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Computational approaches for effective CRISPR guide RNA design and evaluation

Guanqing Liu,^a,^bYong Zhang,^a,^c,^⁎ and Tao Zhang^a,^b,^d,^⁎

Guanqing Liu

^aJiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, China

^bJiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China

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Yong Zhang

^cDepartment of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China

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Tao Zhang

^bJiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China

^dJoint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China

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Author informationArticle notesCopyright and License informationDisclaimer

^bJiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China

^cDepartment of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China

^dJoint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China

Yong Zhang: nc.ude.ctseu@619gnoygnahz; Tao Zhang: nc.ude.uzy@oatgnahz

^⁎Corresponding authors. nc.ude.ctseu@619gnoygnahz, nc.ude.uzy@oatgnahz

Received 2019 Aug 29; Revised 2019 Nov 9; Accepted 2019 Nov 15.

This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

Abstract

The Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/ CRISPR-associated (Cas) system has emerged as the main technology for gene editing. Successful editing by CRISPR requires an appropriate Cas protein and guide RNA. However, low cleavage efficiency and off-target effects hamper the development and application of CRISPR/Cas systems. To predict cleavage efficiency and specificity, numerous computational approaches have been developed for scoring guide RNAs. Most scores are empirical or trained by experimental datasets, and scores are implemented using various computational methods. Herein, we discuss these approaches, focusing mainly on the features or computational methods they utilise. Furthermore, we summarise these tools and give some suggestions for their usage. We also recommend three versatile web-based tools with user-friendly interfaces and preferable functions. The review provides a comprehensive and up-to-date overview of computational approaches for guide RNA design that could help users to select the optimal tools for their research.

1. Introduction

Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/CRISPR-associated (Cas) systems, such as Cas9 [46] and Cas12a (formerly Cpf1) [118], are the primary tools used for genome editing due to their various abilities to manipulate, detect, and image certain DNA and RNA sequences in the cell [50]. The CRISPR/Cas system was first adapted for genome editing in 2012 [31], [46], and subsequent studies have transformed the CRISPR RNA (crRNA) and trans-activating crRNA (tracrRNA) into a single guide RNA (sgRNA) that can bind to both the Cas9 protein and the target DNA sequence. Cas9 protein and sgRNA complex first scans the appropriate PAM sequence and binds to the targeted genome loci, then the activated HNH and the RuvC nuclease domain of Cas9 function to make a DNA double-strand break (DSB) in the specific region [22], [69].

The most frequently used CRISPR nuclease is type II endonuclease Cas9, which recognises the 5′-NGG-3′ PAM (SpCas9) [73]. Another popular nuclease is CRISPR type V endonuclease Cas12a (Cpf1), which recognises the 5′-TTTV-3′ PAM, and shows high efficiency in both animal and plant organisms [25], [48], [49], [71], [97], [118], [124]. Recently, several other Cas family proteins have also been discovered and adapted for DNA or RNA editing events, including Cas12b, Cas13a and Cas14 [2], [37], [94].

CRISPR-based gene editing is implemented with sequence-specific nucleases (SSNs) and a sgRNA to achieve precise gene knock-out (KO) or gene knock-in (KI). Additionally, researchers developed a catalytically inactive Cas9 (dCas9) that loses endonuclease activity, and has been adapted for gene expression regulation (CRISPRa/i) and 3D genome studies [33], [66], [67], [70], [84], [88]. Furthermore, base editing using modified nCas9 has greatly broadened application of the CRISPR system [32], [52], [123]. Compared with previous mature gene editing tools such as zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) [9], [10], [13], [100], [121], which use engineered proteins to target and cleave specific genome loci, CRISPR is lower in cost of both time and money. This advancing technology is increasingly being deployed, and has great potential for clinical detection, gene therapy and agricultural improvement [3], [21], [50], [126].

However, two major challenges hinder the development and application of the CRISPR/Cas system: potential off-target effects, and on-target efficiency (Fig. 1) [112], [120]. Successful CRISPR guide RNA (gRNA) design can resolve these issues [23], [96], and powerful computational approaches facilitate in silico gRNA design [19], [34], [104], thereby enabling the design of specific gRNAs for particular experiments.

In this review, we summarise existing approaches for CRIPSR guide RNA design and evaluation, and assist users in choosing favourable tools for their research. Moreover, it aims to make users aware of the latest computational CRISPR tools and resources.

2. Evaluation of CRISPR cleavage efficiency

In theory, the CRISPR/Cas protein scans the PAM sequence, and sgRNA recognises target loci and activates endonuclease activity to cleave specific sites. However, cleavage efficiency varies greatly among different target sites and/or cell lines [14], [21], [27], [28], [51], [78], [87], [98], [99], [103], [115], [117], [122], [125], suggesting that several features may influence the binding and cutting efficacy of the sgRNA-Cas complex. Numerous studies have revealed that gRNA sequence features (sequence composition, nucleotide position, GC content), genetic and epigenetic features (chromatin accessibility, gene expression) and energetics properties (RNA secondary structure, melting temperature, free energy) all contribute to gRNA efficacy. Based on these features, many computational tools have been developed for designing highly efficient gRNAs. Herein, we introduce these tools based on their features, and evaluate their efficiency (Table 1).

Table 1

Computational methods for evaluation of guide RNA efficiency.

Tool	Enzymes	Data source	Main features	Quantitative metrics
E-CRISP [38]	Cas9	–	SC, GF	–
CRISPRscan [78]	Cas9, Cpf1	Zebrafish	SC	Spearman correlation = 0.309, from [36]
evaluateCrispr [40]	Cas9	Drosophila	SC	Spearman correlation = 0.074, from [36]
sgRNAScorer [14], [15]	Cas9, Cpf1	Human	SC, EGF	Spearman correlation = 0.225, from [36]
SSC [112]	Cas9	Human, Mouse	SC	Spearman correlation = 0.274, from [36]
WU-CRISPR [106]	Cas9	Human, Mouse	SC, EP	Spearman correlation = 0.215, from [36]
Azimuth [23], [29]	Cas9	Human, Mouse	SC, GF, EP	Spearman correlation = 0.366, from [36]
CRISPRater [55]	Cas9	Human	SC, GF	Pearson correlation = 0.399, from [55]
CRISPRpred [86]	Cas9	Human, Mouse	SC, EP	ROC-AUC = 0.85, from [86]
CASPER [75]	Cas9, Cpf1	–	SC	Pearson correlation = 0.443, from [75]
DeepCpf1 [47]	Cpf1	Human	SC, EGF	Spearman correlation = 0.748, from [47]
TSAM [82]	Cas9	Human, Mouse, Zebrafish	SC, GF, EP	Spearman correlation = 0.4, from [82]
TUSCAN [105]	Cas9	Human, Mouse, Zebrafish	SC, GF	Spearman correlation = 0.12, from [105]
uCRISPR [119]	Cas9	–	SC, EP	Spearman correlation = 0.3, from [119]

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2.1. Guide RNA sequence features

The nucleotide composition of a target sequence is one of the most important determinants of gRNA efficiency [24], [103], [107], [112]. Large-scale CRIPSR-based screens in mammals have shown that guanines are preferred in positions 1 and 2 before the PAM sequence [103], while thymines are disfavoured within +/-4 nucleotides surrounding the PAM sequence [107]. Additionally, sequences downstream of PAMs can influence gRNA efficiency, while sequences upstream have no significant effect [24]. Cytosine is preferred at the CRISPR/Cas9 cutting site (-3 position proximal to PAM) [21], [112], and the GC content of the region 4–13 bases downstream of the PAM sequence contributes to gRNA efficiency. Based on this key information, several efficiency prediction models have been constructed.

Rule Set 1 is a predictive model built using data derived from 1,841 sgRNAs in human and mouse [24], the score is predicted by a support vector machine (SVM) model, and a supervised learning method classifies data in a generalised linear manner. Rule Set 1 is mainly used to investigate sequence features that influence CRISPR cutting efficiency. Results predicted by this model show a high correlation with experimental results. To improve the accuracy, the authors adapted more datasets and built a new model in 2016 called Rule Set 2 [23]. In this model, position-independent nucleotide counts and the location of the sgRNA target site within the gene were considered to improve predictions based on their observations. These optimised models were applied for gRNA design for both CRISPR KO and CRISPRa/i experiments. A package to predict the gRNA efficiency based on the models was also developed and implemented in Broad Institute GPP sgRNA Designer [29].

To unravel the nucleotide preference of gRNA target sites in different CRISPR-based editing events, both CRISPR KO and CRISPRa/i libraries in mammals were screened [112], and significant differences in nucleotide preference between CRISPR KO and CRISPRa/i were detected. Elastic Net is a regularised regression method for fitting and classifying data that performs better than SVM in some cases [128]. The Elastic Net algorithm was used to construct models for both CRISPR KO and CRISPRa/i, and they were applied in Spacer Scoring for CRISPR (SSC) software to predict the efficiency of gRNA. Platforms such as E-CRISP, CHOPCHOP and CRISPR-FOCUS also include this model [12], [38], [57].

Moreno-Mateos and his colleagues observed that the loading and activity of sgRNA increased with guanine enrichment and adenine depletion [78]. They measured >1,000 sgRNAs targeting 128 genes in zebrafish and used the logistical regression method to construct a predictive model that was integrated into CRISPRscan. WU-CRISPR takes advantage of this data and adds some novel features [24], [106], resulting in a model with higher precision than several other predictive models [14], [24], [112]. Labuhn et al. identified PAM-distal GC content-dependent activity and constructed a model named CRISPRater [55] that was integrated into CRISPR/Cas9 target online predictor (CCTop), a platform for CRISPR target prediction [93].

The Church laboratory developed software called sgRNA scorer to calculate sgRNA on-target scores based on their SVM model [14]. A second version of the sgRNA scorer software was proposed that improved the on-target prediction power and added prediction for other Cas systems such as SaCas9 and AsCpf1 [15]. Housden et al. then used a drug target method to screen CRISPR KO efficiency in Drosophila and developed an efficiency prediction tool [40]. CASPER integrated scores from CRISPRscan and added some new features to maximise correlations between scores and on-target experimental data [75]. This tool can also detect off-target scores and perform multipopulational analysis.

2.2. Genetic and epigenetic features

Genetic and epigenetic features like chromatin accessibility, gene position and expression are also important factors that influence sgRNA binding and Cas nucleases cleavage. Many researches have demonstrated that nucleosomes inhibit Cas9 target cleavage, and DNase I hypersensitivity and epigenomic markers alter gRNA efficacy [23], [39], [44], [101], [116]. Based on these features, several tools have been developed. By borrowing knowledge from oligonucleotide design and nucleosome occupancy models, an R package called predictSGRNA was proposed for evaluation of sgRNA efficacy [53], and this performed better than other models such as Azimuth and sgRNA scorer [14], [23], [29].

Non-homologous end joining (NHEJ) and microhomology-mediated end joining (MMEJ) are two major pathways which produce heterogeneous repair outcomes when repairing Cas9-mediated DSBs. People use CRISPR/Cas9 system to knock out genes by inducing indels into target genome location. However, CRISPR-based gene KO may induces in-frame variants in which gene functions are retained. Thus, microhomology-based prediction of CRISPR on-target efficiency should be considered. To this end, Bae et al. developed Microhomology-Predictor to improve KO efficiency by reducing in-frame editing [7]. Recent researches have showed that template-free Cas9-editing outcomes are predictable. inDelphi was the first model for precise prediction of CRISPR editing genotype [90]. Soon after, a computational predictor called FORECasT was developed using >40,000 sgRNAs in different cell lines [5]. It was shown that most reproducible mutations are single base insertion, short deletions or longer microhomology-mediated deletions, in addition, Cas9-editing outcomes were cell-line-dependent. The Shendure laboratory also built a predictive model called Lindel for prediction of the insertions and deletions of CRISPR/Cas9-mediated DSB repair based on local sequence context [16]. All these approaches are sure to assist users in guide RNAs selection for gene disruption.

CRISPR-Cpf1 achieves high efficiency and suffers minor off-targets, besides, Cpf1 prefers AT-enriched regions. Hence, more and more studies have adapted Cpf1 for KO screens. However, models for evaluation of Cpf1 cleavage efficiency are lacking. DeepCpf1 is an algorithm especially for prediction of Cpf1 activity [47]. It is implemented within the deep-learning framework and chromatin accessibility data. This program can significantly improve the accuracy of Cpf1 activity prediction. In addition, models for other Cas experiments, such as Cas9, xCas9, and base edition are also provided on the author’s GitHub (https://github.com/MyungjaeSong/Paired-Library). CRISPR-DT is a recently developed platform for prediction of Cpf1 target efficiency [127]. This SVM model displayed better performance than the deep learning-based model employed in DeepCpf1.

2.3. Energetics properties

The energetics associated with the formation of the DNA, gRNA and Cas protein complex are regular and can be analysed to eliminate bias among different models, since some energetics methods may better illustrate the Cas9 editing efficacy [95], [107], [113]. CRISPRpred includes the positions of nucleotides as well as secondary structures of sgRNAs to predict the cleavage efficiency, and this performs better than Rule Set 1 [24], [86]. Zhang et al. recently demonstrated a free energy scheme called uCRISPR for evaluating the Cas9 editing efficacy, as well as off-target effects [119]. This model is thought to apply to any cleavage-activity Cas9 dataset.

2.4. Other considerations for gRNA efficiency

Of note, these predictive models were trained by individual experiments and rules, and each model generates different on-target scores for sgRNAs, hence users must be careful when evaluating or designing guide RNAs using these models in their own experiments. However, several key features are reliable, such as guanine preference, GC content, seed region and the secondary structure of gRNAs [65], [91], [106], [112].

The accuracy of different models is controlled by their learning methods or the approaches of CRISPR activity measurement. Doench et al. tested multiple training methods and selected the best-performing one as the kernel of their model [23]. TUSCAN, a random forest-based model, outperformed models built solely by linear regression [78], [105]. A two-step averaging method (TSAM) for the regression of cleavage efficiencies also performed better than many other models [14], [23], [82], [112]. Additionally, measurement using sequencing data rather than phenotypic data may generate fewer false positive results, albeit at a cost [105].

It is critical for users to know which tool best suits their research. A comprehensive evaluation of different efficiency prediction tools was conducted to examine differences among models [36], and it revealed differences in the correlation between different datasets and models. Furthermore, no model performed excellently across all datasets, suggesting that a careful selection of CRISPR gRNA design tools is necessary. Users can also evaluate gRNAs using multiple models and select the best one for their experiments. Among the available tools, Rule Set 2 and DeepCpf1 are the most used and accurate scoring methods for evaluating Cas9 and Cpf1 cutting efficacy, and uCRISPR may be more accurate than some other methods, but it requires further experimental testing.

3. Prediction of CRISPR cutting specificity

The main obstacle for the application of CRISPR is off-target effects. CRISPR nucleases may cleave unintended genomic sites and cause unexpected mutations due to sgRNAs recognising DNA sequences with a few mismatches and/or DNA/RNA bulges, referred to as off-target cleavage [41], [120]. Off-target effects can be effectively relieved by predicting CRISPR cutting specificity and designing optimal gRNAs [41]. To predict the specificity of CRISPR gRNAs, two main methods have been proposed: (1) alignment-based method. Based on conventional or specialized algothrims, gRNAs are aligned to a given genome and off-target sequences and sites are returned. This method is mainly used for find out all potential off-targets in silico, (2) Scoring-based method. sgRNAs should be further scoring and ranking using identified off-targets from alignment process to select the most specific one for experiments. Two scoring approaches are shown: hypothesis-driven, where off-targets are scored based on the contribution of specific genome context factors to gRNA specificity; learning-based, where gRNAs are scored and predicted from a training model that considers the different features affecting specificity. These methods for prediction of gRNA specificity are discussed below and some of them are summarised in Table 2.

Table 2

Computational methods for prediction of guide RNA specificity.

Tool	Enzymes	Methods	Main features	Quantitative metrics
CasOT [108]	Cas9	alignment	unlimited mismatch number, paired-gRNA mode, annotation	slow
Cas-OFFinder [8]	costom	alignment	unlimited mismatch number, GPU acceleration, web support	middle, fast (use GPU)
sgRNAcas9 [110]	Cas9	alignment	max 5 mismatches, paired-gRNA mode, annotation, risk evaluation	slow
FlashFry [74]	costom	alignment	unlimited mismatch number, multiple on/off-target scores, annotation	fast
Crisflash [43]	Cas9	alignment	unlimited mismatch number, variant data support	fast
MIT [41]	Cas9	scoring	20 bp sgRNA without PAM	ROC-AUC = 0.87, from [36]
CCTop [93]	Cas9, Cpf1	scoring	empirically score based on number of mismatches	ROC-AUC = 0.77, from [36]
CFD [23]	Cas9	scoring	20 bp sgRNA with PAM (enable non-canonical PAM)	ROC-AUC = 0.91, from [36]
CRISPRoff [4]	Cas9	scoring	energetics property and sequences composition	ROC-AUC = 0.98, from [4]
uCRISPR [119]	Cas9	scoring	energetics property and sequences composition	Pearson correlation = 0.75, from [119]
CRISTA [1]	Cas9	scoring	machine learning, sequences composition and epigenetic feature	ROC-AUC = 0.96, from [1]
Elevation [62]	Cas9	scoring	machine learning, integrate both CFD model and epigenetic features	ROC-AUC = 0.98, from [62]
DeepCRISPR [18]	Cas9	scoring	deep learning, sequences composition and epigenetic feature	ROC-AUC = 0.98, from [18]

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3.1. Alignment-based methods

In theory, potential off-target sites can be identified by aligning gRNA sequences to the reference genome based on sequence homology. Bowtie [59] and BWA [61] are traditional tools for short sequence alignment that are capable of off-target detection [36], [104]. However, there are several potential issues when using these tools. First, tools like Bowtie and BWA cannot identify small PAMs, since these alignment tools were developed for next-generation sequencing (NGS) read alignment. Second, these tools allow very limited mismatches in their seed regions, making alignment with default parameters impractical for identifying all potential off-target sites. A survey using bowtie2 [58] to detect off-targets failed to find all possible off-target sites, and could only find off-targets with up to one mismatch [23].

Despite the defects, some gRNA design methods utilise these tools, and parameters have been modified to fit the demand for off-target prediction. CCTop uses Bowtie to find off-target sites by first identifying PAM sites, and matches and mismatches in protospacer sequences are then searched for by bowtie with modified parameters [93]. Up to five mismatches are allowed in the protospacer as more mismatches may prevent DSB induction. CCTop also implements an off-target score for each candidate sgRNA. CHOPCHOP detects off-target sites using Bowtie with parameters -v and -L for searching sgRNA core regions [77]. CRISPOR uses BWA to find all potential off-target sites in iterative mode (“-N”), and can find all validated off-targets as well as Cas-OFFinder [8], [36].

In addition to these traditional tools, many other tools and algorithms have been developed for off-target site detection. Cas-OFFinder is one of the most popular tools for searching potential off-target sites, and advantages include no limit to the number of mismatches, PAM types, gRNA length or high running speed with GPUs. Cas-OFFinder can also predict off-target sites with 1 bp deletions or insertions (i.e. DNA/RNA bulges). CasOT is implemented to find Cas9 on-target sites from input sequences, as well as potential off-target sites with up to six mismatches in the seed region (12 nt adjacent to the PAM). This tool can also determine whether off-targets are within a coding exon [108]. Meanwhile, sgRNAcas9 utilises the ultrafast short sequence mapping tool SeqMap [45] to find off-targets, and classifies all sites into three categories to generate a final output of the best candidate gRNAs [110]. Recently, two new alignment-based tools have been developed. Crisflash utilises a tree-based algorithm to rapidly design CRISPR guide RNAs and optimise guide accuracy by incorporating user-supplied variant data [43]. FlashFry rapidly searches off-target sites and provides much useful information (annotation of off-target sites, on/off-target scores, GC content, etc.) for candidate gRNAs [74]. Here we still classified Crisflash and FlashFry as alignment-based methods since they both propose novel algorithms for off-target searching, whereas the scoring approaches they use are borrowed from others [23], [24], [41], [78].

Among these tools, Cas-OFFinder may be the best choice for identifying all potential off-target sites with any Cas nucleases, and FlashFry is also worth a try for its high speed and comprehensive outputs.

3.2. Scoring-based methods

3.2.1. Hypothesis-driven methods

Alignment-based methods are reliable for detection of most potential off-targets, however, not all nucleotide positions containing mismatches have the same decisive effect on off-target cleavage. Additionally, alignment-based prediction always outputs redundant off-target sites, many which are false-positives, although users can reduce the number of outputs by restricting the maximum mismatches when exploring off-target cleavage. One study compared experimentally validated off-targets and off-targets predicted by Cas-OFFinder and CCTop, and the results showed that off-targets detected by the prediction tools only covered some of the validated sites, while some off-target sites cannot be predicted solely based on sequence homology [11]. Thus, features that influence the nonspecific binding of CRISPR gRNAs need to be considered to increase the accuracy of off-target detection.

MIT (Hsu-Zhang) score was proposed for off-target evaluation during the early stages of gene editing by CRISPR. Hsu et al. evaluated >700 guide RNA variants and SpCas9-induced indel mutation levels at >100 predicted genomic off-target loci [41]. They evaluated the contributions made by different mismatch positions and numbers in the target 20 bp, and calculated a weight matrix to determine off-target efficiency for each sgRNA. The authors claimed that this score accounts for >50% of the variance in cutting frequency. The MIT score has been integrated into many CRISPR gRNA design tools such as CHOPCHOP and CRISPOR [36], [56].

Cutting frequency determination (CFD) is another popular score for off-target evaluation. It is noticeable that sgRNA can also bind genome loci with non-canonical PAMs such as NAG, NCG and NGA, which may cause off-target cleavage. Doench et al. added PAM features in their scoring metrics [23]. sgRNAs with mismatches and indels in target sequences were also included for examining correlations between sgRNAs and off-targets. CFD score was validated with GUIDE-seq and proved to perform better than MIT score, hence it was adopted by CRISPRscan [78], GuideScan [83] and CRISPOR [36].

The prediction of sgRNA specificity based on the structural features of the Cas9-sgRNA complex proved to be superior to prediction solely based on sequence features. CRISPRoff [4] and uCRISPR [119] both utilise energetics properties for off-target evaluation. Compared with other scoring methods like MIT and CFD, they both yielded better accuracy in off-target prediction. Nevertheless, neither have not been systematically evaluated by large-scale experiments, and caution should be exercised when using them.

3.2.2. Learning-based methods

Sometimes, empirical algorithms cannot effectively evaluate off-targets since they only consider minor features, whereas learning-based methods build complex models using combinations of multiple features, and they may better predict off-targets. In recent years, several new approaches for off-target prediction based on machine learning have been developed.

CRISPR Target Assessment (CRISTA) software uses BWA as the off-target search tool and implements multiple features (PAM type, nucleotide composition, GC content, chromatin structure, DNA methylation, RNA secondary structure, etc.) to predict cleavage propensity [1]. CRISTA exhibits better performance than MIT, CCTop and CFD.

The Doench laboratory also developed a linear regression model for prediction of off-target activity called Elevation that takes both sequence and chromatin accessibility features into consideration, as well as observations from others [62]. Elevation predicts individual scores for each off-target site, as well as an aggregate score for gRNAs. This method performs best among MIT, CFD and CCTop. However, this software can only compute off-target scores for the human exome (GRCh38) and cannot support other organisms on their website.

DeepCRISPR is a state-of-the-art computational platform that unifies sgRNA on-target and off-target site prediction into one framework with deep learning [18]. It identifies all possible sequence and epigenetic features that may affect sgRNA KO efficacy by learning from large data. This method was proved to surpass other available off-target prediction tools [23], [41], [92], [93].

3.3. Benchmark of scoring-based methods

Different scoring methods are based on different characteristics applied by each individual laboratory. In order to compare the accuracy of different scores, Haeussler et al. assessed four hypothesis-driven methods for off-target prediction using the same datasets [36]. CFD score exhibited the best prediction accuracy, whereas CCTop performed the worst. Data imbalance, where the number of true observed off-target sites (OTS) identified by off-target detection experiments is much less than that of all potential off-target sites recognized by alignment-based methods, is a common issue in the learning-based methods. To address the problem, a systematic survey was conducted to assess the influence of data imbalance [30]. The authors used bootstrapping sampling and PR-AUC methods to evaluate two well-established models. They emphasized the importance of using symmetric data for model construct and taking unbiased datasets for benchmark. According to current assessment results, we recommend people to use CFD score for off-target prediction. Elevation and DeepCRISPR are suitable for human genome editing, but CRISPRoff and uCRISPR may need further evaluation before use.

4. Tools for CRISPR guide RNA design

A CRISPR/Cas complex typically contains a Cas protein and a sgRNA, both of which determine the cutting activity. However, protein engineering is a complicated and uncertain strategy for most researchers, and optimising gRNAs is more feasible and efficient. A robust gRNA requires maximum on-target efficiency as well as minimum off-target activity. Basing on these two criteria, numerous computational tools have been developed for high-efficiency CRISPR gRNA design. However, each tool possesses distinct features, and user-friendliness is also important. To acquaint users with existing gRNA design tools, we provide an overview of most that are available based on the strength of their features, and this help users to make appropriate selections. Furthermore, we recommend several functional and user-friendly websites for gRNA design (Fig. 2,Table 3).

4.1. A comprehensive overview of CRISPR guide RNA design tools

The CRISPR/Cas system was first adapted for gene editing in 2012, and several tools were developed immediately thereafter, such as Zinc Finger Targeter (ZiFiT) [89], Cas9 guide RNA Design [68] and CRISPR (http://crispr.mit.edu/) [41]. All these platforms have been implemented in the design of gRNAs for model organisms. ZiFiT is also used to design Zinc Finger and TALEN modules, but Cas9 guide RNA Design and CRISPR are now unavailable.

In the following years, various tools for CRISPR gRNA design emerged, due to both urgent demand for these tools, and because people have learned more and more about how the CRISPR system functions and what influences the efficiency and specificity of Cas cleavage. Many of these tools combine multiple scoring methods and provide alternative options for users. Some others have also proposed their own algorithms to rank designed sgRNAs, and this can assist users in gRNA selection. CHOPCHOP [56], [57], [77] provides alternative scores for users such as Rule Set ½ [23], [24], SSC [112], CRISPRscan [78] and deepCpf1 [47]. E-CRISP utilises its own SAE (Specificity, Annotation, Efficacy) score to determine the quality of each sgRNA, while Rule Set 1 [24] and SSC [112] are also included in E-CRISP. CCTop [93] assigns off-target scores for each sequence empirically, while the CRISPRater score [55] is also included to predict the efficiency of sgRNAs. CRISPOR [36] is a versatile platform that ranks gRNAs according to different scores for evaluating potential off-targets in the genome of interest, and for predicting on–target activity.

A large number of CRISPR/Cas-derived RNA-guided Endonucleases (RGENs) have been identified or modified to improve the cutting efficiency and enlarge the editing range. Some tools enable the design of gRNAs for RGENs. For example, Cas-Designer [79] allows users to choose 20 PAM types from different RGENs, while CRISPOR [20] also offers various PAMs from a defined list. To best serve the specialised purposes of different experiments, several web-based tools have been developed. CRISPR-ERA [64] and CHOPCHOP v3 [57] support sgRNA design for the CRISPRa/i system. CRISPETa [85] is mainly used for genome deletion with paired gRNAs, and BE-Designer [42] can be used for designing gRNA for base editing. Recently, three methods have been employed for successively predicting Cas9-editing outcomes: inDelphi [90], FORECasT [5] and Lindel [16]. These approaches can help to identify gRNAs based on forecasting results.

Researchers should choose suitable tools with caution since different tools are in favour of different genomes or cell types. For instance, Yeastriction [72] is specialised for yeast, FlyCRISPR [35] is specific for Drosophila, EuPaGDT [81] is recommended for eukaryotic pathogens, and CRISPR-P [60], [63], CRISPR-PLANT [76], [109] and CRISPR-GE [111] are all implemented for genome editing in plants. Also, user-friendliness is essential for these web-based design tools. Based on these considerations, we propose three comprehensive web-based platforms for CRISPR gRNA design.

4.2. Three comprehensive web platforms for CRISPR guide RNA design

4.2.1. CHOPCHOP

CHOPCHOP has a succinct interface with well-rounded functions, >200 genomes are available on the website, and users can provide gene names, genomic coordinates or target sequences as inputs. If a gene is given, users can set specific regions of the gene as targets, such as coding sequences or promoters. Before designing gRNAs, two off-target detection methods and seven efficiency scores can be chosen, which aids users in selecting optimal gRNAs for their research.

To satisfy different experimental purposes, CRISPR Cas9 nuclease/nickase, Cpf1, CasX, C2C2 and TALEN are all supported by CHOPCHOP, and various modes of DNA targeting are optional such as KO/KI, gene activation/repression, and nanopore enrichment. In activation/repression mode, gRNAs are designed to target the promoter region and its flanking sites in order to bring the activating/repressing domain into close proximity with the transcription start site [17], [54]. Meanwhile, nanopore enrichment mode is implemented to design sgRNAs for long fragment excision within 40 kb. Additionally, the inDelphi model has been integrated into CHOPCHOP for repair profile prediction by Cas9 in five cell types [90].

After clicking the ‘Find Target Sites’ button, a results table is shown, and each candidate gRNA has a rank, genomic information, GC content, self-complementarity score, mismatch number (0–3) and an efficiency score. A graphical view of all gRNAs is also provided in the UCSC Genome Browser, which helps users to select optimal gRNAs.

4.2.2. CRISPR RGEN tools

CRISPR RGEN tools, computational tools and libraries for RNA-guided endonucleases, are maintained by the Bae laboratory, and libraries comprise nine useful tools including Cas-OFFinder [8], Cas-Designer [79] and Digenome-Seq [80]. Herein, we mainly discuss the two gRNA design tools Cas-Designer and BE-Designer [42].

Compared with other designer tools, Cas-Designer allows DNA/RNA bulges when performing off-target detection. Additionally, this detection method is more rapid than others due to the Cas-OFFinder algorithm. Genomic sequences or coordinates and fasta file formats are allowed as inputs. Over 350 genomes and 20 PAM types are specified for users, and outputs include target sequences as well as out-of-frame score (calculate by microhomology), mismatch number (0–2) and off-target sites with up to 1 bp bulge. On/off-target sites are redirected to the Ensembl genome browser [26], which is capable of further inspection.

Unlike Cas-Designer, BE-Designer is primarily implemented for base editing. In this tool, four methods of base editing are specified, and the editing window region is also adjustable. After the design phase, three outcomes are based on different coding types, and gRNAs, editing window sequences and amino acids are highlighted in a user-friendly manner. This tool is a good choice for base editing.

4.2.3. CRISPOR

Since many tools have been developed for highly efficient CRISPR gRNA design, an ensemble of multiple tools can be useful, and CRISPOR does this well [20], [36]. At present, CRISPOR contains 417 genomes and 19 PAM types, and can meet the needs of most users. CRISPOR takes genome coordinates and sequences <2,000 bp as inputs and provides comprehensive information as outputs. By default, results are shown in two parts; visualisation of PAM sites along the given sequence, which allows for downloading using multiple formats including fasta, GenBank and SnapGene; a table including all information for each predicted gRNA is also generated. In the table, two specificity scores (MIT and CFD) and 10 efficiency scores (Rule Set 2, CRISPRscan, etc.) are calculated [23], [41], [78]. Furthermore, Microhomology and Lindel scores are also provided for outcome prediction [7], [16]. Warnings such as extreme GC content and poly-T values are indicated, the table is downloadable, and candidate off-target sites with up to four mismatches can be visualised and downloaded.

In addition to gRNA design, CRISPOR designs primers for each gRNA as well as off-target sites. These primers are useful when conducting on/off-target validation or in vitro expression experiments. Furthermore, CRISPOR enables filtering of gRNAs with genomic variants based on well-known variant databases or marked input sequences with N characters. Thus, CRISPOR may be the best tool for designing gRNAs.

5. Summary and perspectives

CRISPR/Cas technology has emerged as an advanced strategy for functional genomics, crop breeding and precise medicine. Guide RNAs are indispensable for CRISPR-based editing, and computational approaches provide assistance for efficient gRNA design. Numerous tools have been developed for CRISPR gRNA design and evaluation. However, many issues remain. For example, experimental datasets used to build models for predicting sgRNA specificity or efficiency are disparate; CRISPRscan score performs worse in mammals than in zebrafish, the genome the predictive model was trained in [36]. Researchers should therefore know the strengths and weaknesses of each scoring method, and select the optimal tool for their research.

As we become more aware of the mechanisms by which Cas proteins recognise gRNAs, and bind to and cleave target loci, more and more novel features contributing to cutting efficiency and specificity are being identified, including sequence composition. For instance, low chromatin accessibility may block access of Cas9, while open chromatin regions are more likely to cause undesired mutations [39], [92]. In practice, specificity is more important than efficiency for application of CRISPR. However, several off-targets remain indecipherable using current tools, and discovery of novel features may minimise off-target effects.

Too much choice is not always desirable, and an unbiased evaluation can provide guidance. To this end, the Liu laboratory has conducted the benchmarking [30], [114], and Haeussler et al. performed a comparison of different predictive scores and integrated most into CRISPOR [36]. None of the tools excel when using heterogeneous data, due to cell-specific or species-specific training models. Therefore, more cell types need to be evaluated. Also, plant and some animal genomes should be analysed thoroughly, since human or mouse have dominated to date. Moreover, it will be beneficial if useful features of multiple tools are combined in future software packages.

The major outcomes of Cas9 cleavage is non-random and predictable [102], and several tools have been created for prediction of CRISPR-Cas9 outcomes [5], [16], [90]. Such findings facilitate more accurate gene editing. However, existing tools cannot account for large indels, homozygous sites and the activity of nucleases other than SpCas9, and this should be resolved in future [6].

In summary, the development of computational approaches has revolutionised the design of effective gRNAs, and CRISPR-based gene therapies and customised gene editing may come within reach. It is likely that CRISPR technology will continue to become more powerful in the coming years.

Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Acknowledgements

This work was supported by the National Transgenic Major Project (2019ZX08010003-001-002, 2018ZX08020-003), Jiangsu Province Government Project (BK2018003)/The open funds of the Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding (PL201801) for T.Z. and Y.Z.; the Fund of Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD) for T.Z.

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DesktopStaffCrystalMakerModelling Software A fully-interactive visualization and analysis of crystal and molecular structures.CrystalMakerDesktop@UCL Anywhere
DesktopPCEndnoteReference Management Reference management software package, used to manage bibliographies and references when writing essays and articles.Thomson ScientificStaff WTS 20107ZipUtilities 7-Zip is a file archiver with a high compression ratio.7 ZipStaff WTS 2010Acrobat ProfessionalPDF Designed to view, create, manipulate and manage files in Adobe's Portable Document Format (PDF).AdobeActivTestUtilities Used for the ECDL Driving Licence examinations.Activ Training LtdDesktopPCAdlib Demo ArchiveLibrary Intended specifically for managing collections in archives and records officesAdlibAdobe AirUtilities A cross-platform runtime environment for building rich Internet applications using Adobe Flash, Adobe Flex, HTML, or Ajax, that can be deployed as a desktop applicationAdobeAleph ClientLibrary Aleph provides academic, research, and national libraries with the efficient, user-friendly tools and workflow supportEx LibrisAmaseisGeographic The IRIS AmaSeis program is for use with the AS-1 seismometerIRISDesktop@UCL Anywhere
DesktopPCAntiochUtilities Antioch is a utility which allows you to type classical Greek, Hebrew and Coptic in WordAntiochDesktop@UCL Anywhere
DesktopPCAquachemGeographic AquaChem is a groundwater software package specifically tailored for anyone working with water data.Schlumberger Water ServicesAquifer Test ProGeographic An advanced and easy-to-use groundwater software package for graphical analysis and reporting of pumping test and slug test data.Schlumberger Water ServicesAtlas.tiStatistical ATLAS.ti is a computer software program used mostly, but not exclusively, in qualitative research or qualitative data analysis.Atlas.tiDesktop@UCL Anywhere
DesktopPCAudacitySound Recording Open source software for recording and editing soundsAudacityAutocadCAD Software AutoCAD is a CAD (Computer Aided Design or Computer Aided Drafting) software application for 2D and 3D design and drafting. Now available on Mac and WindowsAutodeskDesktopPCInventor Robot Structual Analysis, student home use, autodeskBarcode font 3 of 9Utilities A Font that format characters as Bar codes.NetlabelsBioConductorApplications
Statistical For the analysis and comprehension of genomic data. Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language - see below for information about R on Legion.BioConductorLegionBusiness Objects Planning ClientReporting Tools SAP BusinessObjects Planning and Consolidation application unifies and streamlines the planning, budgeting, and forecasting process and can enable a faster closeSAPC2 DataGeographic C2 is a Microsoft Windows program for analysing and visualising palaeoenvironmental data.University of NewcastleDesktop@UCL Anywhere
DesktopPCCamtasiaScreen Capture
Video Capture Camtasia Studio is a screen video capture programTechSmithBB flashCano DrawStatistical CanoDraw supports thoroughly all the visual aspects of multivariate data analysis with linear and unimodal ordination methodsPlant Research InternationalCanocoStatistical The most popular tool for constrained and unconstrained ordination in ecological applications.Microcomputer PowerCDBurnerXPUtilities CDBurnerXP is a free application to burn CDs and DVDs, including Blu-Ray and HD-DVDsCDBurnerXPDesktopPCChemSketchModelling Software Visualize a chemically intelligent drawing interface that provides a portal to an entire range of analytical tools, and facilitates the transformation of structural or analytical data into professional, easy-to-decipher reports or presentationsAdvanced Chemistry DevelopmentCorel Draw Graphics SuiteGraphic Editing With vector illustration, page layout, photo-editing and tracing software, CorelDRAW Graphics Suite is ideal for professional and occasional designers tackling any type of graphics projectCorelCrimeStatStatistical A spatial statistics program for the analysis of crime incident locations,CrimstatDesktop@UCL Anywhere
DesktopPCCrystal ReportsReporting Tools Used to design and generate reports from a wide range of data sources.SAPCVFITStatistical Curve fitting Software used in PharmacologyUniversity College LondonCygWinUtilities Cygwin is a Unix-like environment and command-line interface for Microsoft Windows.Red HatDesktopPCDemoGraphicsStatistical DemoGraphics is a software package, which makes it easy to browse, analyse and present (global) demographic data from the United Nations Population Assessments and Projections (1996 edition).Gerhard K. HeiligDepthMapStatistical Depthmap is a single software platform to perform a set of spatial network analyses designed to understand social processes within the built environmentUniversity College LondonDesktopPCDigimapGIS / Mapping Digimap is a collection of EDINA services that deliver maps and map data of Great Britain to UK tertiary education.EdinaDigital Shoreline Analysis SystemStatistical The Digital Shoreline Analysis System (DSAS) is computer software that computes rate-of-change statistics from multiple historic shoreline positions residing in a GIS. It is also useful for computing rates of change for just about any other boundary changUSGSDinermoStatistical Convert diary information into nutrient data, and are described in the data processing section.University of CambridgeDjvu BrowserPlug Ins A digital document format with advanced compression technology and high performance valueLizardtechDesktop@UCL Anywhere
DesktopPCDocumentumDocument Management A Document management system used in UCLEMCEarth Sciences - self learningGeographic Earth science CoursewareUK Earth Science Courseware ConsortiumDesktopPCEclipseProgramming A multi-language software development environment comprising an IDE and a plug-in system to extend it.EclipseDesktop@UCL Anywhere
DesktopPCElibLibrary Legacy service which uses Citrix to serve out a handful of index/abstract resources which don't have a web front end.University College LondonEmbryonic DiskModelling Software Contains detailed, illustrated coverage of the first two months of human embryonic development and charts the emergence of the head and neck, nervous system, special senses and all the major organ systems of the thorax and abdomen.University College LondonDesktop@UCL Anywhere
DesktopPCEnvi with RunTimeGIS / Mapping ENVI is the premier software solution for processing and analyzing geospatial imagery used by scientists, researchers, image analysts, and GIS professionals around the world.ITT Visual Information SolutionsDesktop@UCL Anywhere
DesktopPCidl, student home use, staff home useEpidataStatistical Performs basic statistical analysis, graphs, and comprehensive data management.EpidataEstimateSStatistical Computes a variety of biodiversity functions, estimators, and indices based on biotic sampling dataEstimateSDesktop@UCL Anywhere
DesktopPCExceedUtilities PC X server that empowers Windows users with cost-effective access to X Window applications on UNIX and Linux hosts with unparalleled performance and strong securityHumming BirdDesktopPCFilemaker ProDatabase Database management software for people, projects, assets and moreFilemakerFirefoxWeb Browser Is a free open source web browserMozillaStaff WTS 2010Flash PlayerMultimedia Software for viewing animations and movies using computer programs such as a web browser.AdobeStaff WTS 2010Flowpath IIGeographic Software for modelling groundwater flow, re mediation, and wellhead protection.Scientific Software GroupFSecureAnti Virus F-secure anti-virus, Firewall and computer security software.F SecureDesktopStafff secure, anti virus, securityGAMSStatistical A high-level modelling system for mathematical programming and optimizationGAMSGeoDaGeographic EDA, ESDA & ML Spatial RegressionArizona State UniversityDesktop@UCL Anywhere
DesktopPCGeoModelGeographic Collects underground surveysGeoModel IncGeoStudioGeographic Primarily intended for analysing the stability of natural and man-made earth slopesGeo-SlopeDesktop@UCL Anywhere
DesktopPCGeoTrigGeographic GeoTrig is a collection of geologically-related geometric and trigonometric problem solversRockwareGhostscriptUtilities An interpreter for the PostScript (TM) language, with the ability to convert PostScript language files to many raster formats, view them on displays, and print them on printers that don't have PostScript language capability built iGhostscriptDesktopPCGhostviewUtilities A graphical interface for GhostscriptGhostscriptDesktop@UCL Anywhere
DesktopPCGNU PGUtilities GnuPG allows to encrypt and sign your data and communication, features a versatile key management system as well as access modules for all kind of public key directories.GNUPGGoogle EarthGIS / Mapping A virtual globe, map and geographic information programGoogleDesktopPCSketchUpCAD Software A 3D modelling program designed for architects, civil engineers, film makers, game developers, and related professions.DesktopPCGrassGIS / Mapping A free, open source geographical information system (GIS) capable of handling raster, topological vector, image processing, and graphic data.GRASSGW ContourGeographic GW Contour offers the perfect combination of tools and techniques for groundwater and environmental professionals.Schlumberger Water ServicesDesktopPCHot PotatoesUtilities Hot Potatoes suite includes six applications, enabling you to create interactive multiple-choice, short-answer, jumbled-sentence, crossword, matching/ordering and gap-fill exercises for the World Wide Web.Half Baked Software IncDesktop@UCL Anywhere
DesktopPCICECUPTreeBank software ICE-GB consists of a million words of spoken and written English and adheres to the common corpus design. 200 written and 300 spoken texts make up the million words. Every text is grammatically annotated, permitting complex and detailed searches across thUniversity College LondonIHMC Cmap toolsModelling Software Empowers users to construct, navigate, share and criticize knowledge models represented as concept mapsCmap ToolsInspirationAccessibility
Modelling Software Inspiration is the essential visual thinking and learning tool students rely on to plan, research and complete projects successfully.Inspiration Software IncInternet ExplorerWeb Browser Graphical web browserMicrosoftDesktop@UCL Anywhere
DesktopPC
DesktopStaff
Staff WTS 2010IrfanViewGraphic Editing An image viewer that can view, edit, and convert image files and play video/audio formats.Ifran ViewJavaProgramming Java is a programming language and computing platform. This products license has changed please review before installing and understand your usage rightsOracleDesktop@UCL Anywhere
DesktopPCJava, OracleJdiskreportUtilities JDiskReport enables you to understand how much space the files and directories consume on your disk drives, and it helps you find obsolete files and folders.JavaJinitiatorUtilities Allows a web enabled Oracle Forms client application to be run inside a web browser.OracleLabviewProgramming
Statistical Is a platform and development environment for a visual programming language from National Instruments.National InstrumentsDesktop@UCL Anywhere
DesktopPCmultisim niLAPT(London Agreed Protocol for Teaching) uses Certainty-Based Marking (CBM - see below) in the presentation of teaching material.University College LondonDesktop@UCL AnywhereLISRELStatistical For structural equation modelling now includes statistical methods for complex survey dataSSIDesktop@UCL Anywhere
DesktopPCLL2dxfgeospatial processing & analysis LL2DXF translates OS Land-Line in NTF format to DXF format for use in CAD and graphics applicationsGeoToolsMathematicaApplications
Mathematical A computational software program used in scientific, engineering, and mathematical fields and other areas of technical computing.Wolfram ResearchDesktop@UCL Anywhere
DesktopPC
Unitystaff home use, student home useMesquiteStatistical Mesquite is software for evolutionary biology, designed to help biologists analyse comparative data about organisms.MesquiteDesktop@UCL Anywhere
DesktopPCMikTexUtilities An up-to-date implementation of TeX and related programs for Windows (all current variants).Miktex ProjectDesktop@UCL Anywhere
DesktopPCMind GeniusModelling Software Based around the concept of Mind Mapping, which allows the user to capture large amounts of disparate information and gives them the ability to view content from different viewpoints.MindgenuisDesktopPCMySQL BrowserProgramming
Utilities ?Sun MicrosystemNAGLibraries
Mathematical
Programming
Statistical
Utilities The product is a software library of numerical analysis routines. It comprises a collection of 1500 mathematical and statistical algorithms. Areas covered include linear algebra, optimization, quadrature, differential equations, regression analysis.NAGstudent home use, staff home useNDP.viewApplications
Utilities Viewing software specially designed for digital slide observation. Allows making observations just as if operating a microscope.Hamamatsu PhotonicsDesktop@UCL Anywhere
DesktopPCNeuronModelling Software NEURON is a simulation environment for modelling individual neurons and networks of neurons.NeuronDesktop@UCL Anywhere
DesktopPCNotepad ++Programming
Utilities Source code editor and Notepad replacement that supports several languages.Notepad++NVivoMultimedia
Statistical It has been designed for qualitative researchers working with very rich text-based and/or multimedia information, where deep levels of analysis on small or large volumes of data are required.QSRStaff WTS 2010staff home use, student home useOffice Professional PlusDatabase
Email
Multimedia
Office Suite Share information and work across geographical or organisational boundaries with Office Professional Plus. Access, Excel, Outlook, OneNote, PowerPoint, Publisher, WordMicrosoftMicrosoft Office,Open OfficeDesk Top Publishing
Graphic Editing
Office Suite A free productivity Suite, includes Write, Calc, Impress, Draw, BaseSun MicrosystemOxcalUtilities To provide radiocarbon calibration and analysis of archaeological and environmental chronological informationUniversity of OxfordCorel Paintshop ProGraphic Editing A raster graphics editorCorelPASTStatistical Data analysis package originally aimed at palaeontology but now also popular in ecology and other fields.PASTDesktop@UCL Anywhere
DesktopPCPharmacologyModelling Software
Statistical Different Pharmacology software.CoAcSPhotoshop ElementsGraphic Editing Adobe Photoshop Elements software combines power and simplicity so you can make your photos look extraordinary, share your life stories in unique print creations and web experiences, and easily manage and protect all your photos and video clips.AdobeMicrosoft ProjectProject Management A project management software programMicrosoftPublish Web PagesFTP A application to publish files to an FTP site.University College LondonPuttyUtilities PuTTY is a client program for the SSH, Telnet and Rlogin network protocolsPuTTYPymolModelling Software PyMOL is a molecular visualization systemPymolQuick Time PlayerMultimedia Capable of handling various formats of digital video, media clips, sound, text, animation, music, and interactive panoramic imagesAppleDesktop@UCL Anywhere
DesktopPCRApplications
Statistical Software environment for statistical computing and graphicsRDesktop@UCL Anywhere
UnityRASMOLModelling Software A program for molecular graphics visualisationRasMolReal PlayerMultimedia Plays a number of multimedia formats including MP3, MPEG-4, QuickTime, Windows Media, and multiple versions of proprietary RealAudio and RealVideo formatsRealDesktop@UCL Anywhere
DesktopPCReference ManagerReference Management A reference management software packageThomson ScientificRemedy ARSService Management Service management software used, by various helpdesks throughout UCL.BMCResource LinkUtilities An integrated range of HR and Payroll modulesNorthgateSASApplications
Financial
Programming
Statistical Is an integrated system of software products. That enables the programmer to perform: data entry, retrieval, management, and mining report writing and graphics statistical analysis business planning, forecasting, and decision support operationsSASLegionstaff home use, student home useSeismic EruptionsGeographic A program for the visualization of seismicity and volcanic activity in space and time.Alan L JonesDesktop@UCL Anywhere
DesktopPCSeismic WavesGeographic Seismic Waves is a Windows program which illustrates how wave propagate from an earthquake hypocenter to seismic stations throughout the earth.Alan L JonesDesktop@UCL Anywhere
DesktopPCSigma PlotScientific Graphing SigmaPlot provides more than 100 different 2-D and 3-D graph types. From simple 2-D scatter plots to compelling contour plots, SigmaPlot gives you the exact technical graph type you need for your demanding research.Scientific Graphing SoftwareSnagItScreen Capture Capture anything you see on the screen. Edit and combine those captures. Share them via your favorite applications. Organize and find them again later.TechSmithSophosAnti Virus An anti-virus and computer security software for Macs and Windows, only available for certain departmentsSophosSpeech filling systemSpeech Capture SFS 4/Windows is a free computing environment for PCs for conducting research into the nature of speechUniversity College LondonStataStatistical Integrated statistical package that provides everything you need for data analysis, data management, and graphics.Stataic se mp, home useStatTransferStatistical Designed to simplify the transfer of statistical data between different programs.Circle SystemsStellaGeographic STELLA offers a practical way to dynamically visualize and communicate how complex systems and ideas really work.Isee Systems LtdDesktop@UCL Anywhere
DesktopPCStrataBugsGeographic Biostratigraphic data management for both data generators and data usersStratDataTex nic centreUtilities LaTeX is a high-quality typesetting system; it includes features designed for the production of technical and scientific documentation.LatexTG ViewStatistical A Windows (95 and above) program that views and prints *.tgf files generated by the DOS version of Tilia*Graph.Illinois State MuseumThunderbirdEmail A legacy email client.MozillaTreepadUtilities TreePad is a Personal Information Manager, Organizer, Database, and Word ProcessorFreebyte.comTWINSPANStatistical A program for classifying species and samples, producing an ordered two-way table of their occurrence.CanodrawMicrosoft VisioDiagramming A diagramming program for Microsoft Windows that uses vector graphics to create diagramsMicrosoftDesktopPCVisual Basic Express EditionProgramming An object-oriented computer programming language that can be viewed as an evolution of Microsoft's Visual Basic (VB) which is implemented on the Microsoft .NET Framework.MicrosoftVLCMultimedia VLC is a portable multimedia player, encoder, and streamer supporting many audio and video codecs and file formats as well as DVDs, VCDs, and various streaming protocolsVideoLANDesktop@UCL Anywhere
DesktopPCWinbugsStatistical WindBugs is statistical software for Bayesian analysis using Markov chain Monte Carlo (MCMC) methods.Imperial College School of MedicineDesktop@UCL Anywhere
DesktopPCWindows Media PlayerMultimedia A digital media player and media library application developed by Microsoft that is used for playing audio, video and viewing images on personal computersMicrosoftDesktop@UCL Anywhere
DesktopPC
Staff WTS 2010WinkystStatistical Adds non-metric multidimensional scaling method to the Canoco for Windows packageCanodrawWinPHUtilities WinPH is a winsock-based CCSO PH (phonebook) client program. It runs under windows, and is a 32bit program.WInPHWinSCP3FTP An open source SFTP and FTP client for Microsoft Windows. Its main function is secure file transfer between a local and a remote computer. Beyond this, WinSCP offers basic file manager and file synchronization functionalityWinSCPDesktop@UCL Anywhere
DesktopPCWinTwinsThe program classifies species and samples, producing an ordered two-way table of their occurrence. The process of classification is hierarchical; samples are successively divided into categories, and species are then divided into categories on the basisThe Centre for Ecology & HydrologyDesktop@UCL Anywhere
DesktopPCCorel WordperfectOffice Suite Corel WordPerfect Office is the ideal office software for home and business users, delivering more productivity tools that make your work go faster and your life go easierCorelWorkraveAccessibility
Utilities Workrave is a program that assists in the recovery and prevention of Repetitive Strain Injury (RSI).WorkraveVisual PestStatistical Used extensively for automated model calibration and data interpretation in groundwater and surface-water hydrology, geophysics, geotechnical, mechanical and mining engineering as well as many other fields.Scientific Software GroupDesktop@UCL Anywhere
DesktopPCPhotoshop LightroomUtilities Adobe Photoshop Lightroom software is essential for today's digital photography workflow. Now you can quickly import, process, manage, and showcase your images Ã¢â¬â from one shot to an entire shoot. With Lightroom 2, you spend less time in front of the coAdobeCaptivateMultimedia With Adobe Captivate software, you can rapidly author professional eLearning content with advanced interactivity, software and scenario simulations, quizzes, and other engaging experiences Ã¢â¬â no programming or multimedia skills required. Boost your produAdobeWindows UpgradeOperating System Microsoft Windows is a series of software operating systems and graphical user interfacesMicrosoftDesktop@UCL Anywhere
DesktopPC
DesktopStaffwindows, Operating system, windows 10, windows 7, windows 11ColdFusionMultimedia Adobe ColdFusion and Adobe ColdFusion BuilderÃ¢âÂ¢ enable developers to rapidly build, deploy, and maintain robust Internet applications for the enterprise. ColdFusion allows developers to condense complex business logic into fewer lines of code.AdobePremiereÂ ElementsVideo Editing With Adobe Premiere Elements software, making incredible movies is easier than ever. Enhance your stories with professional style. Share virtually anywhere. And easily manage and protect all your video clips and photos.AdobeSQL Server Standard EditionDatabase SQL Server Standard edition includes the core database engine, along with the stand-alone services. It differs from Enterprise edition in that it supports fewer active instances (number of nodes in a cluster).MicrosoftWindows Server StandardOperating System Windows Server is one of Microsoft Windows' server line of operating systemsMicrosoftVisual Studio ProfessionalProgramming Microsoft Visual Studio is an Integrated Development Environment (IDE) from Microsoft. It can be used to develop console and graphical user interface applications along with Windows Forms applications, web sites, web applications, and web services.MicrosoftTurning PointMultimedia The voting system at UCL uses software called TurningPoint.Turning PointDesktopPCBioPerlStatistical Perl code which is useful in biologyBioPerlECRC Weather TutorialGeographic A learning tool on understanding past climates.DesktopPCMinitabStatistical Statistical softwareMinitabDesktop@UCL Anywhere
DesktopPCstaff home use, student home useOrigin ProScientific Graphing
Statistical Origin is an easy-to-use software application that provides powerful data analysis and publication-quality graphing capabilities tailored to the needs of scientists and engineers.OriginLabDesktop@UCL Anywhere
DesktopPCstaff home use, student home useAllway SyncUtilities Allway Sync is free file and folder synchronization software for Windows. Allway Sync uses innovative synchronization algorithms to synchronize your data between desktop PCs, laptops, USB drives and more. Allway Sync combines bulletproof reliability wiFetchUtilities Fetch for Mac OS X provides file transfer using both FTP and secure FTP. The client is available at no charge to educational institutionsfetch softworksiSpring FreeUtilities iSpring Free PowerPoint to Flash converter promptly creates web-friendly Flash (.SWF) presentations from your PowerPoint content (.PPT, .PPS, .PPTX, .PPSX) keeping its visual parameters, animation effects and slide transitions, audio narrations, video anISpring SolutionsMoodleTeaching & Learning UCL Moodle is the centrally supported virtual learning environment (VLE) used in over 2000 of UCL's courses and programmes to support and enhance teaching, learning and research. All members of UCL are able to login to Moodle. The Moodle service is proMoodle.orgMapInfoGeographic MapInfo Professional has the ability to combine and display, on a single map, data from a variety of sources that are in different formats and projections. The software is capable of overlaying raster and vector layers on the same map.Pitney BowesDesktop@UCL Anywhere
DesktopPCPLASModelling Software
Statistical PLAS is a software tool for modelling integrative systems in which the dynamics can be described by differential equations.JMPStatistical JMP (pronounced "jump") is a computer program that was first developed by John Sall and others to perform simple and complex statistical analyses. It dynamically links statistics with graphics to interactively explore, understand, and visualize data.SASStaff Home use, student home useVMware WorkstationUtilities virtualization software.VMwareTestUtilities These packages are for testing purposes only.Oracle DatabaseDatabase a relational database management system (RDBMS).OracleCitrix RecieverUtilities provides remote access services to multiple users across a wide range of platforms.CitrixPreviewPDF
Utilities application for displaying images and Portable Document Format (PDF) documents. (mac)ParallelsUtilities A software package providing hardware virtualization for Mac's.Exchange Server EnterpriseEmail Exchange server Enterprise Edition enables rich and productive collaboration among its users and is designed for larger organisations that may require a greater number of mailbox databases.MicrosoftRead & Write GOLDAccessibility
Utilities A literacy support software designed to assist users of all ages who require extra assistance when reading or composing text. The software provides users with dyslexia, literacy difficulties and English as a Second Language with literacy support.TextHELPExchange Server StandardEmail Exchange Server Standard Edition enables rich and productive collaboration among its users and is designed for the mailbox needs of small to medium organisations. Also appropriate for non-mailbox roles in a larger Exchange deployment.Gaussian 09Applications
Modelling Software Gaussian 09 (g09) is a system of linked programs for electronic structure modeling.Gaussian Inc.Legion
UnitySGI MPTDevelopment Tools Message Passing Toolkit from SGI (includes SHMEM implementation of MPI)UnityMPICHDevelopment Tools MPI-1 implementation (uses GNU compilers)UnityGaussian 03Applications
Modelling Software Gaussian 03 (G03) is a system of linked programs for electronic structure modeling.Gaussian Inc.Legion
UnityMolproApplications
Modelling Software Molpro is a complete system of ab initio programs for molecular electronic structure calculationsUniversity College Cardiff Consultants LimiteLegionGNU MakeDevelopment Tools Utility to maintain and automate the building of groups of programsUnityGCCDevelopment Tools GNU Compiler CollectionLegionNAG Fortran compilerDevelopment Tools
Programming Fortran compiler by NAGNAGLegionQ Logic MPI for Intel compilersDevelopment Tools MPI-1 implementationLegionOpen MPIDevelopment Tools MPI-2 implementationLegionPythonDevelopment Tools Scripting languageLegionCmakeDevelopment Tools multi-platform make utilityLegionACMLLibraries ACML (AMD Core Maths Library) provides optimized and threaded math routines.LegionARPACK/PARPACKLibraries ARPACK is a library that is designed to help solve eigenvalue problems. PARPACK is a parallel version of ARPACK for MPI.LegionBonnie++Libraries Bonnie++ is a benchmark suite that is aimed at performing a number of simple tests of hard drive and file system performance.LegionBLACSLibraries BLACS is a linear algebra orientated message passing interface. It is built for GCC and GCC 4.4.0, both with OpenMPI. Users of Intel compilers should use MKL.LegionFFTWLibraries FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST).LegionGSLLibraries The GNU Scientific Library provides numerical routines. On Legion, there are versions for all the supported compilers.LegionHDFLibraries NCSA's Hierarchical Data FormatLegionIntel-tbbLibraries Intel Threading Building Blocks.LegionIOzoneLibraries IOzone is a filesystem benchmark tool.LegionMKLLibraries The Intel MKL contains numerical libraries optimised for Intel processors.LegionNetCDFLibraries NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.LegionNetperfLibraries Netperf is a benchmark that can be used to measure the performance of many different types of networking. It provides tests for both unidirecitonal throughput, and end-to-end latencyLegionPLplotLibraries PLplot is a cross-platform software package for creating scientific plots. To help accomplish that task it is organized as a core C library, language bindings for that library, and device drivers which control how the plots are presented in non-interactivLegionScaLAPACKLibraries ScaLAPACK is a parallel subset of LAPACK. There are versions on Legion for system GCC and GCC 4.4.0 compilers with OpenMPI. This library depends on the corresponding ATLAS, OpenMPI and BLACS libraries.LegionBLASTApplications BLAST is a tool for comparing sequence information.LegionCmguiApplications Cmgui is an advanced 3D visualisation software package with modelling capabilities.LegionCP2KApplications CP2K performs atomistic and molecular simulations. There are two versions on Legion: The most recent branch version (2_1) and the trunk release as of 15th February 2011. CP2K has considerable dependencies (including a special version of OpenMPI) anLegionDL_Poly ClassicApplications DL_Poly Classic is the open source release of DL_Poly 2.LegionDL_Poly 4Applications DL_poly 4 is the latest release of DL_Poly. Please read the license before using this software.LegionLAMMPSApplications LAMMPS is an open source parallel molecular dynamics code which exhibits good scaling in a wide range of environments. The version deployed on Legion has been built as both an executable ("lmp_legion") and as a library ("liblmp_legion.a").LegionNAMDApplications NAMD is a parallel molecular dynamics package which shows exceptional scaling on a variety of systems. NAMD was developed by the Theoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the UniversityLegionGnuplotApplications Gnuplot is a commonly used command-line plotting tool.LegionGraceApplications Grace (sometimes referred to as XMGrace) is a commonly used graphing tool.LegionR & BioconductorApplications R (GNU S) is an integrated suite of software for data manipulation, analysis and graphical display with strong support for a wide range of statistical methods. A number of add-on packages are also installed. Bioconductor provides tools for the analysiCondor
Legion
UnityROOTApplications ROOT provides a set of OO frameworks for handling, analysing, and visualising large amounts of data. Included are specialised storage methods, methods for histograming, curve fitting, function evaluation, minimization etc. ROOT includes a built-in CINT C+LegionVASPApplications VAMP/VASP (Build and run instructions only) is a package for performing ab-initio quantum-mechanical molecular dynamics (MD) using pseudopotentials and a plane wave basis set.LegionVMware FusionUtilities With VMware Fusion, run the most demanding Mac and Windows applications side-by-side at maximum speeds without rebooting.VMwareQuarkXPressDesk Top Publishing QuarkXPress is design software that lets anyone create and publish rich, compelling materials for print, the Web, e-readers, tablets, and other digital media in one easy-to-use tool Ã¢â¬â no coding or programming required.GraphPad PrismStatistical A powerful combination of biostatistics, curve fitting (nonlinear regression) and scientific graphing in one comprehensive program. Easily organize, analyze and graph repeated experiments; pick appropriate statistical tests and interpret the results.AmberStatistical a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demosGreenfootProgramming Greenfoot is an Integrated Development Environment (IDE) for use by students with no previous programming experience. It includes a class browser, editor, compiler, execution, etc.G*PowerStatistical G*Power 3 is a major extension of, and improvement over, G*Power 2. It covers statistical power analyses for many different statistical testsDesktop@UCL Anywhere
DesktopPCGeoToolsProgramming Java ProgrammingDesktopPCDietPlanModelling Software
Statistical a comprehensive, high-quality and easy-to-use nutrition analysis software package for professional dietitians and nutritionistsDesktop@UCL Anywhere
DesktopPCsimplantModelling Software Dental Implant softwareDesktopPCNyquistModelling Software
Programming Nyquist is a language for sound synthesis and music composition. It is implemented in C and C++ and runs on Win32, OSX, and Linux. Nyquist combines a powerful functional programming style with efficient signal-processing primitives.Desktop@UCL Anywhere
DesktopPCBlueJProgramming BlueJ is an integrated Java environment specifically designed for introductory teaching.Desktop@UCL Anywhere
DesktopPCMPlusStatistical a statistical modeling program that provides researchers with a flexible tool to analyze their data. Only the Demo version is available on ISD ServicesRookcaseStatistical Rooks Case: Calculates Spatial Autocorrelation, Moran's I, Geary's C, Join-Count, Gi, G*i, Import IDRISI, Randomization for Monte Carlo Simulation.Desktop@UCL Anywhere
DesktopPCDispersion CalculatorStatistical This program will calculate Offense Dispersion Index and associated values for specific crime data in a fixed formatDesktop@UCL Anywhere
DesktopPCNear Repeat CalculatorStatistical calculates the risk of near repeat events in crime dataDesktop@UCL Anywhere
DesktopPCAVS4U ConverterMultimedia Convert audio between various formats: WAV, PCM, MP3, WMA, OGG, AAC, M4A, AMR and others. Add text information to your audio files.PureDataProgramming a real-time graphical programming environment for audio, video, and graphical processing.Decision Tools SuiteRisk Management The DecisionTools Suite is an integrated set of programs for risk analysis and decision making under uncertainty that runs in Microsoft Excel.PalisadeDesktopPCdtsSQL Server Enterprise CoreDatabase SQL Server Enterprise CoreMicrosoftSQL Server Standard CoreDatabase SQL Server Standard CoreMicrosoftWindows Server DatacenterDatabase Windows Server Datacenter is an advanced server platform that provides more cost-effective and reliable support for mission-critical workloads. It offers innovative features for virtualization, power savings, and manageability and helps make it eaMicrosoftLotus NotesIBM Lotus Notes is the client of a collaborative client-server platform. IBM Lotus Domino is the application server.HypathiaModelling Software the study of elementary constituents of matter and of their interactions.JMOLModelling Software an open-source Java viewer for chemical structures in 3DDesktop@UCL Anywhere
DesktopPCChem Bio Office UltraStatistical The ChemBioOffice software suite combines ChemBioDraw, ChemBio3D, ChemFinder, BioViz, BioAssay, Inventory and E-Notebook in the worldâs premier desktop suite designed for both chemists and biologists.Chem Bio Ultra, ChemOffice, CambridgesoftCasaXPSModelling Software CasaXPS processing software offers powerful analysis techniques for both spectral and imaging dataCASASystem CenterDevelopment Tools Microsoft System Center std or datacenter makes it easier for IT to empower users to be productive with a unified infrastructure that delivers and manages rich user experiences across corporate and consumer devices.MicrosoftRed HatOperating System RedHat is a UCL site licensed Linux product for servers and Workstation. If you would like to use Red Hat you must first contact your local IT Team or email isd-itpurchasing@ucl.ac.ukRed HatSharePoint ServerSharePoint Server: enables organizations to create web sites to share information with others, manage documents from start to finish, and publish reports to help make better decisions.MicrosoftOasysGeographic
Statistical Suite of Engineering SoftwaresOasysAdminStudioDevelopment Tools AdminStudio provides enterprise IT teams, including the MSI packager, with the most advanced software packaging tools to efficiently prepare reliable application packages for deployment with a complete suite of automated MSI packaging, customization, testIntel Cluster StudioDevelopment Tools Comprising: IntelÂ® C / C++ Compiler IntelÂ® Fortran Compiler IntelÂ® Integrated Performance Primitives3 IntelÂ® Math Kernel Library3 IntelÂ® Cilkâ¢ Plus IntelÂ® Threading Building Blocks IntelÂ® Inspector XE IntelÂ® VTuneâ¢ Amplifier XE Static SecurityLegion
UnityPGI Fortran/C/C++ ServerDevelopment Tools
Programming Contains The Portland Group's native parallelizing/optimizing Fortran 2003, C and C++ compilers and tools for 64 bit Linux systems.The Portland Group, Inc.LegionAccelrys DrawAccelrys Draw enables scientists to draw and edit complex molecules, chemical reactions and biological sequences with ease, facilitating the collaborative searching, viewing, communicating, and archiving of scientific information.Desktop@UCL Anywhere
DesktopPCAppGiniAppGini is a program that helps you develop web database applications instantly. You do not need to have any programming background to use it. Just define your database, set some options, click the Generate button, and you're done!CogToolCogTool is a general purpose UI prototyping tool with a difference - it automatically evaluates your design with a predictive human performance modeDesktop@UCL Anywhere
DesktopPCDistanceDistance is a Windows-based computer package that allows you to design and analyze distance sampling surveys of wildlife populations.Desktop@UCL Anywhere
DesktopPCEViewsEViews 8 offers access to powerful statistical, forecasting, and modeling tools through an innovative, easy-to-use object-oriented interfaceGDISGDIS is a GTK based program for the display and manipulation of isolated molecules and periodic systemsDesktop@UCL Anywhere
DesktopPCNetBeans IDEProgramming NetBeansTM IDE is a modular, standards-based integrated development environment (IDE), written in the JavaTM programming languageOracleCoulombGIS / Mapping Coulomb 3.0 is designed to investigate Coulomb stress changes on mapped faults and earthquake nodal planes, and is intended both for publication-directed research and for university teaching and instruction. Available with Matlab.Desktop@UCL Anywhere
DesktopPCEasy ScanModelling Software Your Surface Analysis Tool for Science and Industrial Researchenthought EPD FreeProgramming The Enthought Python Distribution provides scientists with a comprehensive set of tools to perform rigorous data analysis and visualizationGBI ClientStatistical Business IntelligenceGitHubProgramming GitHub is a web-based hosting service for software development projects that use the Git revision control systemMicrosoftchrome BrowserUtilities Google's web browserKdiffStatistical KDiff is a diff and merge programDesktop@UCL Anywhere
DesktopPCLatin drillLibrary Latin Flash Drill is an advanced system for drilling grammatical forms and for making a self-diagnosis of where help and practice is most neededDesktop@UCL Anywhere
DesktopPCMicrosoft SilverlightUtilities Microsoft Silverlight is an application framework for writing and running rich Internet applications, with features and purposes similar to those of Adobe Flash.Desktop@UCL Anywhere
DesktopPC
DesktopStaffMorphologicaModelling Software is a set of integrated tools for examining size and shape variation among objects described by sets of landmark coordinates. These tools provide for 2 and 3 dimensional visualisation of shape and shape differences.Oxygen XML editorWeb Editing oXygen XML Editor is a cross platform XML Editor providing tools for XML authoring, XML conversion, XSL, XSLT, XQuery, XML Schema, DTD, Relax NGDesktop@UCL Anywhere
DesktopPCParaViewStatistical ParaView is an open-source, multi-platform application designed to visualize data sets of size varying from small to very large.DesktopPCpetraCAD Software
Geographic Petra is an integrated application with a common database and interface for project and data management, well log analysis, mapping, cross-sections, seismic integration, production and reservoir analysis and 3D visualization.psych toolboxDevelopment Tools
Statistical Psychophysics Toolbox Version 3 (PTB-3) is a free set of Matlab and GNU/Octave functions for vision research. It makes it easy to synthesize and show accurately controlled visual and auditory stimuli and interact with the observerQuantum GISGIS / Mapping Quantum GIS (QGIS) is a user friendly Open Source Geographic Information SystemRASCWUtilities n/aDesktop@UCL Anywhere
DesktopPCRev ManUtilities Review Manager (RevMan) is the software used for preparing and maintaining Cochrane Reviews.RStudioStatistical Powerful IDE for R. RStudio IDE is a powerful and productive user interface for R. It's free and open source, and works great on Windows, Mac, and Linux.SafariWeb Browser Apple's Web BrowserDesktop@UCL AnywhereSenseModelling Software Sense software to be used with a SenseBoardSignProcModelling Software Sign-proc is a CUI-based (command line) tool to process gene network files, including converting file formats, extracting sub networks, colouring the specified nodestpsDIGModelling Software Digitize coordinates of landmarks and capture outlines.Desktop@UCL Anywhere
DesktopPCVisITStatistical VisIt is a free interactive parallel visualization and graphical analysis tool for viewing scientific data on Unix and PC platforms.Visual Studio expressProgramming Visual Studio Express tools, you can build the next great app for Windows 8, Windows Phone, and the webDesktop@UCL Anywhere
DesktopPCwin ptUtilities WinPT or Windows Privacy Tray is frontend to the Gnu Privacy Guard (GnuPG) for the Windows platform.Desktop@UCL AnywhereWindows LiveUtilities Windows Live is the former collective brand name for a set of services and software products from Microsoft; part of their software plus services platformWSxM DevelopUtilities WSxM (Windows Scanning (where x = Force, Tunneling, Near Optical, ...) Microscope) is a powerful and user-friendly Windows application for Data Acquisition and Processing in Scanning Probe Microscopy (SPM).Dragon NaturallySpeaking PremiumUtilities Dragon NaturallySpeaking Premium ignites new levels of productivity by letting you interact with your PC by voice at work, home or school. Dictate or modify documents, spreadsheets and presentations, send email, search the Web and more. Even captureNuanceKaleidagraphUtilities KaleidaGraph contains the comprehensive toolset you need to get your graphing and data analysis done quickly and easilyNAG Toolbox for MatlabApplications
Mathematical
Programming
Statistical The NAG Toolbox for MATLAB is a large and comprehensive numerical toolkit that both complements and enhances MATLAB. It contains over 1,500 functions that provide solutions to a vast range of mathematical and statistical problems.NAGLegionAdobe Creative Cloud CCApplications
Capture
Desk Top Publishing
Graphic Editing
Multimedia
PDF
Screen Capture
Video Capture
Video Editing
Web Editing Creative Cloud is a collection of 20+ desktop and mobile apps and services for photography, design, video, web, UX and more.Adobecc suite, Indesign, Photoshop, Dreamweaver, Illustrator, Acrobat, staff home use, student home use, corel, presenter, indesign, premiere pro, acrobat Pro, audition, spark,Cambridge Crystallographic Data CentreLibraries Comprehensive of the published literature and highly curated, the Cambridge Structural Database (CSD) is an essential resource to scientists around the worldCCDCLabTutorTeaching & Learning With LabTutor you can create and manage feature-rich courses and conduct lessons either in a traditional laboratory setting, or over the web.ADInstrumentsDesktopPCLINGOUtilities Lingo for Windows has been designed to meet the needs of translators, localizers and businesses that need to create and maintain their own terminology bases, dictionaries or glossaries, whether monolingual or multilingual.LexicoolMemoQApplications
Utilities MemoQ is a computer-assisted translation software suite which runs on Microsoft Windows operating systems. MemoQ provides translation memory, terminology, machine translation integration and reference information management in desktop, client/serverKilgray FordÃtÃ¡stechnolÃ³giai Kft.DesktopPCMendeleyPDF
Reference Management Mendeley is a desktop and web program for managing and sharing research papers, discovering research data and collaborating online. It combines Mendeley Desktop, a PDF and reference management application with Mendeley Web, an online social network foElsevierDesktop@UCL Anywhere
DesktopPCModel BuilderModelling Software ModelBuilder is used to build, validate, execute and deploy high-fidelity predictive models of chemical processes, which can be validated against experimental or plant data using built-in advanced parameter estimation techniques.Process Systems EnterpriseOmegaTApplications
Utilities OmegaT is a free translation memory application written in Java. It is a tool intended for professional translators.pgAdminDatabase
Development Tools
Utilities PGAdmin is an Open Source administration and development platform for PostgreSQLProtege DesktopApplications
Diagramming
Utilities ProtÃ©gÃ© Desktop supports creation and editing of one or more ontologies in a single workspace via a customizable user interface.AB TutorUtilities AB Tutor is the perfect teaching tool for networked classrooms and labs, allowing you to simply and effectively control, manage, monitor, demonstrate, support and collaborate with your students. Computers in the classroom have created amazing opportunDesktopPCAnaconda PythonDevelopment Tools Completely free enterprise-ready Python distribution for large-scale data processing, predictive analytics, and scientific computingAntConcQualitative Analysis A freeware corpus analysis toolkit for concordancing and text analysis.DesktopPCBB Flashback ExpressMultimedia
Sound Recording
Video Capture
Video Editing Create great demos and tutorials, with BB FlashBack Express. The free screen recorderDesktop@UCL Anywhere
DesktopPCBentley MicrostationCAD Software 3D CAD Design and Modeling Software for Architecture, Engineering, Construction and OperationsChemCADModelling Software CHEMCAD is Chemstationsâ intuitive suite of chemical process simulation software that broadens an engineerâs capabilities and increases productivity. CHEMCAD supercharges an engineerâs efficiency when facing the toughest chemical process models or addressDesktop@UCL Anywhere
DesktopPCDROIDUtilities DROID is a software tool developed by The National Archives to perform automated batch identification of file formats. Developed by our Digital Preservation department as part of its broader digital preservation activities, DROID is designed to meet the fDesktop@UCL Anywhere
DesktopPCEnthought CanopyDevelopment Tools Enthought Canopy is a comprehensive Python analysis environment that provides easy installation of the core scientific analytic and scientific Python packages, creating a robust platform you can explore, develop, and visualize on. In addition to its pre-bFileOpenDocument Management FileOpen provides tools to decide exactly who can view documents and files, when and from which devices.DesktopPCDeja VuUtilities DÃ©jÃ Vu is is a customizable Computer Aided Translation (CAT) system.Desktop@UCL Anywhere
DesktopPCEclipse IDE for Java DevelopersDevelopment Tools The essential tools for any Java developer, including a Java IDE, a CVS client, Git client, XML Editor, Mylyn, Maven integration and WindowBuilder This package includes: â¢Eclipse Git Team Provider â¢Eclipse Java Development Tools â¢Maven IntegratiEclipseDesktop@UCL Anywhere
DesktopPCFree OCRUtilities Free-OCR.com is a free online OCR (Optical Character Recognition) tool. You can use this service to extract text from any image you supply. This service is free, no registration necessary. We also do not need your email address. Just upload your iDesktop@UCL Anywhere
DesktopPCGIMPDevelopment Tools GIMP is an acronym for GNU Image Manipulation Program. It is a freely distributed program for such tasks as photo retouching, image composition and image authoring. It has many capabilities. It can be used as a simple paint program, an expert quality Desktop@UCL Anywhere
DesktopPCGITGit is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency. Git is easy to learn and has a tiny footprint with lightning fast performance. It outclasses SCDesktopPCProTrackProject Management ProTrack is a project management software tool.OR-ASProTrack PSGProject Management
Teaching & Learning The Project Scheduling Game (PSG) is an IT-supported simulation game to get acquainted with dynamic project scheduling using the critical path method.OR-ASDesktopPCSafeView PluginPlug Ins SafeView is a Digital Rights Management plugin for IE and FirefoxDesktop@UCL Anywhere
DesktopPCSDL Trados and MultiTerm DesktopApplications
Utilities SDL MultiTerm Desktop is a desktop terminology management tool.SDLDesktopPCSDL MultiTerm ExtractApplications
Utilities SDL MultiTerm Extract is a tool used to build searchable glossaries.SDLDesktopPCSimpleOCRApplications
Document Management
Utilities This software converts black and white scans or TIFF images to editable text files or MS Word documents.Google Chinese Pinyin input MethodApplications The pinyin method (simplified Chinese: æ¼é³è¾å¥æ³; traditional Chinese: æ¼é³è¼¸å¥æ³; pinyin: pÄ«nyÄ«n shÅ«rÃ¹ fÇ) refers to a family of input methods based on the pinyin method of romanization. In the most basic form, the pinyin method allows a user to input ChineseGoogleDesktop@UCL Anywhere
DesktopPCGradeProQualitative Analysis
Statistical This software allows you to create a Summary of Findings (SoF) table. You can import data from a Review Manager 5 file, edit the data, and then export a Summary of Findings table or import it into a Review Manager 5 file. GRADEpro performs many of the calIntellijDevelopment Tools IntelliJ IDEA is a Java integrated development environment (IDE) for developing computer software. It is developed by JetBrains, and is available as an Apache 2 Licensed community edition,[1] and in a proprietary commercial edition.K-Lite CodecApplications
Multimedia K-Lite Codec Pack is a collection of audio and video codecs for Microsoft Windows that enables the operating system and its software to play various audio and video formats generally not supported by the operating system itself. K-Lite Codec Pack also incSQL DeveloperDatabase
Development Tools Oracle SQL Developer is a development environment that simplifies the development and management of Oracle Database.OracleSWI-PrologDevelopment Tools
Programming SWI-Prolog offers a comprehensive free Prolog programming environment.System QuirkApplications
Utilities System Quirk is a flexible package of integrated tools for building and managing term bases.Desktop@UCL Anywhere
DesktopPCTiliaScientific Graphing
Utilities Tilia is spreadsheet and graphics software orginally developed for fossil pollen and for producing stratigraphic pollen diagramsDesktop@UCL Anywhere
DesktopPCUnity Web PlayerMultimedia The Unity Web Player enables you to view 3D content created with Unity directly in your browser.Unity TechnologiesDesktopPCVPythonProgramming VPython is the Python programming language plus a 3D graphics module called Visual. VPython allows users to create objects in 3D space and displays these objects in a window.DesktopPCLexTermUtilities Lexicography and Terminology Management SystemDesktopPCPhet Membrane ChannelsModelling Software Insert channels in a membrane and see what happens. See how different types of channels allow particles to move through the membrane.PhETKCVFITApplications Curve fitting software for PharmacologyDesktop@UCL Anywhere
DesktopPCQuickTime PlayerMultimedia Plays a number of multimedia formats including MP3, MPEG-4, QuickTime, Windows Media, and multiple versions of proprietary RealAudio and RealVideo formatsAppleDesktop@UCL Anywhere
DesktopPCSMART NotebookTeaching & Learning SMART Notebook software provides the tools to create and deliver interactive learning experiences across year group levels, subjects and learning styles.SMART TechnologiesDesktopPCStopWatchUtilities A Flash based stop watch.Desktop@UCL Anywhere
DesktopPCNernst/Goldman Equation SimulatorScientific Graphing A program which graphs the Nernst/Goldman Equation in real time based on user defined K+, Na+ and Cl- parameters.Michael BranchMySQL WorkbenchDatabase MySQL Workbench provides DBAs and developers an integrated tools environment for: Database Design & Modeling SQL Development Database Administration Database MigrationLanguage, Proof and LogicTeaching & Learning Language, Proof and Logic covers topics such as the boolean connectives, formal proof techniques, quantifiers, basic set theory, and induction.DesktopPCMicro Drainage EducationalModelling Software MicroDrainage PRODUCTS MicroDrainage New in MicroDrainage 2014 Micro Drainage Brochure Video Demos XPDRAINAGE XPSTORM MicroDrainage 2014 MicroDrainage is a world class drainage design tool. Used for 30 years, thiDesktopPCSimaProModelling Software SimaPro, the leading LCA tool, can help you put the metrics behind your sustainable product development and sustainability goals. You can make solid decisions to positively change your productâs life cycle.Interactive Ground Water 2DModelling Software IGW is a real-time, interactive and visual software system for unified deterministic and stochastic groundwater modelingToad for OracleDatabase Toad for Oracle is the a productivity solution for Oracle database development and administration.DesktopStaffSibeliusSound Recording Create and share scores quickly with easy-to-use notation software designed for beginning and intermediate composersTechtool ProUtilities Techtool Pro s a robust hardware diagnostic tool available for Macintosh. Drive Repair and Data Recovery, so you can get back to work. Repair damaged volumes, identify files in bad blocks, recover deleted filesECRI Rigel Anaylstgeospatial processing & analysis The most accurate and reliable geographic profiling available. Now, easier to use than ever. Create custom layouts with free placement of floating and docked windows across multiple monitors, collapse windows to tabs, save case-specific layouts. CustomizDesktopPCEKKO ProjectGeographic EKKO_Project features unique managing and display of GPR line data and ancillary data, enhanced viewing of file attributes, and the biggest benefit â use of a single file to store all information in a GPR project. All GPR data, GPS, topography, photos, nDesktopPCSubtitle WorkshopUtilities Subtitle Workshop is a free application for creating, editing, and converting text-based subtitle files.DesktopPCAnsysCAD Software Ansys publishes engineering analysis software across a range of disciplines including finite element analysis, structural analysis, computational fluid dynamics, explicit and implicit methods, and heat transfer.SolidworksCAD Software SOLIDWORKS solutions cover all aspects of your product development process with a seamless, integrated workflowâdesign, verification, sustainable design, communication and data managementstudent home useDragon Pro for MacUtilities Dragon for Mac delivers fast speech recognition, along with versatile transcription and mobility features, to drive individual productivity at workNuancenuance3ds MaxModelling Software 3ds Max is 3D modelling, rendering and animation softwareInventorCAD Software Inventor 3D CAD software offers an easy-to-use set of tools for 3D mechanical design, documentation, and product simulationAutodeskautodeskCaptivaCapture
Scanning
Utilities UCL scanning solutionOpenTextScanning, Capture, UtilitiesGaussian 16Applications
Modelling Software Gaussian 16 is a system of linked programs for electronic structure modeling.Gaussian Inc.Tableau Desktop professionalQualitative Analysis Tableau is a business intelligence (BI) toolPDF SAM BasicPDF a free, open source, multi-platform software designed to split, merge, extract pages, mix and rotate PDF filesstudent home use, staff home usePower PDF AdvancedPDF Power PDF is the ultimate PDF solution. Perfect for the individual or the enterprise, itâs simply the best way to gain control over PDF files. Power PDF provides superior accuracy, industry standard PDF compatibility and is exceptionally easy to useNuance, power PDF, PDFGurobi OptimizerMathematical
Modelling Software
Statistical The Gurobi Optimizer is a solver for mathematical programming.DeepsoilDiagramming
Mathematical
Modelling Software DEEPSOIL is a unified 1D equivalent linear and nonlinear site response analysis platformRapidSetApplications RapidSet allows easy and quick change of the color of the background and the font of all applications without having to go through the Screen Properties dialogs, making the computer more convenient for people with visual impairments.BalabolkaAccessibility
Utilities free text to speech programme which can also save text in a sound formatOratoAccessibility
Utilities Orato is a free text-to-speech engine with highlighting.ssOverlayAccessibility
Utilities ssOverlay (the ss stands for Scotopic Sensitivity), places a coloured overlay onto the screen with customisable transparency.Virtual Magnifying GlassAccessibility
Utilities Virtual Magnifying Glass is designed for visually-impaired and others who need to magnify a part of the screen. It zooms the screen through a lens that follows your mouse.NVDAAccessibility
Utilities screen reader for blind and vision impairedLastPass EnterpriseUtilities LastPass, a password manager, password generator and vault.Last passthink-cellOffice Suite
Reporting Tools think-cell is a presentation software which makes the task of creating professional PowerPoint presentations easy and efficient. It contains an Excel add-in for consistently rounding numbers across complex calculations and multiple worksheets, and integraSophos Home EditionAnti Virus An Anti Virus recommended for use with UCL's VPN. Not for use on UCL machines.Sophos, Home, personal, Anti Virus, student home use, staff home usef.luxUtilities f.lux is a program that adjusts a display's color temperature according to location and time of day, offering functional respite for the eyes. The program is designed to reduce eye strain during night-time useTrelisModelling Software Trelis is a high-end, commercial-grade pre-processor for complex FEA and CFD simulationStructurizrDiagramming The quickest way to create software architecture diagramsPLS_toolboxUtilities PLS_Toolbox software is the worldâs most extensive suite of essential and advanced chemometric multivariate analysis tools for use within the MATLABÂ® computational environmentAdobe Creative Cloud sharedApplications
Desk Top Publishing
Graphic Editing
Multimedia
Screen Capture
Video Capture
Video Editing
Web Editing Adobe Creative Cloud suite for open space areas onlyAdobecc suite, Indesign, Photoshop, Dreamweaver, Illustrator, Acrobat, staff home use, student home use, corel, presenter, indesign, premiere pro, acrobat Pro, audition, spark,Microsoft TeamsOffice Suite Microsoft Teams allows you to collaborate with your co-workers through instant messaging, online meetings and sharing of documents.MicrosoftSkype, teams, Zoom, webinarMicrosoft Teams dial in featureOffice Suite This is needed to allow people to dial in to a meeting. Good to be used with externals.MicrosoftSkype, teams, Conferencing, meetings, teamviewer, zoomOffice 365 Desktop AppsOffice Suite Office 365 is a line of subscription services offered by Microsoft as part of the Microsoft Office product lineMicrosoftOffice, word, excel,accessArticulate 360Teaching & Learning Articulate 360 includes both Storyline 360 and Rise 360, plus a slew of other authoring apps. Use Storyline 360 to develop custom, interactive courses that work on every deviceâwithout any manual tweaking.Cubase Pro 10.5Sound Recording Used by star producers and musicians for composing, recording, mixing and editing music, Cubase Pro combines outstanding audio quality, intuitive handling and a collection of highly advanced audio and MIDI tools.Avantage softwareModelling Software Complete Surface Analysis SoftwareTableau Public VersionFree public version of TableauTableau AcademicTableau Desktop and Tableau Prep Builder are free for students and instructors around the worldZoom MeetingsUtilities A remote conferencing service that combines video conferencing, online meetings, chat, and mobile collaboration. Use as alternative to Microsoft Teams or Blackboard Collaborate to support global synchronous teaching events. Also integrated into Moodle.webinarTableau ReaderOpen visualisations built in Tableau Desktop1FuzionUtilities Secure Real-Time Text Streaming PlatformPhoneGapApplications Adobe PhoneGap is a standards-based, open-source development framework for building cross-platform mobile apps with HTML, CSS and JavaScript for iOS, Androidâ¢ and WindowsÂ® Phone 8.AdobeDWG TrueViewApplications View DWG files or convert them to work with older versions of AutoCAD software.AutodeskNavisworks ManageApplications Navisworks Manage project review software helps you holistically review integrated models and data with stakeholders to gain better control over project outcomes. Integration, analysis, and communication tools help teams coordinate disciplines, resolve coAutodeskRevitApplications Use Revit to produce consistent, co-ordinated and complete model-based building designs and documentationAutodeskAxure RP ProApplications Axure RP Pro is a wireframing, rapid prototyping, documentation and specification software tool aimed at web, mobile and desktop applications. It offers drag and drop placement, resizing, and formatting of widgets.InVivoStatApplications InVivoStat is a powerful, free to use, statistical software package which uses R as its statistics engine.InkscapeApplications Inkscape is a free and open-source vector graphics editor. This software can be used to create or edit vector graphics such as illustrations, diagrams, line arts, charts, logos, icons and complex paintingsItasca FLACModelling Software A numerical modelling software for advanced geotechnical analysis of soil, rock, groundwater, and ground support in two dimensionsAvidemuxApplications Avidemux is a free and open-source transcoding and video editing software, designed for easy-to-use and simple video editing and video processingJorg Muller FreeMindProject Management
Reporting Tools A premier free mind-mapping software written in JavaGSViewApplications GSview is a graphical interface for GhostscriptJulian Spencer CatsCradle 4.0Utilities
Web Editing A web page editor for professional language translators.KCP Technologies FathomStatistical
Teaching & Learning Learning and teaching statisticsMissionMakerApplications MissionMaker is a game-authoring software tool for making 3D videogamesKudlanSoft I Can AnimateMultimedia
Video Capture
Video Editing Stop Motion Animation SoftwareMedia SubtitlerApplications Media Subtitler is the best choice for creating, editing and fixing external subtitle files for all video types fast and easilyAegisubApplications Aegisub is a free, cross-platform open source tool for creating and modifying subtitles. Aegisub makes it quick and easy to time subtitles to audio, and features many powerful tools for styling them, including a built-in real-time video preview.HaploViewApplications Haploview is designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses.TopSpinApplications TopSpin for NMR data analysis and the acquisition and processing of NMR spectra.Cabri 3DApplications Cabri 3D is a software application which provides you with tools for creating and manipulating objects in a 3D environment.ThinLincApplications ThinLinc is a remote desktop server tailored for Linux distributions.Foxit ReaderApplications PDF readerInkscapeApplications Inkscape is an multi-platform, Open-Source Vector Graphics Editor that uses SVG as its native file format.2Simple SuiteApplications Creative educational software suite including 2Animate, 2Connect, 2Create, 2Create A Story, 2Draw, 2Investigate, 2Simulate, Developing Tray and Infant Video ToolkitLingoes Project Lingoes TranslatorUtilities An easy and intuitive dictionary and text translation softwareLittleRiverInst KinemageMotion Graphic
Utilities An interactive graphic scientific illustrationMartinKulldorff SatScangeospatial processing & analysis
Statistical Analyzes spatial, temporal and space-time data using the spatial, temporal, or space-time scan statistics.McNeel RhinocerosModelling Software 3-D ModelingMemsource EditorTeaching & Learning
Utilities Computer Aided Translation toolMicrosoft Essentials 2012Video Capture
Video Editing Movie MakerMicrosoft Kodu Game LabDevelopment Tools
Programming A visual programming language for creating gamesMicrosoft Photo Story 3Utilities To create audiovisual presentations out of your photos and images.Microsoft Small BasicProgramming A simplified programming language and environment to help teach programming to beginners.Microsoft Access Database EngineUtilities To facilitate transfer of data between Microsoft Office System files and non-Microsoft Office applications.MIT Scratch 2Utilities offline editorMIT StarLogo TNGProgramming To create 3D games and simulations for understanding complex systems.MLwiNStatistical A statistical software package for fitting multilevel modelsModelistica TranusModelling Software An integrated land use and transport modelling systemImageJApplications
Programming
Utilities A Java-based image processing programNatural Resources Canada RETScreen SuiteModelling Software
Utilities A Clean Energy Management Software system for energy efficiency, renewable energy and cogeneration project feasibility analysis as well as ongoing energy performance analysis.Ocean Informatics OpenEHR Archetype EditorUtilities A tool to develop archetypes for use in both point-of-care and research settings.OhbotModelling Software
Utilities Educational robotics systemOoonaUtilities
Video Capture
Video Editing Professional online tool for subtitling and captioningOpenBUGSStatistical A statistical tool to perform Bayesian inference Using Gibbs SamplingOpen Proof Project Language Proof LogicApplications
Utilities Application of software to problems in logicOpenText Webtop pluginUtilities pluginPortico (SITS) ClientUtilities Portico (SITS) ClientPraat with Charis & Doulos SIL FontsUtilities fontsQueen Mary University Sonic VisualiserMultimedia
Sound Recording
Utilities Visualisation, analysis, and annotation of audio recordings.Rockefeller University LINKAGEStatistical Statistical genetics program - Two-locus linkage analysisSafe FME Desktopgeospatial processing & analysis
Utilities To facilitate data integration workflowsScion Corporation Scion ImageCapture
Utilities It is used for capture, showing, analyzing, enhancing, measuring digital pictures.SeismoSoft SeismoSignalgeospatial processing & analysis To process strong-motion data, featuring a user-friendly visual interface and the capability of deriving a number of strong-motion parameters often required by engineer seismologists and earthquake engineers.Stanford University ePADDUtilities A quantitative imaging informatics platformStrathclyde University WinEDRSound Recording
Utilities A Windows program with continuous recording to disk features for single-channel, noise and miniature synaptic current analysis.Strathclyde University WinWCPUtilities A Windows program for recording and analysing signals from whole cell voltage and current clamp experiments.TechSmith Jing (Capture)Screen Capture
Utilities To create basic screenshots and screen recordings and share them with others.TeXStudioUtilities An integrated writing environment for creating LaTeX documentsThe National Archives Digital Record Object IUtilities To automatically profile a wide range of file formatsThermo Fisher Scientific SeqScannerUtilities It allows you to view, edit, print, and export data generated using Applied Biosystems genetic analyzer instruments after data has been processed by Sequencing Analysis Software.TRL JunctionsGeographic
geospatial processing & analysis
Modelling Software Modelling and analysis of roundabouts, priority junction and signalised junctionsTRL OSCADY PROGeographic
geospatial processing & analysis
GIS / Mapping
Modelling Software Prediction of capacities, queues, delays at isolated signalised junctionsTRL TRANSYTGeographic
geospatial processing & analysis
GIS / Mapping
Modelling Software A macroscopic software package for designing, evaluating and modelling everything from single isolated road junctions to large mixed signal-controlled and priority control traffic networks.UCL B100 Cell Equilibrium Sim 1Utilities UCL B100 Cell Equilibrium Sim 1UCL Biochemical Simulations 1Utilities UCL Biochemical Simulations 1UCL Histology WebPagesUtilities UCL Histology WebPagesUCL WindkesselUtilities UCL WindkesselUCSF ChimeraUtilities An extensible program for interactive visualization and analysis of molecular structures and related dataUK Science Consortium EarthScienceUtilities UKScienceConsortium EarthScienceVisual Computing Lab MeshLabUtilities Processing and editing 3D triangular meshesWordQ + SpeakQSpeech Capture
Utilities Assistive technology toolXMindAccessibility
Project Management
Utilities Mind mapping toolFileZillaApplications FileZilla is a cross-platform FTP applicationVu-BarApplications Vu-Bar is a tool that can be used by people that suffer from dyslexia. The application allows the user to select the bar width, 25%, 50%, 75% or 100% of screen width and set the slot height to the required font size.T-BarApplications A simple text reading helper for people with Scotopic SensitivityBioeditApplications BioEdit is a biological sequence alignment editorSketchpadApplications Sketchpad is an interactive geometry software program for exploring Euclidean geometry, algebra, calculus, and other areas of mathematicsSPSS AMOSStatistical Amos is a powerful structural equation modeling software helping support your research and theories by extending standard multivariate analysis methods, including regression, factor analysis, correlation, and analysis of variance.SPSS, AMOsMagMapApplications MagMap is a post acquisition processing software used to analyze and process data from a number of different instrumentsMagPickApplications MagPick is designed to edit, process, interpret and present land, marine or airborne magnetometer survey data.CSAZApplications Cesium Sensor Active Zone Software (CSAZ) provides a graphical solution for proper sensor orientationInQuestApplications InQuest is designed to convert between the ETRS89 (WGS84) and OSGB36 National Grid coordinate systems using the same transformation modelsAutographApplications Autograph is a comprehensive and lightweight software that helps you to easily and quickly generate mathematical graphs.GPlatesApplications GPlates is an application for the interactive visualisation of plate-tectonics.QualtricsUtilities Survey ToolsurveyOpinioUtilities A survey tool - supported by ISDQualtrics, surveyAxiomReporting Tools Axiom is a reporting product used to report on financial dataFLOWJOScientific Graphing platform for single-cell flow cytometry analysis.Autodesk Fusion 360CAD Software Fusion 360 CAD/CAM software connects your entire product design & development process in a single toolAutodeskautodesk, autocadRobot Structural Analysis ProfessionalCAD Software AutodeskÂ® Robotâ¢ Structural Analysis Professional software provides structural engineers with advanced building simulation and analysis capabilities for large, complex structures. The software offers a smooth workflow, enabling engineers to more quickly pAutodeskautodeskDesignBuilderDesignBuilder is now the most widely used energy modelling toolAsta PowerprojectProject Management Construction scheduling software for construction project management. Construction planning softwareFigshare UploaderUtilities figshare is a repository where users can make all of their research outputs available in a citable, shareable and discoverable manner. Used for UCL Research Data Repositorystorage, Figshare, UCL Research Data RepositoryMS Visual Studio CodeUtilities Visual Studio Code is a code editor redefined and optimised for building and debugging modern web and cloud applicationscodeNCBI OsirisOSIRIS is a public domain quality assurance software package that facilitates the assessment of multiplex short tandem repeat (STR) DNA profiles based on laboratory-specific protocolsNeo4j Graph PlatformNeo4j is purpose-built to work with highly connected data, delivers lightning-fast performance and enables powerful, actionable insightsAurdinoApplications open-source IDECodeBrowserApplications CodeBrowser is a folding and syntax highlighting text editorEasySenseApplications EasySense allows data to be displayed and analysed in many different ways.CytoscapeApplications Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating with gene expression profiles and other state dataDynareApplications Dynare is a software platform for handling a wide class of economic models, in particular dynamic stochastic general equilibrium (DSGE) and overlapping generations (OLG) models.NetLogoModelling Software NetLogo is a multi-agent programmable modelling environment. It is used by many tens of thousands of students, teachers and researchers worldwideCootModelling Software Coot is for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data.FolditModelling Software Foldit is a revolutionary crowdsourcing computer game enabling you to contribute to important scientific researchSeismoMatchModelling Software SeismoMatch is an application capable of adjusting earthquake accelerograms to match a specific target response spectrumSeismoStructCAD Software Civil Engineering Software for Structural Assessment and Structural RetrofittingMembrane Action Potential.Passive Design AssistantA software tool that demonstrates the principles of the passive thermal design of buildings.Tallis ComposerApplications Tallis Composer is a graphical editor that supports the authoring process.Focus on Bee-BotApplications Focus on Bee-Bot software suiteSalsa JApplications Salsa J software data analysisTarsiaApplications Formulator Tarsia is an editor designed for puzzlesGeoGebraApplications math tools for graphing, geometry and 3DDMDXApplications DMDX is used to measure reaction times to visual and auditory stimuliFacilityCMISApplications timetabling softwareBioSolveApplications BioSolve suiteCellProfilerApplications CellProfiler is software for measuring and analyzing cell images.MentimeterCreate presentations with real-time feedbackpresentations meetingsSlidointeractive web platform, aimed at the audience during various meetings or conferencesMinecraft EducationMinecraft for educationDocuSignDocument Management allows organizations to manage electronic agreements.Adobe sign, Doc u sign, Dropbox, signDropboxDocument Management Dropbox is a file hosting servicedropbox, storageoverleafOverleaf Professional accounts are available for all UCL students and staff. Overleaf Professional is a collaborative, online LaTeX editor that is designed to make the process of writing, editing and producing research papers and project reports much quiclatex, sharelatexLabsterOnline, interactive, virtual science lab simulationsLTOnline, interactive, customisable virtual science lab simulations.Talis ElevateOnline collaborative annotation software. Can annotate websites. Cannot annotate graphic based text.Hypothes.isOnline collaborative annotation software. Cannot annotate websites. Can annotate graphic based text.OTIS â the virtual patientAudiometry training with virtual patientsCoCalcVirtual online workspace for calculations, coding and collaboration.OverleafA collaborative cloud-based LaTeX editor used for writing, editing and publishing scientific documentsSnapGeneMolecular Cloning Toolpavlovia.orgModelling Software Pavlovia is a place for the wide community of researchers in the behavioural sciences to run, share, and explore experiments online.SimcenterModelling Software Simcenter FloEFD: a premier frontloading CFD simulation toolCFDAWSAmazon Web Services offers reliable, scalable, and inexpensive cloud computing services.Storage, AmazonJIRA cloudJira Software is built for every member of your software team to plan, track, and release great software.JIRA, Atlassian, AgileArcGIS OnlineAccess to UCL Online ArcGIS Page, for ArcGIS pro and ESRI training.Arcgis Pro, Online, ESRI trainingScrintalSpeech Capture Transcription software and morerefinitiv WorkspaceFinancial Access unmatched financial data, news and content coverage in a highly customized workflow experienceBiorenderBioRender is a web-based program that helps you create scientific figures up to 50x faster than traditional tools. The tool combines a library of over 50,000 scientifically accurate, expert-validated life science icons and templates with intuitive drag-anPresentations; Lab & Team Meetings; Publications; Posters; Visual Protocols; Whiteboarding; Educational Materialsensor AccessAccessibility
PDF Convert PDFs, JPEGs and other files into an e-book, text file, audio or braille. You can combine more than one .JPG into a single file.Sensus ApS

Computational Tools

This list was seeded by the participants of the 2008 workshop on Standards and Specifications in Synthetic Biology.

Please feel free to add information about a computation tool for synthetic biology (CADs, simulators, databases, lab managements systems, automation software, anything) to the list. Place it alphabetically, name the main project contributors, provide a canonical link to the program, and add a paragraph of descriptive text. Please date your entry.

Antimony

http://antimony.sourceforge.net/Lucian Smith, Deepak Chandran, Herbert Sauro

Antimony is a human-readable and human-writable language for describing biological modules. The modules can be connected together by declaring overlapping molecular species between two modules or via the PoPS in/PoPS out interface. The language is similar to the Jarnac language introduced by Herbert Sauro several years ago.

Athena

http://www.washington.edu/staff/deepakc/downloads/InstallAthena.exeDeepak Chandran, Frank Bergmann, Herbert Sauro

Athena is a tool for building, simulating, and analyzing genetic circuits (as well as metabolic/signaling networks, such as SBML files). It provides a visual interface for building biological modules that can be saved and later connected together. The connection can be achieved using either the PoPS interface or by defining overlapping molecular species (similar to the concept of module in CellML and SBML). In addition to simulation, Athena supports a few other useful features: Database of Ecoli regulatory network from RegulonDB, Graphical view of part sequence, Automated derivation of transcription rate equations, Interface to all Systems Biology Workbench programs, Interface with R statistical language, Easy plugin architecture

Note: Athena has been succeeded by Tinkercell

TinkerCell is a highly flexible visual tool. Although still in development, it will have all the features in Athena. In addition, TinkerCell allows a family tree of biological parts to be loaded from a database. TinkerCell comes with a drawing program that allows users to draw their own graphical representations (if they do not like the defaults). C libraries, such as simulations or graph analysis, can easily be incorporated into TinkerCell. New plug-ins can also be added very easily.

BioJade

http://web.mit.edu/jagoler/www/biojade/Jonathan Goler

BioJADE is a design and simulation tool for synthetic biological systems. BioJADE is written in Java, and makes interactive use of BioBrick Repositories. BioJADE enables system designers to specify a system abstractly, tune it, simulate its behavior using a variety of simulators, and finally package the part for use by either the designer or the public.

BioMortar

http://igem.uwaterloo.ca/BioMortarAndre Masella

BioMortar is a lab management system designed specifically to deal with BioBricks. It is also capable of generating cookie-cutter protocols from user-specified templates and tracking the results, including gel images. It is released under the MIT License.

BioStudio

Sarah Richardson, Joel Bader, Jef Boeke

BioStudio is both an integrated development environment and a genome version control system, with the ability to modify nucleotide sequences automatically or manually at multiple resolutions. It uses Gbrowse from the GMOD project for its user interface and is currently able to locate and manipulate potential and existing restriction enzyme recognition sites, identify and incorporate unique sequences for PCR identification of wildtype and synthetic sequence, edit existing genome features, and incorporate and annotate user-created genome features. Each version of the genome is encoded in a Gene Feature Format (GFF) file, which is then displayed by the open source annotation viewer GBrowse and stored in a branching version control system. Collaboration and transparency is accomplished through the use of a wiki. Each feature in a GFF file will have a corresponding article in the wiki, where registered users can actively discuss its treatment. To ensure that BioStudio actually meets the needs of synthetic biologists, it is under development alongside the design of a synthetic Saccharomyces cerevisiae genome, SC2.0.

BrickIt

http://brickit.wiki.sourceforge.net/Raik Gruenberg and you?

BrickIt aims to create a portable web-based registry that helps synthetic biologists to plan, organize and track their local biobrick samples. The database-backed web server can be downloaded as virtual machine to quickly set up a local registry which coordinates the work within a lab, institute or community. Although the data remain local, the web server itself is an open-source project and new functions or improvements can be easily exchanged between the different local registries. BrickIt thus also offers a platform for the shared development of tools and infrastructure that foster the collaboration within the Synthetic Biology community. BrickIt and everything it relies on are open source and free. BrickIt itself is licensed under the GPL.

Clotho

http://www.clothocad.orgDouglas Densmore, J. Christopher Anderson, Alberto Sangiovanni-Vincentelli

Clotho presents a design environment to manipulate DNA sequence information and store the manipulated data as packaged "parts" back to part repositories. It provides a robust sequence editing environment (highlighting, restriction enzyme library, basic DNA analysis features), a parts management system (database browsing, search, and manipulation), and an algorithm manager which allows the introduction of user developed algorithms (currently includes assembly algorithms). The tool is very much in the early stages of development but an alpha release is available. Clotho is part of a larger development of platform-based design tools for synthetic biology. The tool is open source under a BSD license.

Cytostudio

http://moleculamaxima.com/Molecula Maxima

DilutionMagic

http://www.dilutionmagic.org/dilutionMagic

DilutionMagic is a clever dilution calculator which can calculate your serial dilution steps. It can do it for arbitrary concentrations values and arbitrary volumes.

GeneDesign

http://www.genedesign.orgSarah Richardson, Joel Bader, Jef Boeke

GeneDesign is a suite of algorithms that allow users to edit several features of protein coding sequences, including codon usage and restriction enzyme recognition site presence. It will then generate a list of oligos and a road map for the assembly of the sequence by PCR It is written in Perl and is served over the internet; the code is available for local installations. A new, improved version is due before the end of 2008. PMID: 16481661

Gene Designer

https://www.dna20.com/tools/genedesigner.phpDNA2.0

This integrated, stand-alone secure software helps you create DNA constructs on your desktop with unprecedented ease and speed. Available for Mac and PC. For details see Villalobos et al.

GeNetDes

http://soft.synth-bio.org/genetdes.htmlGuillermo Rodrigo, Javier Carrera, Alfonso Jaramillo

GeNetDes is a tool to design transcriptional networks with targeted behavior that could be used to better understand the design principles of genetic circuits. It is a Simulated Annealing optimization algorithm that explores throughout the space of transcription networks to obtain a specific behavior. The software outputs a transcriptional network with all the corresponding kinetic parameters in SBML format. Our tool can also be applied to design networks with multiple external input and output genes. The software, a tutorial manual, parameter sets and examples are freely available in our website. We are currently extending Genetdes to design networks by assembling standardized biological part models. The models contain data obtained from part characterizations. We will evolve such circuits by replacing model parts to reach the imposed design specifications. In addition, we will incorporate the effect of the chassis by including the interaction with the cellular resources.

GenoCAD

http://www.genocad.orgYizhi Cai, Michael Czar, Julie Marchand, Jean Peccoud

GenoCAD is a web-based application guiding users through the design of part-based genetic systems. GenoCAD uses context-free grammars to formalize design strategies for synthetic genetic systems. This approach provides a path to organizing libraries of genetic parts according to their biological functions. It also provides a framework for the systematic design of new genetic constructs consistent with the design principles expressed in the grammar. Using parsing algorithms, GenoCAD enables the verification of existing constructs.doi:10.1093/bioinformatics/btm446

Genome Compiler

Genome Compiler is an intuitive all-in-one software platform for life scientists in the genetic engineering, molecular biology and synthetic biology fields, and provides a comprehensive tool for:

DNA design and visualization
Data management
Collaboration platform
Seamless DNA ordering

Genome Compiler is free for academia users and is available online and in a downloadable version so you can easily access your data on Genome Compiler from anywhere you are. The software supports Windows and Mac. In addition, the software supports common file formats such as: FASTA, Vector NTI, SnapGene, Geneious, Clone Manager, Serial Cloner, Plasma DNA, ApE, DNAStar, etc.

Metabolic Tinker

http://osslab.lifesci.warwick.ac.uk/Tinker.aspxKent McClymont, Orkun S Soyer

TINKER is a metabolic pathway design/search tool. It compiles the entire set of known reactions and compounds from the latest version of the Rhea database and converts this data into a directed graph. Nodes and edges on this graph correspond to metabolites and reactions, respectively, and thus the entire graph corresponds to the current known metabolic universe. Within this graph, TINKER searches for thermodynamically feasible paths between user defined "source" and "target" compounds and returns the found paths as metabolic pathways (rank-ordered by thermodynamic feasibility)

Operon Calculator

http://salislab.net/softwareDaniel Cetnar, Tian Tian, Iman Farasat, and Howard M. Salis

The Operon Calculator combines 15 biophysical models and design rules to automatically design synthetic operon sequences for maximum tunable control over RNA and protein expression levels. The algorithm also eliminates the presence of several overlapping, undesired genetic elements that will inevitably break the operon's function.

https://salislab.net/software/OperonCalculator_ForwardDesign

ProMoT

http://www.mpi-magdeburg.mpg.de/projects/promot/Katrin Kolczyk, Sebastian Mirschel, Michael Rempel, Mario A. Marchisio

ProMoT is the process modeling tool designed for the convenient setup of synthetic biology models in a modular fashion. Genetic circuits are built just by placing biological parts on a canvas (using drag and drop) and by connecting them through ”wires” that enable ﬂow of signal carriers, as it happens in electrical engineering. ProMoT supports two different modeling approaches -- a quantitative and a qualitative modeling approach. The quantitative approach is based on differential algebraic equations (DAEs) whereas the qualitative approach is a description of the system in the form of logical equations. The final code associated with a circuit can be exported into Matlab or SBML format (Level-1 and Level-2) allowing to run both deterministic and stochastic simulation.

For more detailed information, please refer to the recent papers ProMoT: Modular Modeling for Systems Biology and Computational design of synthetic gene circuits with composable parts or the synthetic biology research page Synthetic Biology at ETH Zurich.

Ribosome Binding Site (RBS) Calculator

http://salislab.net/softwareHoward Salis, Ethan Mirsky, and Christopher Voigt, Nature Biotechnology, v27, 2009

The Ribosome Binding Site (RBS) Calculator is an engineering design method that predicts the translation initiation rate of a protein coding sequence in bacteria. You can use the RBS Calculator to generate synthetic ribosome binding site sequences and to rationally control the production rate of any protein in bacteria from 0.1 to 100,000+ on a proportional scale.

https://salislab.net/software/forward

The RBS Calculator is used by GenScript to synthesize DNA sequences with custom-designed ribosome binding sites.

The RBS Calculator is embedded into Genome Compiler, an intuitive all-in-one software platform for DNA design, which is free for academics to use.

Relevant papers: Translation Rate is Controlled by Coupled Trade-offs between Site Accessibility, Selective RNA unfolding and Sliding at Upstream Standby Sites

A Predictive Biophysical Model of Translational Coupling to Coordinate and Control Protein Expression in Bacterial Operons

Automated Design of Synthetic Ribosome Binding Sites to Control Protein Expression

Riboswitch Calculator

http://salislab.net/softwareBreakthrough Article: Espah Borujeni A., D.M. Mishler, J. Wang, W. Huso, and H.M. Salis. Nucleic Acids Research. v44(1). 2016

Riboswitches are shape-changing regulatory RNAs that bind chemicals and regulate gene expression, directly coupling sensing to cellular actuation. The Riboswitch Calculator designs synthetic translation-regulating riboswitches that bind to specific chemicals and activate gene expression. Starting with a known RNA aptamer, the algorithm automatically optimizes the (up to) 30 nucleotide sequences that appear before and after the RNA aptamer to maximize the activation of gene expression. The algorithm combines a statistical thermodynamic model of translation with genetic algorithm optimization. The algorithm's predictions were validated by constructing and characterizing 62 synthetic riboswitches that utilized six different RNA aptamers to sense a diverse range of chemicals (theophylline, tetramethylrosamine, fluoride, dopamine, thyroxine, 2,4-dinitrotoluene). The riboswitches' activation ratios were the highest reported to-date for their respective RNA aptamers.

https://salislab.net/software/RiboswitchCalculator_EvaluateMode

Relevant paper: Automated Physics-based Design of Synthetic Riboswitches from Diverse RNA Aptamers

RBS Library Calculator

Iman Farasat, Manish Kushwaha, Jason Collens, Michael Easterbrook, Matthew Guido, and Howard Salis, Molecular Systems Biology, v10(6). 2014

The RBS Library Calculator designs the smallest RBS library sequence that uniformly searches a desired translation rate space, enabling one to efficiently identify optimal protein expression levels in plasmid- or chromosomally-encoded genetic systems. The algorithm has three modes. Search mode allows one to explore the largest possible translation rate space, across a 100,000-fold proportional scale, using the smallest RBS library (16 to 32 variants). Zoom mode allows one to design a minimal RBS library to search a targeted translation rate space between a minimum and maximum. Genome Editing mode designs genomic RBS libraries with a minimal number of consecutive mutations, suitable for designing the mutagenic oligonucleotides needed for MAGE genome mutagenesis. The method has been used to efficiently tune genetic circuits and optimize metabolic pathways.

Relevant paper: Efficient Search, Mapping, and Optimization of Multi-protein Genetic Systems in Diverse Bacteria

https://salislab/software/RBSLibraryCalculatorSearchMode

RoVerGeNe

http://iasi.bu.edu/~batt/rovergene/rovergene.htmGregory Batt, Calin Belta

RoVerGeNe is a software tool for the analysis of dynamical properties of gene networks. Unlike conventional ODE numerical simulation tools, it allows

to test whether a dynamical property holds for ranges of parameters
and to find parameter sets for which a given dynamical property hold

The tool is thus useful for robustness analysis and tuning of gene networks. See Bioinformatics paper.

SBW

SBW (Systems Biology Workbench)

SimThyr

http://simthyr.sf.netJohannes W. Dietrich

SimThyr is a continuous numeric simulation program for thyroid homeostasis. It is based on a parametrically isomorphic model of the overall system. Applications of this program cover research, including development of hypotheses, and education of students in biology and medicine, nurses and patients.

Relevant papers:

Citation: Dietrich JW (1994-2016) SimThyr 4.0. Fairfax, VA: sourceforge, http://simthyr.sf.net. RRID:SCR_014351.

SynBioSS

http://synbioss.sourceforge.net/Yiannis Kaznessis, Tony Hill, Vassilis Sotiropoulos, Jonathan Tomshine

SynBioSS (Synthetic Biology Software Suite) is a software suite for the quantitative simulation of biochemical networks using hybrid stochastic algorithms. We believe that one shouldn’t need to know how to program (or use command-line) to use sophisticated numerical methods. Through this software, we intend to put the most powerful techniques for simulating chemically reacting networks into the hands of biologists (or any scientist who can put them to good scientific use). SynBioSS can accurately simulate any system modeled as a network of reactions. In order to achieve this result, we wrapped up state-of-the-art algorithms inside a user friendly graphical interface (GUI) that handles input data, runs the simulations and vividly visualizes simulation results, without requiring any programming background from the user. The software is open and runs on any of the three platforms most used by scientists: Windows, Macintosh, and Linux.

Synbiotools

http://synbiotools.orgSwapnil Bhatia (Boston University)

Synbiotools hosts a free and growing software suite for engineering biology including tools for visualization, combinatorial genetic design generation, circuit design, and build automation.

TinkerCell

Engineering platform for building and testing cellular circuits (Deepak Chandran, UW, Seattle)

TinkerCell is an extensible platform for editing and simulating cellular networks. Users can operate the software at different levels including graphical point and click or via an interactive console. While the main interface is visual, programmers may add new features by writing custom programs in C or Python. TinkerCell is designed to incorporate information from database(s), thus the models store information such as rate constants, gene sequences and promoter strengths. Networks can be "modularized" and connected to one another. TinkerCell is cross platform and written in C++. A Python console is provided for interactive control.

http://www.tinkercell.com/Home

TinySeq.com

http://tinyseq.comJason Morrison, Mackenzie Cowell

TinySeq is the minimal minimal part storage tool. It assigns a unique url to a given sequence, and stores the sequence's construction format & plasmid. TinySeq supports part composition via the url, so you can get the assembled sequence of two parts simply by asking for something like tinyseq.com/mlc:1+mlc:2. We built tinyseq to reveal what other features besides assigning an accession number (mlc:1) to a sequence would be useful for users at a lab bench who are looking for tools to help them keep their assemblies in order.

PCEnv

http://www.cellml.org/tools/pcenv/Andrew Miller, Justin Marsh, Alan Garny

PCEnv is an environment for creating and simulating arbitrary mathematical models, including mathematical models in the fields of systems and synthetic biology. PCEnv uses CellML as a native format for storing models.

PROTDES

http://soft.synth-bio.org/protdes.htmlMaria Suarez, Pablo Tortosa, Alfonso Jaramillo

Synthetic Biology will benefit from future efforts using first-principles to design biological macromolecules. Ideally, this would mean using the same software and parameters to fold a protein than to design a protein with a given fold (inverse folding problem). Recent work has demonstrated that it is possible to experimentally validate such approaches, by using appropriate physical modelling. We have developed a tool able to incorporate such successful procedures by using a leading molecular dynamics software. Our tool PROTDES is an open-source toolbox for computational protein design using the CHARMM package. This allows the integration of molecular dynamics within the protein design, allowing to extend the physical description more than it has been possible with current software. The procedure automatically finds the suitable mutations optimizing a protein folding free energy. It mutates residue positions to find the best amino acids in an arbitrary protein structure without requiring pairwise approximations. It implements an heuristic optimization algorithm that iteratively searches the best amino acids and their conformations for a an arbitrary set of positions within a structure. The users will be able to create their own procedures for protein design using their own physical protocol, which we exemplify by already incorporating three alternative effective energy functions.Our versatile software will allow synthetic biologists using physical models to use a standard molecular dynamics software for protein design.

j5

http://j5.jbei.orgNathan J. Hillson

Recent advances in Synthetic Biology have yielded standardized and automatable DNA assembly protocols that enable a broad range of biotechnological research and development. Unfortunately, the experimental design required for modern scar-less multipart DNA assembly methods is frequently laborious, time-consuming, and error-prone. A web-based software tool, j5, automates the design of scar-less multipart DNA assembly protocols including SLIC, Gibson, CPEC, and Golden Gate. The key innovations of the j5 design process include cost optimization, leveraging DNA synthesis when cost-effective to do so, the enforcement of design specification rules, hierarchical assembly strategies to mitigate likely assembly errors, and the instruction of manual or automated construction of scar-less combinatorial DNA libraries. j5 can be used to build combinatorial libraries and applied to the preparation of linear gene deletion cassettes. These innovations save researchers time and effort, reduce the frequency of user design errors and off-target assembly products, decrease research costs, and enable scar-less multipart and combinatorial DNA construction at scales unfeasible without computer-aided design. The j5 software has been exclusively licensed to TeselaGen Biotechnologies for commercial use and distribution.

DeviceEditor

http://j5.jbei.orgJoanna Chen, Douglas Densmore, Timothy Ham, Zinovii Dmytriv

A web-based bioCAD software tool, DeviceEditor, provides a graphical design environment that mimics the intuitive visual whiteboard design process practiced in biological laboratories. The key innovations of DeviceEditor include visual combinatorial library design, direct integration with scar-less multi-part DNA assembly design automation, and a graphical user interface for the creation and modification of design specification rules. DeviceEditor liberates researchers from DNA base-pair manipulation, and enables users to create successful prototypes using standardized, functional, and visual abstractions. Open and documented software interfaces support further integration of DeviceEditor with other bioCAD tools and software platforms. DeviceEditor saves researcher time and institutional resources through correct-by-construction design, the automation of tedious tasks, design reuse, and the minimization of DNA assembly costs. The DeviceEditor software has been exclusively licensed to TeselaGen Biotechnologies for commercial use and distribution.

VectorEditor

https://public-registry.jbei.org/static/vesa/VectorEditor.htmlZinovii Dmytriv, Timothy Ham, Hector Plahar, Joanna Chen

Open source, web based cross platform and cross browser DNA sequence editing and analysis tool.

iGEM Software

http://igem.synbioreview.com/Michal Galdzicki

A reference collection of iGEM software projects 2007-2011. This is a compilation of all the software projects large and small created throughout the iGEM competition. On this site you can find the description of the computational tool, a link to the project page and source code.

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change decision load job for Slate to include decisionJointProgram 3/29/2016 DITR LIte Touch PROD Update Windows 7 Base WIM to (2016-03-17) Patches 3/25/2016 Touchstone PROD CAMS application update 3/24/2016 Atlas PROD Atlas 8 - enhancements and release 3/24/2016 Admissions PROD CHG0033934 - Load undergrad veteran data into MITSIS 3/23/2016 Summer Catalog PROD MAJOR UPDATE: Use Courseleaf to replace the paper process of creating the summer catalog 3/21/2016 GitHub PROD Update to 2.3.10 3/20/2016 Storage PROD EMC VNX2 code upgrade (OC11 NIST) 3/17/2016 WTW (Who's Teaching What) PROD CHG0033904 - Online Subject Evaluation - Change to a filter on a report, CopyToUSB License key a change to a snapshot that's taken at the end of a survey window and is used to create that report. 3/16/2016 Developer Portal PROD Converting Anypoint portal to require Touchstone for access, URL will change to https://anypoint.mit.edu/ 3/15/2016 Admissions PROD Annual acceptances go live 3/14/2016 SAP (all services) PROD Downtime for security patches 3/13/2016 Grade20 PROD Preparation for yearly Admissions decisions 3/10/2016 Learning Modules PROD Spring semester patch release 3/10/2016 SAP Facilities PROD Correct Plant Mit snapgene Crack Key For U printing issue 3/10/2016 SAP Finance PROD Return hard error when posting document to customer marked for deletion 3/10/2016 SAP Finance PROD Text edits to 'RWBP Trial balance' report 3/10/2016 SAP Payroll PROD Apply SAP Year End 2015 Phase II for U.S. Tax Reporter 3/10/2016 SAP Logistics PROD Correct false duplicate invoice kickouts in eShip feed 3/10/2016 SAP Payroll PROD Change text on termination reason for action code HF 3/10/2016 SAP Facilities PROD Correct issues with ZPM_NOTIF_WO_RPT report 3/10/2016 SAP Facilities PROD Shop paper for events should display activity code 3/10/2016 SAP Finance PROD New role for transaction 'FD06' 3/10/2016 Admissions PROD RA Verify page go live on new decisions app 3/7/2016 MITnet PROD ROLLOUT: Network edge switch cutover to UPS power -- Building 35 3/4/2016 Distributed Software Diskdigger license key free Announce Mac OS X 10.11 known issues 3/4/2016 MITnet PROD ROLLOUT: Network edge switch cutover to UPS power -- Building 18 3/3/2016 MITnet PROD ROLLOUT: Network edge switch cutover to UPS power -- Building 11 3/2/2016 Drupal Cloud PROD 3.9 Release 3/1 - 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Computational approaches for effective CRISPR guide RNA design and evaluation

Guanqing Liu,^a,^bYong Zhang,^a,^c,^⁎ and Tao Zhang^a,^b,^d,^⁎

Guanqing Liu

^bJiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China

Find articles by Guanqing Liu

Yong Zhang

^cDepartment of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China

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Tao Zhang

^bJiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China

^dJoint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China

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Author informationArticle notesCopyright and License informationDisclaimer

^bJiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China

^cDepartment of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China

^dJoint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China

Yong Zhang: nc.ude.ctseu@619gnoygnahz; Mit snapgene Crack Key For U Zhang: nc.ude.uzy@oatgnahz

^⁎Corresponding authors. nc.ude.ctseu@619gnoygnahz, nc.ude.uzy@oatgnahz

Received 2019 Aug 29; Revised 2019 Nov 9; Accepted 2019 Nov 15.

This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

Abstract

The Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/ CRISPR-associated (Cas) system has emerged as the main technology for gene editing. Successful editing by CRISPR requires an appropriate Cas protein and guide RNA. However, mit snapgene Crack Key For U, low cleavage efficiency and off-target effects hamper the development and application of CRISPR/Cas systems. To predict cleavage efficiency and specificity, numerous computational approaches have been developed for scoring guide RNAs. Most scores are empirical or trained by experimental datasets, and scores are implemented using various computational methods. Herein, we discuss these approaches, focusing mainly on the features or computational methods they utilise. Furthermore, we summarise these tools and give some suggestions for their usage. We also recommend three versatile web-based tools with user-friendly interfaces and preferable functions. The review provides a comprehensive and up-to-date overview of computational approaches for guide RNA design that could help users to select the optimal tools for their research.

1. Introduction

Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/CRISPR-associated (Cas) systems, such as Cas9 [46] and Cas12a (formerly Cpf1) [118], are the primary tools used for genome editing due to their various abilities to manipulate, detect, and image certain DNA and RNA sequences in the cell [50]. The CRISPR/Cas system was first adapted for genome editing in 2012 [31], [46], and subsequent studies have transformed the CRISPR RNA (crRNA) and trans-activating crRNA (tracrRNA) into a single guide RNA (sgRNA) that can bind to both the Cas9 protein and the target DNA sequence. Cas9 protein and sgRNA complex first scans the appropriate PAM sequence and binds to the targeted genome loci, mit snapgene Crack Key For U, then the activated HNH and the RuvC nuclease domain of Cas9 function to make a DNA double-strand break (DSB) in the specific region [22], [69].

CRISPR-based gene editing is implemented with sequence-specific nucleases (SSNs) and a sgRNA to achieve precise gene knock-out (KO) or gene knock-in (KI). Additionally, mit snapgene Crack Key For U, researchers developed a catalytically inactive Cas9 (dCas9) that loses endonuclease activity, and has been adapted for gene expression regulation (CRISPRa/i) and 3D genome studies [33], [66], [67], [70], [84], [88]. Furthermore, base editing using modified nCas9 has greatly broadened application of the CRISPR system [32], [52], [123]. Compared with previous mature gene editing tools such as zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) [9], [10], [13], [100], [121], which use engineered proteins to target and cleave specific genome loci, CRISPR is lower in cost of both time and money. This advancing technology is increasingly being deployed, and has great potential for clinical detection, gene therapy and agricultural improvement [3], [21], [50], [126].

However, two major challenges hinder the development and application of the CRISPR/Cas system: potential off-target effects, and on-target efficiency (Fig. 1) [112], [120], mit snapgene Crack Key For U. Successful CRISPR guide RNA (gRNA) design can resolve these issues [23], [96], mit snapgene Crack Key For U, and powerful computational approaches facilitate in silico gRNA design [19], [34], mit snapgene Crack Key For U, [104], thereby enabling the design of specific gRNAs for particular experiments.

2. Evaluation of CRISPR cleavage efficiency

In theory, the CRISPR/Cas protein scans the PAM sequence, and sgRNA recognises target loci and activates endonuclease activity to cleave specific sites. However, cleavage efficiency varies greatly among different target sites and/or cell lines [14], [21], [27], [28], [51], [78], [87], [98], [99], [103], [115], [117], [122], [125], suggesting that several features may influence the binding and cutting efficacy of the sgRNA-Cas complex. Numerous studies have revealed that gRNA sequence features (sequence composition, nucleotide position, GC content), genetic and epigenetic features (chromatin accessibility, gene expression) and energetics properties (RNA secondary structure, melting temperature, free energy) all contribute to gRNA efficacy. Based on these features, many computational tools have been developed for designing mit snapgene Crack Key For U efficient gRNAs. Herein, we introduce these tools based on their features, and evaluate their mit snapgene Crack Key For U (Table 1).

Table 1

Computational methods for evaluation of guide RNA efficiency.

Tool	Enzymes	Data source	Main features	Quantitative metrics
E-CRISP [38]	Cas9	–	SC, GF	–
CRISPRscan [78]	Cas9, Cpf1	Zebrafish	SC	Spearman correlation = 0.309, from [36]
evaluateCrispr [40]	Cas9	Drosophila	SC	Spearman correlation = 0.074, from [36]
sgRNAScorer [14], [15]	Cas9, Cpf1	Human	SC, EGF	Spearman correlation = 0.225, from [36]
SSC [112]	Cas9	Human, Mouse	SC	Spearman correlation = 0.274, from [36]
WU-CRISPR [106]	Cas9	Human, Mouse	SC, EP	Spearman correlation = 0.215, from [36]
Azimuth [23], [29]	Cas9	Human, Mouse	SC, GF, EP	Spearman correlation = 0.366, from [36]
CRISPRater [55]	Cas9	Human	SC, GF	Pearson correlation = 0.399, from [55]
CRISPRpred [86]	Cas9	Human, Mouse	SC, EP	ROC-AUC = 0.85, from [86]
CASPER [75]	Cas9, Cpf1	–	SC	Pearson correlation = 0.443, from [75]
DeepCpf1 [47]	Cpf1	Human	SC, EGF	Spearman correlation = 0.748, from [47]
TSAM [82]	Cas9	Human, Mouse, Zebrafish	SC, GF, EP	Spearman correlation = 0.4, from [82]
TUSCAN [105]	Cas9	Human, Mouse, Zebrafish	SC, GF	Spearman correlation = 0.12, from [105]
uCRISPR [119]	Cas9	–	SC, EP	Spearman correlation = 0.3, from [119]

Open in a separate window

2.1. Guide RNA sequence features

The nucleotide composition of a target sequence is one of the most important determinants of gRNA efficiency [24], [103], [107], [112]. Large-scale CRIPSR-based screens in mammals have shown that guanines are preferred in positions 1 and 2 before the PAM sequence [103], while thymines are disfavoured within +/-4 nucleotides surrounding the PAM sequence [107]. Additionally, sequences downstream of PAMs can influence gRNA efficiency, while sequences upstream have no significant effect [24]. Cytosine is preferred at the CRISPR/Cas9 cutting site (-3 position proximal to PAM) [21], [112], and the GC content of the region 4–13 bases downstream of the Mit snapgene Crack Key For U sequence contributes to gRNA efficiency. Based on this key information, several efficiency prediction models have been constructed.

Rule Set 1 is a predictive model built using data derived from 1,841 sgRNAs in human and mouse [24], the score is predicted by a support vector machine (SVM) model, and a supervised learning method classifies data in a generalised linear manner, mit snapgene Crack Key For U. Rule Set 1 is mainly used to investigate sequence features that influence CRISPR cutting efficiency. Results predicted by this model show a high correlation with experimental results. To improve the accuracy, the authors adapted more datasets and built a new model in 2016 called Rule Set 2 [23]. In this model, position-independent nucleotide counts and the location of the sgRNA target site within the gene were considered to improve predictions based on their observations. These optimised models were applied for gRNA design for both CRISPR KO and CRISPRa/i experiments. A package to predict the gRNA efficiency based on the models was also developed and implemented in Broad Institute GPP sgRNA Designer [29].

To unravel the nucleotide preference of gRNA target sites in different CRISPR-based editing events, both CRISPR KO and CRISPRa/i libraries in mammals were screened [112], mit snapgene Crack Key For U significant differences in nucleotide preference between CRISPR KO and CRISPRa/i were detected. Elastic Net is a regularised regression method for fitting and classifying data that performs better than SVM in some cases [128]. The Elastic Net algorithm was used to construct models for both CRISPR KO and CRISPRa/i, and they were applied in Spacer Scoring for CRISPR (SSC) software to predict the efficiency of gRNA. Platforms such as E-CRISP, CHOPCHOP and CRISPR-FOCUS also include this model [12], [38], [57].

The Church laboratory developed software called sgRNA scorer to calculate sgRNA on-target scores based on their SVM model [14]. A second version of the sgRNA scorer software was proposed that improved the on-target prediction power and added prediction for other Cas systems such as SaCas9 and AsCpf1 [15]. Housden et al. then used a drug target method to screen CRISPR KO efficiency in Drosophila and developed an efficiency prediction tool [40]. CASPER integrated scores from CRISPRscan and added some key for beyond compare features to maximise correlations between scores and on-target experimental data [75]. This tool can also detect off-target scores and perform multipopulational analysis.

2.2. Genetic and epigenetic features

Genetic and epigenetic features like chromatin accessibility, gene position and expression are also important factors that influence sgRNA binding and Cas nucleases cleavage. Many researches have demonstrated that nucleosomes inhibit Cas9 target cleavage, and DNase I hypersensitivity and epigenomic markers alter gRNA efficacy [23], [39], mit snapgene Crack Key For U, [44], [101], [116]. Based on these features, several tools have been developed. By borrowing knowledge from oligonucleotide design and nucleosome occupancy models, an R package called predictSGRNA was proposed for evaluation of sgRNA efficacy [53], and this performed better than other models such as Azimuth and sgRNA scorer [14], [23], [29].

Non-homologous end joining (NHEJ) and microhomology-mediated end joining (MMEJ) are two major pathways which produce heterogeneous repair outcomes when repairing Cas9-mediated DSBs. People use CRISPR/Cas9 system to knock out genes by inducing indels into target genome location. However, CRISPR-based gene KO may induces in-frame variants in which gene functions are retained. Thus, microhomology-based prediction of CRISPR on-target efficiency should be considered. To this end, Bae et al. developed Microhomology-Predictor to improve KO efficiency by reducing in-frame editing [7]. Recent researches have showed that template-free Cas9-editing outcomes are predictable. inDelphi was the first model for precise prediction of CRISPR editing genotype [90]. Soon after, a mit snapgene Crack Key For U predictor called FORECasT was developed using >40,000 sgRNAs in different cell lines [5]. It was shown that most reproducible mutations are single base insertion, short deletions or longer microhomology-mediated deletions, in addition, Cas9-editing outcomes were cell-line-dependent. The Shendure laboratory also built a predictive model called Lindel for prediction of the insertions and deletions of CRISPR/Cas9-mediated DSB repair based on local sequence context [16]. All these approaches are sure to assist users in guide RNAs selection for gene disruption.

CRISPR-Cpf1 achieves high efficiency and suffers minor off-targets, besides, Cpf1 prefers AT-enriched regions. Hence, more and more studies have adapted Cpf1 for KO screens. However, models for evaluation of Cpf1 cleavage efficiency are lacking. DeepCpf1 is an algorithm especially for prediction of Cpf1 activity [47]. It is implemented within the deep-learning framework and chromatin accessibility data. This program can significantly improve the accuracy of Cpf1 activity prediction. In addition, models for other Cas experiments, such as Cas9, xCas9, and base download express vpn cracked version for pc Crack Key For U are also provided on the author’s GitHub (https://github.com/MyungjaeSong/Paired-Library). CRISPR-DT is a recently developed platform for prediction of Cpf1 target efficiency [127]. This SVM model displayed better performance than the deep learning-based model employed in DeepCpf1.

2.3. Energetics properties

The energetics associated with the formation of the DNA, gRNA and Cas protein complex are regular and can be analysed to eliminate bias among different models, since some energetics methods may better illustrate the Cas9 editing efficacy [95], mit snapgene Crack Key For U, [107], [113]. CRISPRpred includes the positions of nucleotides as well as secondary structures of sgRNAs to predict the cleavage efficiency, and this performs better than Rule Set 1 [24], [86], mit snapgene Crack Key For U. Zhang et al. recently demonstrated a free energy scheme called uCRISPR for evaluating the Cas9 editing efficacy, as well as off-target effects [119]. This model is thought to apply to any cleavage-activity Cas9 dataset.

2.4. Other considerations for gRNA efficiency

Of note, these predictive models were trained by individual experiments and rules, and each model generates different on-target scores for sgRNAs, hence users must be careful when evaluating or designing guide RNAs using these models in their own experiments. However, several key features are reliable, such as guanine preference, GC Corel PaintShop Pro 24.0.0.113 Crack with Product Key Free Download, seed region and the secondary structure of gRNAs [65], [91], [106], [112].

The accuracy of different models is controlled by their learning methods or the approaches of CRISPR activity measurement. Doench et al. tested multiple training methods and selected the best-performing one as the kernel of their model [23]. TUSCAN, a random forest-based model, outperformed models built solely by linear regression [78], mit snapgene Crack Key For U, [105]. A two-step averaging method (TSAM) for the mit snapgene Crack Key For U of cleavage efficiencies also performed better than many other models [14], [23], [82], [112]. Additionally, measurement using sequencing data rather than phenotypic data may generate fewer false positive results, albeit at a cost [105].

3. Prediction of CRISPR cutting specificity

The how to install autodesk inventor 2019 crack Free Activators obstacle for the application of CRISPR is off-target effects. CRISPR nucleases may cleave unintended genomic sites and cause unexpected mutations due to sgRNAs recognising DNA sequences with a few mismatches and/or DNA/RNA bulges, referred to as off-target cleavage [41], [120]. Off-target effects can be effectively relieved by predicting CRISPR cutting specificity and designing optimal gRNAs [41]. To predict the specificity of CRISPR gRNAs, two main methods have been proposed: (1) alignment-based method. Based on conventional or specialized algothrims, gRNAs are aligned to a given genome and off-target sequences and sites are returned. This method is mainly used for find out all potential off-targets in mit snapgene Crack Key For U, (2) Scoring-based method. sgRNAs should be further scoring and ranking using identified off-targets from alignment process to select the most specific one for experiments. Two scoring approaches are shown: hypothesis-driven, where off-targets are scored based on the contribution of specific genome context factors to gRNA specificity; learning-based, where gRNAs are scored and predicted from a training model that considers the different features affecting specificity. These methods for prediction of gRNA specificity are discussed below and some of them are summarised in Table 2.

Table 2

Computational methods for prediction of guide RNA specificity.

Tool	Enzymes	Methods	Main features	Quantitative metrics
CasOT [108]	Cas9	alignment	unlimited mismatch number, mit snapgene Crack Key For U, paired-gRNA mode, annotation	slow
Cas-OFFinder [8]	costom	alignment	unlimited mismatch number, GPU acceleration, web support	middle, fast (use GPU)
sgRNAcas9 [110]	Cas9	alignment	max 5 mismatches, paired-gRNA mode, annotation, risk evaluation	slow
FlashFry [74]	costom	alignment	unlimited mismatch number, multiple on/off-target scores, mit snapgene Crack Key For U, annotation	fast
Crisflash [43]	Cas9	alignment	unlimited mismatch number, variant data support	fast
MIT [41]	Cas9	scoring	20 bp sgRNA without PAM	ROC-AUC = 0.87, from [36]
CCTop [93]	Cas9, Cpf1	scoring	empirically score based on number of mismatches	ROC-AUC = 0.77, from [36]
CFD [23]	Cas9	scoring	20 bp sgRNA with PAM (enable non-canonical PAM)	ROC-AUC = 0.91, from [36]
CRISPRoff [4]	Cas9	scoring	energetics property and sequences composition	ROC-AUC = 0.98, from [4]
uCRISPR [119]	Cas9	scoring	energetics property and sequences composition	Pearson correlation = 0.75, from [119]
CRISTA [1]	Cas9	scoring	machine learning, sequences composition and epigenetic feature	ROC-AUC = 0.96, from [1]
Elevation [62]	Cas9	scoring	machine learning, integrate both CFD model and epigenetic features	ROC-AUC = 0.98, from [62]
DeepCRISPR [18]	Cas9	scoring	deep learning, sequences composition and epigenetic feature	ROC-AUC = 0.98, from [18]

Open in a separate window

3.1. Alignment-based methods

In theory, potential off-target sites can be identified by aligning gRNA sequences to the reference genome based on sequence homology. Bowtie [59] and BWA [61] are traditional tools for short sequence alignment that are capable of off-target detection [36], [104]. However, there are several potential issues when using these tools. First, mit snapgene Crack Key For U, tools like Bowtie and BWA cannot identify small PAMs, since these alignment tools were developed for next-generation sequencing (NGS) read alignment. Second, these tools allow very limited mismatches in their seed regions, making alignment with default parameters impractical for identifying all potential off-target sites. A survey using bowtie2 [58] to detect off-targets failed to mit snapgene Crack Key For U all possible off-target sites, and could only find off-targets with up to one mismatch [23].

Despite the defects, some gRNA design methods utilise these tools, and parameters have been modified to fit the demand for off-target prediction. CCTop uses Bowtie to find off-target sites by first identifying PAM sites, and matches and mismatches in protospacer sequences are then searched for by bowtie with modified parameters [93]. Up to five mismatches are allowed in the protospacer as more mismatches may prevent DSB induction. CCTop also implements an off-target score for each candidate sgRNA. CHOPCHOP detects off-target sites using Bowtie with parameters -v and -L for searching sgRNA core mit snapgene Crack Key For U [77]. CRISPOR uses BWA to find all potential off-target sites in iterative mode (“-N”), and can find all validated off-targets as well as Cas-OFFinder [8], [36].

In addition to these traditional tools, many other tools and algorithms have been developed for off-target site detection. Cas-OFFinder is one of the most popular tools for searching potential off-target sites, and advantages include no limit to the number of mismatches, PAM types, gRNA mit snapgene Crack Key For U or high running speed with GPUs. Cas-OFFinder can also predict off-target sites with 1 bp deletions or insertions (i.e. DNA/RNA bulges). CasOT is implemented to find Cas9 on-target sites from input sequences, as well as potential off-target sites with up to six mismatches in the seed region (12 nt adjacent to the PAM). This google sketchups can also determine whether off-targets are within a coding exon [108]. Meanwhile, sgRNAcas9 utilises the ultrafast short sequence mapping tool SeqMap [45] to find off-targets, and classifies all sites into three categories to generate a final output of the best candidate gRNAs [110]. Recently, two new alignment-based tools have been developed. Crisflash utilises a tree-based algorithm to rapidly design CRISPR guide RNAs and optimise guide accuracy by incorporating user-supplied variant data [43]. FlashFry rapidly searches off-target sites and provides much useful information (annotation of off-target sites, on/off-target scores, GC content, etc.) for candidate gRNAs [74]. Here we still classified Crisflash and FlashFry as alignment-based methods since they both propose novel algorithms for off-target searching, whereas the scoring approaches they use are borrowed from others [23], [24], [41], [78].

3.2. Scoring-based methods

3.2.1. Hypothesis-driven methods

Alignment-based methods are reliable for detection of most potential off-targets, however, mit snapgene Crack Key For U, not all nucleotide positions containing mismatches have the same decisive effect on off-target cleavage. Additionally, alignment-based prediction always outputs redundant off-target sites, many which are false-positives, although users can reduce the number of outputs by restricting MDaemon Email Server Pro Free Download maximum mismatches when exploring off-target cleavage. One study compared experimentally validated off-targets and off-targets predicted by Cas-OFFinder and CCTop, and the results showed that off-targets detected by the prediction tools only covered some of the validated sites, while some off-target sites cannot be predicted solely based on sequence homology [11]. Thus, features that influence the nonspecific binding of CRISPR gRNAs need to be considered to increase the accuracy of off-target detection.

MIT (Hsu-Zhang) score was proposed for off-target evaluation during the early stages of gene editing by CRISPR. Hsu mit snapgene Crack Key For U al. evaluated >700 guide RNA variants and SpCas9-induced indel mutation levels at >100 predicted genomic off-target loci [41]. They evaluated the contributions made by different mismatch positions and numbers in the target 20 bp, and calculated a weight matrix to determine off-target efficiency for each sgRNA. The authors claimed that this score accounts for >50% of the variance in cutting frequency. The MIT score has been integrated into many CRISPR gRNA design tools such as CHOPCHOP and CRISPOR [36], [56].

Cutting frequency determination (CFD) is another popular score for off-target evaluation. It is noticeable that sgRNA can also bind genome loci with non-canonical PAMs such as NAG, NCG and NGA, which may cause off-target cleavage. Doench et al. added PAM features in their scoring metrics [23]. sgRNAs with mismatches and indels in target sequences were also included for examining correlations between sgRNAs and off-targets. CFD score was validated with GUIDE-seq and proved to perform mit snapgene Crack Key For U than MIT score, hence it was adopted by CRISPRscan [78], GuideScan [83] and CRISPOR [36].

The prediction of sgRNA specificity based on the structural features of the Cas9-sgRNA complex proved to be superior to prediction solely based GOM Player 2.3.68.5332 Crack Plus Registration Code 2021 Download sequence features. CRISPRoff [4] and uCRISPR [119] both utilise energetics properties for off-target evaluation. Compared with other scoring methods like MIT and CFD, they both yielded better accuracy in off-target prediction. Nevertheless, neither have not been systematically evaluated by large-scale experiments, and caution should be exercised when using them.

3.2.2, mit snapgene Crack Key For U. Learning-based methods

The Doench laboratory also developed a linear regression model for prediction of off-target activity called Elevation that takes both sequence and chromatin accessibility features into consideration, as well as observations from others [62]. Elevation predicts individual scores for each off-target site, as well as an aggregate score for gRNAs. Mit snapgene Crack Key For U method performs best among MIT, CFD and CCTop. However, this software can only compute off-target scores for the human exome (GRCh38) and cannot support other organisms on their website.

3.3. Benchmark of scoring-based methods

Different scoring methods are based on different characteristics applied by each individual laboratory. In order to compare the accuracy of different scores, Haeussler et al. assessed four hypothesis-driven methods for off-target prediction using the same datasets [36]. CFD score exhibited the best prediction accuracy, whereas CCTop performed the worst. Data imbalance, mit snapgene Crack Key For U, where the number of true observed off-target sites (OTS) identified by off-target detection experiments is much less than that of all potential off-target sites recognized by alignment-based methods, is a common issue in the learning-based methods. To address the problem, a systematic survey was conducted to assess the influence of data imbalance [30]. The authors used bootstrapping sampling and PR-AUC methods to evaluate two well-established models. They emphasized the importance of using symmetric data for model construct and taking unbiased datasets for benchmark. According to current assessment results, we recommend people to use CFD score for off-target prediction. Elevation and DeepCRISPR are suitable for human genome editing, but CRISPRoff and uCRISPR may need further evaluation before use.

4. Tools for CRISPR guide RNA design

4.1. A comprehensive overview of CRISPR guide RNA design tools

The CRISPR/Cas system was first adapted for gene editing in 2012, and several tools mit snapgene Crack Key For U developed immediately thereafter, such as Zinc Finger Targeter (ZiFiT) [89], Cas9 guide RNA Design [68] and CRISPR (http://crispr.mit.edu/) [41]. All these platforms have been implemented in the design of gRNAs for model organisms. ZiFiT is also used to design Zinc Finger and TALEN modules, but Cas9 guide RNA Design and CRISPR are now unavailable.

Researchers should choose suitable tools with caution since different tools are in favour of different genomes or cell types. For instance, Yeastriction [72] is specialised for yeast, FlyCRISPR [35] is specific for Drosophila, EuPaGDT [81] is recommended for eukaryotic pathogens, and CRISPR-P [60], [63], CRISPR-PLANT [76], [109] and CRISPR-GE [111] are all implemented for genome editing in plants. Also, user-friendliness is essential for these web-based design tools, mit snapgene Crack Key For U. Based on these considerations, we propose three comprehensive web-based platforms for CRISPR gRNA design.

4.2. Three comprehensive web platforms for CRISPR guide RNA design

4.2.1. CHOPCHOP

CHOPCHOP has a succinct interface with well-rounded functions, >200 genomes are available on the website, and users can provide gene names, genomic coordinates or target sequences as inputs. If a gene is given, users can set specific regions of the gene as targets, such as coding sequences or promoters. Before designing gRNAs, mit snapgene Crack Key For U, two off-target detection methods and seven efficiency scores can be chosen, which aids users in selecting optimal gRNAs for their research.

To satisfy different experimental purposes, mit snapgene Crack Key For U, CRISPR Cas9 nuclease/nickase, Cpf1, CasX, C2C2 and TALEN are all supported by CHOPCHOP, and various modes of DNA targeting are optional such as KO/KI, gene activation/repression, and nanopore enrichment. In activation/repression mode, gRNAs are designed to target the promoter region and its flanking sites in order to bring the activating/repressing domain into close proximity with the transcription start site [17], [54]. Meanwhile, nanopore enrichment mode is implemented to design sgRNAs for long fragment excision within 40 kb. Additionally, the inDelphi model has been integrated into CHOPCHOP for repair profile prediction by Cas9 in five cell types [90].

4.2.2. CRISPR RGEN tools

Unlike Cas-Designer, BE-Designer is primarily implemented for base editing. In this tool, four methods of base editing are specified, mit snapgene Crack Key For U, and the editing window region is also adjustable. After the design phase, three outcomes are based on different coding types, and gRNAs, editing window sequences and amino acids are highlighted in a user-friendly manner. This tool is a good choice for base editing.

4.2.3. CRISPOR

5. Summary and perspectives

CRISPR/Cas technology has emerged as an advanced strategy for functional genomics, crop breeding and precise medicine. Guide RNAs are indispensable for CRISPR-based editing, and computational approaches provide assistance for efficient gRNA design. Numerous mit snapgene Crack Key For U have been developed for CRISPR gRNA design and evaluation. However, many issues mit snapgene Crack Key For U. For example, experimental datasets used to build models for predicting sgRNA specificity or efficiency are disparate; CRISPRscan score performs worse in mammals than in zebrafish, the genome the predictive model was trained in [36], mit snapgene Crack Key For U. Researchers mit snapgene Crack Key For U therefore know the strengths and weaknesses of each scoring method, and select the optimal tool for their research.

As we become more aware of the mechanisms by which Cas proteins recognise gRNAs, and bind to and cleave target loci, more and more novel features contributing to cutting efficiency and specificity are being identified, including sequence composition. For instance, mit snapgene Crack Key For U, low chromatin accessibility may block access of Cas9, while open chromatin regions are more likely to cause undesired mutations [39], [92]. In practice, specificity is more important than efficiency for application of CRISPR. However, several off-targets remain indecipherable mcafee internet security download Activators Patch current tools, and discovery of novel features may minimise off-target effects.

Too much choice is not always desirable, and an unbiased evaluation can provide guidance. To this end, the Liu laboratory has conducted the benchmarking [30], mit snapgene Crack Key For U, [114], and Haeussler et al. performed a comparison of different predictive scores and integrated most into CRISPOR [36]. None of the tools excel when using heterogeneous data, due to cell-specific or species-specific training models. Therefore, more cell types need to be evaluated. Also, plant and some animal genomes should be analysed thoroughly, since human or mouse have dominated to date. Moreover, it will be beneficial if useful features of multiple tools are mit snapgene Crack Key For U in future software packages.

Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Acknowledgements

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Computational Tools
This list was seeded by the participants of the 2008 workshop on Standards and Specifications in Synthetic Biology.
Please feel free to add information about a computation tool for synthetic biology (CADs, simulators, databases, lab managements systems, automation software, anything) to the list. Place it alphabetically, name the main project contributors, provide a canonical link to the program, and add a paragraph of descriptive text. Please date your entry.
Antimony
http://antimony.sourceforge.net/Lucian Smith, Mit snapgene Crack Key For U Chandran, Herbert Sauro
Antimony is a human-readable and human-writable language for describing biological mit snapgene Crack Key For U. The modules can be connected together by declaring overlapping molecular species between two modules or via the PoPS in/PoPS out interface. The language is similar to the Jarnac language introduced by Herbert Sauro several years ago.
Athena
http://www.washington.edu/staff/deepakc/downloads/InstallAthena.exeDeepak Chandran, Frank Bergmann, Herbert Sauro
Athena is a tool for building, simulating, and analyzing genetic circuits (as well as metabolic/signaling networks, such as SBML files). It provides a visual interface for building biological modules that can be saved and later connected together. The connection can be achieved using either the PoPS interface or by defining overlapping molecular species (similar to the concept of module in CellML and SBML). In addition to simulation, Athena supports a few other useful features: Database of Ecoli regulatory network from RegulonDB, Graphical view of part sequence, Automated derivation of transcription rate equations, Interface to all Systems Biology Workbench programs, Interface with R statistical language, Easy plugin architecture

Note: Athena has been succeeded by Tinkercell
TinkerCell is a highly flexible visual tool. Although still in development, it will have all the features in Athena. In addition, TinkerCell allows a family tree of biological parts to be loaded from a database. TinkerCell comes with a drawing program that allows users to draw their own graphical representations (if they do not like the defaults). C libraries, such as simulations or graph analysis, can easily be incorporated into TinkerCell. New plug-ins can also be added very easily.
BioJade
http://web.mit.edu/jagoler/www/biojade/Jonathan Goler
BioJADE is a design and simulation tool for synthetic biological systems. BioJADE is written in Java, and makes interactive use of BioBrick Repositories. BioJADE enables system designers to specify a system abstractly, tune it, simulate its behavior using a variety of simulators, and finally package the part for use by either the designer or the public.
BioMortar
http://igem.uwaterloo.ca/BioMortarAndre Masella
BioMortar is a lab management system designed specifically to deal with BioBricks. It is also capable of generating cookie-cutter protocols from user-specified templates and tracking the results, including gel images. It is released under the MIT License.
BioStudio
Sarah Richardson, Joel Bader, mit snapgene Crack Key For U, Jef Boeke
BioStudio is both an integrated development environment and a genome version control system, with the ability to modify nucleotide sequences automatically or manually at multiple resolutions. It uses Gbrowse from the GMOD project for its user interface and is currently able to locate and manipulate potential and existing restriction enzyme recognition sites, identify and incorporate unique sequences for PCR identification of wildtype and synthetic sequence, edit existing genome features, and incorporate and annotate user-created genome features. Each version of the genome is encoded in a Gene Feature Format (GFF) file, which is then displayed by the open source annotation viewer GBrowse and stored in a branching version control system, mit snapgene Crack Key For U. Collaboration and transparency is accomplished through the use of a wiki. Each feature in a GFF file will have a corresponding article in the wiki, where registered users can actively discuss its treatment. To ensure that BioStudio actually meets the needs of synthetic biologists, it is under development alongside the design of a synthetic Saccharomyces cerevisiae genome, SC2.0.
BrickIt
http://brickit.wiki.sourceforge.net/Raik Gruenberg and you?
BrickIt aims to create a portable web-based registry that helps synthetic biologists to plan, organize and track their local biobrick samples. The database-backed web server can be downloaded as virtual machine to quickly set up a local registry which coordinates the work within a lab, institute or community. Although the data remain local, the web server itself is an open-source project and new functions or improvements can be easily exchanged between the different local registries. BrickIt thus also offers a platform for the shared development of tools and infrastructure that foster the collaboration within the Synthetic Biology community. BrickIt and everything it relies on are open source and free. BrickIt itself is licensed under the GPL.
Clotho
http://www.clothocad.orgDouglas Densmore, J. Hitman pro 3.8.11 product key Crack Key For U Anderson, Alberto Sangiovanni-Vincentelli
Clotho presents a design environment to manipulate DNA sequence information and store the manipulated data as packaged "parts" back to part repositories. It provides a robust sequence editing environment (highlighting, restriction enzyme library, basic DNA analysis features), a parts management system mit snapgene Crack Key For U browsing, search, and manipulation), and an algorithm manager which allows the introduction of user developed algorithms (currently includes assembly algorithms). The tool is very much in the early stages of development but an alpha release is available. Clotho is part of a larger development of platform-based design tools for synthetic biology. The tool is open source under a BSD license.
Cytostudio
http://moleculamaxima.com/Molecula Maxima
DilutionMagic
http://www.dilutionmagic.org/dilutionMagic
DilutionMagic is a clever dilution calculator which can calculate your serial dilution steps. It can do it for arbitrary concentrations values and arbitrary volumes.
GeneDesign
http://www.genedesign.orgSarah Richardson, Joel Bader, Jef Boeke
GeneDesign is a suite of algorithms that allow users to edit several features of protein coding sequences, including codon usage and restriction enzyme recognition site presence. It will then generate a list of oligos and a road map for the assembly of the sequence by PCR It is mit snapgene Crack Key For U in Perl and is served over the internet; the code is available for local installations. A new, improved version is due before the end of 2008. PMID: 16481661
Gene Designer
https://www.dna20.com/tools/genedesigner.phpDNA2.0
This integrated, stand-alone secure software helps you create DNA constructs on your desktop with unprecedented ease and speed. Available for Mac and PC. For details see Villalobos et al.
GeNetDes
http://soft.synth-bio.org/genetdes.htmlGuillermo Rodrigo, Javier Carrera, Alfonso Jaramillo
GeNetDes is a tool to design transcriptional networks with targeted behavior that could be used to better understand the design principles of genetic circuits. It is a Simulated Annealing optimization algorithm that explores throughout the space of transcription networks to obtain a specific behavior. The software outputs a transcriptional network with all the corresponding kinetic parameters in SBML format. Our tool can also be applied to design networks with multiple external mit snapgene Crack Key For U and output genes. The software, a tutorial manual, parameter sets and examples are freely available in our website. We are currently extending Genetdes to design networks by assembling standardized biological part models. The models contain data obtained from part characterizations. We will evolve such circuits by replacing model parts to reach the imposed design specifications. In addition, we will incorporate the effect of the chassis by including the interaction with the cellular resources.
GenoCAD
http://www.genocad.orgYizhi Cai, Michael Czar, Julie Marchand, Jean Peccoud
GenoCAD is a web-based application guiding users through the design of part-based genetic systems. GenoCAD uses context-free grammars to formalize design strategies for synthetic genetic systems. This approach provides a path to organizing libraries of genetic parts according to their biological functions. It also provides a framework for the systematic design of new genetic constructs consistent with the design principles expressed in the grammar. Using parsing algorithms, mit snapgene Crack Key For U, GenoCAD enables the verification of existing constructs.doi:10.1093/bioinformatics/btm446
Genome Compiler
Genome Compiler is an intuitive all-in-one software platform for life scientists in the genetic engineering, molecular biology and synthetic biology fields, and provides a comprehensive tool for:
DNA design and visualization
Data management
Collaboration platform
Seamless DNA ordering
Genome Compiler is free for academia users and is available online and in a downloadable version so you can easily access your data on Genome Compiler from anywhere you are. The software supports Windows and Mac. In addition, the software supports common file formats such as: FASTA, Vector NTI, SnapGene, Geneious, Clone Manager, Serial Cloner, Plasma DNA, mit snapgene Crack Key For U, ApE, DNAStar, etc, mit snapgene Crack Key For U.
Metabolic Tinker
http://osslab.lifesci.warwick.ac.uk/Tinker.aspxKent McClymont, Orkun S Soyer
TINKER is a metabolic pathway design/search tool. It compiles mit snapgene Crack Key For U entire set of known reactions and compounds from the latest version of the Rhea database and converts this data into a directed graph. Nodes and edges on this graph correspond to metabolites and reactions, respectively, and thus the entire graph corresponds to the current known metabolic universe. Within this graph, TINKER searches for thermodynamically feasible paths between user defined "source" and "target" compounds and returns the found paths as metabolic pathways (rank-ordered by thermodynamic feasibility)
Operon Calculator
http://salislab.net/softwareDaniel Cetnar, Tian Tian, Iman Farasat, and Howard M. Salis
The Operon Calculator combines 15 biophysical models and design rules to automatically design synthetic operon sequences for maximum tunable control over RNA and protein expression levels. The algorithm also eliminates the presence of several overlapping, undesired genetic elements that will inevitably break the operon's function.
https://salislab.net/software/OperonCalculator_ForwardDesign
ProMoT
http://www.mpi-magdeburg.mpg.de/projects/promot/Katrin Kolczyk, Sebastian Mirschel, Michael Rempel, Mario A. Marchisio
ProMoT is the process modeling tool designed for the convenient setup of synthetic biology models in a modular fashion. Genetic circuits are built just by placing biological parts on a canvas (using drag and drop) and by connecting them through ”wires” that enable ﬂow of signal carriers, as it happens in electrical engineering. ProMoT supports two different modeling approaches -- a quantitative and a qualitative modeling approach. The quantitative approach is based on differential algebraic equations (DAEs) whereas the qualitative approach is a description of the system in the form of logical equations. The final code associated with a circuit can be exported into Matlab or SBML format (Level-1 and Level-2) allowing to run both deterministic and stochastic simulation.
For more detailed information, please refer to the recent papers ProMoT: Modular Modeling for Systems Biology and Computational design of synthetic gene circuits with composable parts or the synthetic biology research page Synthetic Biology at ETH Zurich.
Ribosome Binding Site (RBS) Calculator
http://salislab.net/softwareHoward Salis, Ethan Mirsky, and Christopher Voigt, Nature Biotechnology, v27, 2009
The Ribosome Binding Site (RBS) Calculator is an engineering design method that predicts the translation initiation rate of a protein coding sequence in bacteria. You can use the RBS Calculator to generate synthetic ribosome binding site sequences and to rationally control the production rate of any protein in bacteria from 0.1 to 100,000+ on a proportional scale.
https://salislab.net/software/forward
The RBS Calculator is used by GenScript to synthesize DNA sequences with custom-designed ribosome binding sites.
The RBS Calculator is embedded into Genome Compiler, an intuitive all-in-one software platform for DNA design, which is free for academics to use.
Relevant papers: Translation Rate is Controlled by Coupled Trade-offs between Site Accessibility, Selective RNA unfolding and Sliding at Upstream Standby Sites
A Predictive Biophysical Model of Translational Coupling to Coordinate and Control Protein Expression in Bacterial Operons
Automated Design of Synthetic Ribosome Binding Sites to Control Protein Expression
Riboswitch Calculator
http://salislab.net/softwareBreakthrough Article: Espah Borujeni A., D.M. Mishler, J. Wang, W. Huso, and H.M. Salis. Nucleic Acids Research, mit snapgene Crack Key For U. v44(1). 2016
Riboswitches are shape-changing regulatory RNAs that bind chemicals and regulate gene expression, directly coupling sensing to cellular actuation. The Riboswitch Calculator designs synthetic translation-regulating riboswitches that bind to specific chemicals and activate gene expression. Starting with a known RNA aptamer, the algorithm automatically optimizes the (up to) 30 nucleotide sequences that appear before and after the RNA aptamer to maximize the activation of gene expression. The algorithm combines a statistical thermodynamic model of translation with genetic algorithm optimization. The algorithm's predictions were validated by constructing and characterizing 62 synthetic riboswitches that utilized six different RNA aptamers to sense a diverse range of chemicals (theophylline, tetramethylrosamine, fluoride, dopamine, thyroxine, 2,4-dinitrotoluene). The riboswitches' activation ratios were the mit snapgene Crack Key For U reported to-date for their respective RNA aptamers.
https://salislab.net/software/RiboswitchCalculator_EvaluateMode
Relevant paper: Automated Physics-based Design of Synthetic Riboswitches from Diverse RNA Aptamers
RBS Library Calculator
Iman Farasat, Manish Kushwaha, Jason Collens, Michael Easterbrook, Matthew Guido, and Howard Salis, Molecular Systems Biology, v10(6). 2014
The RBS Library Calculator designs the smallest RBS library sequence that uniformly searches a desired translation rate space, enabling one to efficiently identify optimal protein expression levels in plasmid- or chromosomally-encoded genetic systems. The algorithm has three modes. Search mode allows one to explore the largest possible translation rate space, across a 100,000-fold proportional scale, using the smallest RBS library (16 to 32 variants). Zoom mode allows one to design a minimal RBS library to search a targeted translation rate space between a minimum and maximum. Genome Editing mode designs genomic RBS libraries with a minimal number of consecutive mutations, suitable for designing the mutagenic oligonucleotides needed for MAGE genome mutagenesis. The method has been used to efficiently tune genetic circuits and optimize metabolic pathways.
Relevant paper: Efficient Search, Mapping, and Optimization of Multi-protein Genetic Systems in Diverse Bacteria
https://salislab/software/RBSLibraryCalculatorSearchMode
RoVerGeNe
http://iasi.bu.edu/~batt/rovergene/rovergene.htmGregory Batt, Calin Belta
RoVerGeNe is a software tool for the analysis of dynamical properties of gene networks. Unlike conventional ODE numerical simulation tools, it allows
to test whether a dynamical property holds for ranges of parameters
and to find parameter sets for which a given dynamical property hold
The tool is thus useful for robustness analysis and tuning of gene networks. See Bioinformatics paper.
SBW
SBW (Systems Biology Workbench)
SimThyr
http://simthyr.sf.netJohannes W, mit snapgene Crack Key For U. Dietrich
SimThyr is a continuous numeric simulation program for thyroid homeostasis. It is based on a parametrically isomorphic model of the overall system. Applications of this program cover research, including development of hypotheses, and education of students in biology and medicine, nurses and patients.
Relevant papers:
Citation: Dietrich JW (1994-2016) SimThyr 4.0. Fairfax, VA: sourceforge, http://simthyr.sf.net. RRID:SCR_014351.
SynBioSS
http://synbioss.sourceforge.net/Yiannis Kaznessis, Tony Hill, Vassilis Sotiropoulos, Jonathan Tomshine
SynBioSS (Synthetic Biology Software Suite) is a software suite for the quantitative simulation of biochemical networks using hybrid stochastic algorithms. We believe that one shouldn’t need to know how to program (or use command-line) to use sophisticated numerical methods. Through this software, we intend to put the most powerful techniques for simulating chemically reacting networks into the hands of biologists (or any scientist who can put them to good scientific use). SynBioSS can accurately simulate any system modeled as a network of reactions. In order to achieve this result, we wrapped up state-of-the-art algorithms inside a user friendly graphical interface (GUI) that handles input data, runs the simulations and vividly visualizes simulation results, without requiring any programming background from the user. The software is open and runs on any of the three platforms most used by scientists: Windows, Macintosh, and Linux.
Synbiotools
http://synbiotools.orgSwapnil Bhatia (Boston University)
Synbiotools hosts a free and growing software suite for engineering biology including tools for visualization, combinatorial genetic design generation, circuit design, and build automation.
TinkerCell
Engineering platform for building and testing cellular circuits (Deepak Chandran, UW, Seattle)
TinkerCell is an extensible platform for editing and simulating cellular networks. Users can operate the software at different levels including graphical point and click or via an interactive console. While the main interface is visual, programmers may add new features by writing custom programs in C or Python. TinkerCell is designed to incorporate information from database(s), thus the models store information such as rate constants, gene sequences and promoter strengths. Networks can be "modularized" and connected to one another. TinkerCell is cross platform and written in C++. A Python console is provided for interactive control, mit snapgene Crack Key For U.
http://www.tinkercell.com/Home
TinySeq.com
http://tinyseq.comJason Morrison, Mackenzie Cowell
TinySeq is the minimal minimal part storage tool. It assigns a unique url to a given sequence, and stores the sequence's construction format & plasmid. TinySeq supports part composition via the url, so you can get the assembled sequence of two parts simply by asking for something like tinyseq.com/mlc:1+mlc:2. We built tinyseq to reveal what other features besides assigning an accession number (mlc:1) to a sequence would be useful for users at a lab bench who are looking for tools to help them keep their assemblies in order.
PCEnv
http://www.cellml.org/tools/pcenv/Andrew Miller, Justin Marsh, Alan Garny
PCEnv is an environment for creating and simulating arbitrary mathematical models, including mathematical models in the fields of systems and synthetic biology. PCEnv uses CellML as a native format for storing models.
PROTDES
http://soft.synth-bio.org/protdes.htmlMaria Suarez, Pablo Tortosa, Alfonso Jaramillo
Synthetic Biology will benefit from future efforts using first-principles to design biological macromolecules. Ideally, this would mean using the same software and parameters to fold a protein than to design a protein mit snapgene Crack Key For U a given fold (inverse folding problem). Recent work has demonstrated that it is possible to experimentally validate such approaches, by using appropriate physical modelling. We have developed a tool able to incorporate such successful procedures by using a leading molecular dynamics software. Our tool PROTDES is an open-source toolbox for computational protein design using the CHARMM package. This allows the integration of molecular dynamics within the protein design, allowing to extend the physical description more than it has been possible with current software. The procedure automatically finds the suitable mutations optimizing a protein folding free energy. It mutates residue positions to find the best amino acids in an arbitrary protein structure without requiring pairwise approximations. It implements an heuristic optimization algorithm that iteratively searches the best amino acids and their conformations for a an arbitrary set of positions within a structure. The users will be able to create their own procedures for protein design using their own physical protocol, which we exemplify by already incorporating three alternative effective energy functions.Our versatile software will allow synthetic biologists using physical models to use a standard molecular dynamics software for protein design.
j5
http://j5.jbei.orgNathan J. Hillson
Recent advances in Synthetic Biology have yielded standardized and automatable DNA assembly protocols that enable a broad range of biotechnological research and development. Unfortunately, the experimental design required for modern scar-less multipart DNA assembly methods is frequently laborious, time-consuming, mit snapgene Crack Key For U, and error-prone. A web-based software tool, j5, automates the mit snapgene Crack Key For U of scar-less multipart DNA assembly protocols including SLIC, Gibson, CPEC, and Golden Gate. The key innovations of the j5 design process include cost optimization, leveraging DNA synthesis when cost-effective to do so, the enforcement of design specification rules, hierarchical assembly strategies to mitigate likely assembly errors, and the instruction of manual or automated construction of scar-less combinatorial DNA libraries. j5 can be used to build combinatorial libraries and applied to the preparation of linear gene deletion mit snapgene Crack Key For U. These innovations save researchers time and effort, reduce the frequency of user design errors and off-target assembly products, decrease research costs, and enable scar-less multipart and combinatorial DNA construction at scales unfeasible without computer-aided design. The j5 software has been exclusively licensed to TeselaGen Biotechnologies for commercial use and distribution.
DeviceEditor
http://j5.jbei.orgJoanna Chen, Douglas Densmore, Timothy Ham, Zinovii Dmytriv
A web-based bioCAD software tool, DeviceEditor, provides a graphical design environment that mimics the intuitive visual whiteboard design process practiced in biological laboratories. The key innovations of DeviceEditor include visual combinatorial library design, direct integration with scar-less multi-part DNA assembly design automation, mit snapgene Crack Key For U, and a graphical user interface for the creation and modification of design specification rules. DeviceEditor liberates researchers from DNA base-pair manipulation, and enables users to create successful prototypes using standardized, functional, and visual abstractions. Open and documented software interfaces support further integration of DeviceEditor with other bioCAD tools and software platforms. DeviceEditor saves researcher time and institutional resources through correct-by-construction design, the automation of tedious tasks, mit snapgene Crack Key For U, design reuse, and the minimization of DNA assembly costs. The DeviceEditor software has been exclusively licensed to TeselaGen Biotechnologies for commercial use and distribution.
VectorEditor
https://public-registry.jbei.org/static/vesa/VectorEditor.htmlZinovii Dmytriv, Timothy Ham, Hector Plahar, Joanna Chen
Open source, web based cross platform and cross browser DNA sequence editing and analysis tool.
iGEM Software
http://igem.synbioreview.com/Michal Galdzicki
A reference collection of iGEM software projects 2007-2011. This is a compilation of all the software projects large and small created throughout the iGEM competition. On this site you can find the description of the computational tool, a link to the project page and source code.

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