Computational Tools

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

Antimony

http://staff.washington.edu//deepakc/PartSyntax.pdf 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.exe Deepak 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

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.

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.

GeneDesign

http://www.genedesign.org Sarah 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

GeNetDes

http://soft.synth-bio.org/genetdes.html Guillermo 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.org Yizhi 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

SBW

SBW (Systems Biology Workbench)

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.

TinySeq.com

http://tinyseq.com Jason 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.