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Article

Synthetic Biology Software Tools

 
 

The list below is derived from open wetware computational tools  [Link]Another listing of some tools can also be found here:  

 

1. Antimony

"Antimony is a text-based model definition language originally based on Jarnac  , and extended to be fully modular. Antimony models can be converted to and from SBML, flattening the modularity in the process."  

 

2. ApE - A plasmid Editor

"Highlights restriction sites in the editing window. Accurately reflects Dam/Dcm blocking of enzyme sites. Highlights text using pre-defined and custom feature libraries. Shows translation, Tm, %GC, ORF of selected DNA in real-time. Reads DNA Strider, Fasta, Genbank and EMBL files. Saves files as DNA Strider-compatible or Genbank file format. Highlights and draws graphic maps using feature annotations from genbank and embl files. Directly BLASTs selected sequence at NCBI or worm base."  

 

3. BioJade

"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."  

 

4. BioMortar

This software is no longer available.   "BioMortar is an application to manage BioBricks. It is both a freezer/strain collection manager and it is capable of generation protocols based on Standard Assembly techniques."  

 

5. Brickit

"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."  

 

6. Clotho

"Clotho is for engineering synthetic biological systems and managing the data which is used to create them. It also provides a mechanism to begin the process of creating standardized data, algorithms, and methodologies for synthetic biology."  

 

7 GeneDesign

"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."  

 

8 Gene Designer 2.0

Gene circuit design: "The ideal software developed for you to design sequences de novo without being limited by what nature can provide. Gene Designer 2.0 encompasses a complete and visually rich set of tools to bring your creative ideas to completion."  

 

9 Genetdes

"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."  

 

10 GenoCAD

"GenoCAD is an open-source computer-assisted-design (CAD) application for synthetic biology. The foundation of GenoCAD is to consider DNA as a language to program synthetic biological systems. GenoCAD includes a large database of annotated genetic parts which are the words of the language. GenoCAD also includes design rules describing how parts should be combined in genetic constructs. These rules are used to build a wizard that guides users through the process of designing complex genetic constructs and artificial gene networks. The same rules are used by the GenoCAD compiler to maintain the integrity of existing constructs. GenoCAD provides users with data import and export capabilities using standard formats (FASTA, GenBank, and tab-delimited text) so that users' personal workspaces can be customized to meet their specific needs."  

 

11 OpenCell

"OpenCell 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."  

 

12 ProMoT

"ProMoT is the Pro cess Mo deling T ool, a software for the construction and manipulation of complex technical and biological systems. ProMoT has its origins in process engineering. Together with the simulation environment Diana  it provides capabilities for the development of dynamic models based on differential-algebraic equations, and their simulation and further analysis.For the application in Systems Biology key features of ProMoT are the development of modular models, the use of specialized modeling-libraries, and the support for model-exchange via the international standard SBML  .Of specific importance for successful work in interdisciplinary teams is the availability of graphical methods for model editing and exploration, because this defines a common language for direct communication about models without the need for in-depth mathematical knowledge. ProMoT already implements graphical tools for both the implementation, and the exploration and visualization of models. ProMoT has being used as a modeling tool not only for the setup of dynamic models, but also for the visual construction of Boolean models that can be analyzed with CellNetAnalyzer  ."  

 

13 Ribosome Binding Site Calculator - RBS

"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."  

 

14 RoVerGeNe

"Rovergene is a tool for the analysis of genetic regulatory networks under parameter uncertainty."  

 

15 SynBioSS

"The Synthetic Biology Software Suite (SynBioSS) is a software suite for the generation, storing, retrieval and quantitative simulation of synthetic biological networks. SynBioSS facilitates computational synthetic biology and consists of three independent components: the Desktop Simulator (DS), the Wiki, and the Designer."  

 

16 TinkerCell

"TinkerCell is a Computer-Aided Design software tool for Synthetic Biology. It combines visual interface with programming API (Python, Octave, C, Ruby) and allows users to share their code with each other via a central repository."    

 

17 PROTDES

"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."  

 

18 NanoCAD Java applet

NanoCAD Java applet simulating molecular configuration and inter-atomic forces; necessary to understand how simple molecules are organized  

 

19 Foldit

The Science Behind Foldit  ; a computer simulation based 'game' that lets one predict protein structure & design; designed by the HHMI team.

 

20 DOCK Software

DOCK Version 6.0   molecular docking software package for validating drug discovery.

 

21 Athena

Athena: Modular CAD / CAM Software for Synthetic Biology  

 

22 Synthetic Biology

Synthetic Biology: Semantic web ontology/Software  

 

23 SBML Software Guide

SBML Software Guide ; this Systems Biology mark-up language also applies to SynBio.

 

24 j5  

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  Biotechnology, Inc. for commercial use and distribution.

 

25 DeviceEditor  

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  Biotechnology, Inc. for commercial use and distribution.

 

26 VectorEditor

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

27 GenoGUARD/GenoTHREAT

(by Jean Peccoud and co workers, Virginia Tech) a software tool that helps to detect the use of synthetic DNA as bioterrorism agents.   GenoTHREAT takes a DNA sequence on input, and in return told the user if it's a dangerous sequence which need further investigation or if the sequence can be synthesized. It follows the "best match" screening protocol method recommended by the guidelines of the US Department of Health and Human Services  , and so uses the Blast software for sequence alignment. The sequence screening algorithm was published in Nature Biotechnology 2011. [1] The software was renamed to the more reassuring GenoGUARD  . The software is open source and being released using the Apache License Version 2.0 to ensure broad accessibility.

28 Synthetic Biology Open Language (SBOL)

is a software standard for the electronic exchange of specifications and descriptions of genetic parts, devices, modules, systems, and engineered genomes.  

29 TASBE

A Tool-Chain to Accelerate Synthetic Biological Engineering.

"There is a pressing need for design automation tools for synthetic biological systems. Compared to electronic circuits, cellular information processing has more complex elementary components with a much greater complexity of interactions between components. Moreover, chemical computation within a cell is strongly affected both by other computations taking place within the cell and by the cell's native metabolic processes and its external environment. All this adds up to a design flow that is currently highly iterative, error-prone, and extremely slow: critical problems that must all be addressed in order to realize the potential of synthetic biology.

We have been developing a tool-chain approach to decomposing the problems of design and assembly into automatable fragments. Practitioners using our tool-chain will be able to design organisms using higher level descriptions, which are automatically transformed into genetic regulatory network designs, then assembled into DNA samples ready for in vivo execution. At the same time, the tool-chain is free and open software that will allow researchers to incorporate their own design tools, thereby disseminating their results to the community and enhancing the capabilities of the tool-chain."  

 

30 PaR-PaR Laboratory Automation Platform  

Labor-intensive multistep biological tasks, such as the construction and cloning of DNA molecules, are prime candidates for laboratory automation. Flexible and biology-friendly operation of robotic equipment is key to its successful integration in biological laboratories, and the efforts required to operate a robot must be much smaller than the alternative manual lab work. To achieve these goals, a simple high-level biology-friendly robot programming language is needed. We have developed and experimentally validated such a language - Programming a Robot (PaR-PaR). The syntax and compiler for the language are based on computer science principles and a deep understanding of biological workflows. PaR-PaR allows researchers to use liquid-handling robots effectively, enabling experiments that would not have been considered previously. After minimal training, a biologist can independently write complicated protocols for a robot within an hour. Adoption of PaR-PaR as a standard cross-platform language would enable hand-written or software-generated robotic protocols to be shared across laboratories.

31 iGem software  

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.

 

32 Genome Compiler  

Genome Compiler is built on the idea that biology is information technology.

Just like another information technology - computers, genetic engineers also need tools to design, debug and compile their code: A genome compiler.

Genome Compiler is inspired by the breakthrough research done by the JCVI and Harvard with their achievement of whole bacterial genome engineering, as required for functional changes in the form of new codes, new amino acids, safety and virus-resistance — and a vision of making biological design easier, cheaper, and open to people outside the research labs.

 

33 Some additional useful learning resources and programs:

- BioProject  , collection of a biological database for easy access.

- The NCBI Structure Group  ; developed by NCBI Computational Biology Branch, freely accessible.

- Craig Venter Institute software packages  

References

  1. Strengths and limitations of the federal guidance on synthetic DNA. Adam, L., Kozar, M., Letort, G., Mirat, O., Srivastava, A., Stewart, T., Wilson, M.L., Peccoud, J. Nat. Biotechnol. (2011) [Pubmed]
 
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