Systems Biology Tools and Resources
Comprehensive Systems-Biology Database
http://csbdb.mpimp-golm.mpg.de
The Comprehensive Systems-Biology Database (CSB.DB), provides a useful portal into systems biology by allowing statistical analysis of gene expression data. CSB.DB maintains Databases of various model organisms, namely Escherichia coli, Saccharomyces cerevisiae and Arabidopsis thaliana (this include NASC affymextric data). Comprehensive analyses of these data sets can be achieved via various tools provided by CSB.DB allowing parallel evaluation of a compendium of data.
Gene Ontology Consortium
http://www.geneontology.org/
To aid the need for a consistent description of gene products across databases the gene ontology consortium is working towards a controlled vocabulary of how gene products behave in a cellular context that is species independent
KEGG (Kyoto Encyclopedia of Genes and Genomes)
http://www.genome.jp/kegg/
Collection of databases and software for understanding higher order networks and functions in cell/organisms from existing genome data.
Plant Ontology Consortium
http://www.plantontology.org
Aims to develop and make public controlled vocabularies that accurately reflect biology of plant structures and developmental stages.
Software
AGRIS
http://arabidopsis.med.ohio-state.edu/
Arabidopsis Gene Regulatory Information Server. An information resource of Arabidopsis cis regulatory elements and transcription factors.
Arabidopsis Reactome
http://arabidopsisreactome.org/
A curated knowledge base of plant biological pathways
Ara-Cyc
http://www.arabidopsis.org/biocyc/index.jsp
TAIR package that allows visualisation of biochemical pathways in Arabidopsis thaliana.
At RegNet (Arabidopsis Regulatory Network)
http://arabidopsis.med.ohio-state.edu/RGNet/
Web-based tools to help researchers visualize the complex networks of transcription factor interactions. Simply enter AGI locus and get back target genes nodes and edges of interactions.
AthaMap
http://www.athamap.de/
Provides a genome-wide map of potential transcription factor binding sites in Arabidopsis thaliana.
BioRel
http://mips.gsf.de/proj/biorel/
Software to assess biological relevance of gene networks generated from high through put data.
Celleartor
http://www.cellerator.org/
Cellerator is a Mathematical package designed to facilitate biological modeling via automated equation generation
Cytoscape
http://www.cytoscape.org/
Software for analysing and visualizing biological network data
MapMan
http://gabi.rzpd.de/projects/MapMan/
MapMan is a user-driven tool that displays large datasets (e.g. gene expression data from Arabidopsis Affymetrix arrays) onto diagrams of metabolic pathways or other processes.
MetNetDB
http://metnet.vrac.iastate.edu
The Metabolic Network Exchange contains publicly available software for analysis of genome wide data profiling in Arabidopsis.
ONDEX
http://ondex.sourceforge.net/
ONDEX enables data from diverse biological data sets to be linked, integrated and visualised through graph analysis techniques.
Path-Explore
http://www.cs.nyu.edu/~pathexp/index.html
Supplied by the Coruzzi lab. Allows users to analyse gene expression, metabolic and proteomics data in terms of biochemical reactions and metabolic pathways.
Pathway Tools Omic Viewer
http://www.arabidopsis.org:1555/expression.html
Displays expression or proteomics data onto the Aracyc metabolic diagram
System Biology Workbench (SBW)
http://www.sys-bio.org
Designed by the Sauro Lab, SBW provides a framework for diverse applications, written in differing languages and running on various platforms to interact and communicate.
Package includes:-
Jarnac:- Biochemical network simulation tool
JDesigner:- Designs biochemical networks
MatLab Interface:- Allows interaction between MatLab and SBW
WinSCAMP:- General purpose metabolic and chemical network simulator
Virtual Plant
http://virtualplant-prod.bio.nyu.edu/cgi-bin/virtualplant.cgi
Integrates genomic data and provides visualization and analysis tools for rapid and efficient exploration of Arabidopsis genome wide data.
OpenWetware
http://openwetware.org/wiki/Main_Page
OpenWetWare is an effort to promote the sharing of information, know-how, and wisdom among researchers and groups who are working in biology & biological engineering.
Other sites
Institute for Systems Biology
http://www.systemsbiology.org
Good introduction in to the area not particular plant specific.
Systems Biology
http://systems-biology.org/
Japanese portal site for systems biology
The Systems Biology Researcher Database
http://www.sysbioldb.org
An information and knowledge exchange platform for all systems biology researchers worldwide
