Computational Tools

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
Line 28: Line 28:
'''Sarah Richardson, Joel Bader, Jef Boeke'''
'''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.  [http://www.ncbi.nlm.nih.gov/pubmed/16481661 PMID: 16481661]
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.  [http://www.ncbi.nlm.nih.gov/pubmed/16481661 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 ==
== GenoCAD ==

Revision as of 19:18, 27 April 2008

Contents

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.

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

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.

Personal tools