Computational Tools
Antimony
http://tinyseq.com Jason Morrison, Mackenzie Cowell
TinySeq is the minimal minimal part storage tool. It assigns a unique url to a given sequence, including tracking format & plasmid. TinySeq supports part composition via the url.
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.
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.
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. doi:10.1093/bioinformatics/btm446
LBS
http://tinyseq.com Jason Morrison, Mackenzie Cowell
TinySeq is the minimal minimal part storage tool. It assigns a unique url to a given sequence, including tracking format & plasmid. TinySeq supports part composition via the url.
SBW
SBW (Systems Biology Workbench)
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, including tracking format & plasmid. TinySeq supports part composition via the url.
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.
