Systems Biology
General
- Bioinformatics.ca - Web portal
to bioinformatics resources and activities in Canada.
- Bioinformatics.org - "The
Bioinformatics Organization, Inc. (Bioinformatics.Org) was founded to facilitate
world-wide communications and collaborations between practicing and neophyte
bioinformatic scientists and technicians."
- Bioinformatics Web -
"Comprehensive educational resource on Bioinformatics."
- European Systems Biology
- MacDevCenter.com:
Systems Biology - Basic introduction to systems biology. (Robert Jones,
2004)
- NPG
Web Focus: Systems Biology - A "selection of recently published
Reviews, Perspectives and Highlights on this topic" from the
Nature Publishing Group.
- Protein Lounge - "[I]nteractive web-based databases and software to help
the life-scientists understand the complexity of systems biology," including
pathway, siRNA, peptide-antigen, protein-interaction, kinase-phosphatase,
transcription factors, disease genes and protein databases, as well as pathway,
protein, peptide, siRNA and PCR cloning tools.
- systems-biology.org - Systems
biology information and tools.
- Wikipedia - Free online encyclopedia
with basic overviews. (Beginner's Level)
- Yeast Systems Biology Network -
"The Yeast Systems Biology Network proposes the yeast Saccharomyces
cerevisiae as a model system to develop the field and to advance our understanding
of the rules and principles of the dynamic operation of cellular systems."
Databases, Tools and Simulations
- BioCyc - "BioCyc is a collection
of Pathway/Genome Databases. Each database in the BioCyc collection describes
the genome and metabolic pathways of a single organism, with the exception
of the MetaCyc database, which is a reference source on metabolic pathways
from many organisms."
- Database of Interacting Proteins
(DIP) - A catalog of experimentally determined protein-protein interactions
and related projects like the Database of Ligand-Receptor Partners (DLRP),
LiveDIP and the Java-based JDIP. (David Eisenberg, University of California,
Los Angeles)
- Database of Quantitative Cellular
Signaling - "The Database of Quantitative Cellular Signaling is a
repository of models of signaling pathways." (National Centre for Biological
Science, India)
- Endomesoderm Gene Network - A genomic view of the regulatory gene network for endomesoderm specification
(Davidson Lab, California Institute of Technology)
- Kyoto Encyclopedia of Genes and
Genomes (KEGG) - Graphical and hypertext-based information on biochemical
pathways, including metabolic and regulatory pathways (for instance, cell
cycle and growth factor signaling).
- PathBlast - Tool for aligning two protein interaction networks to elucidate conserved
pathways.
- PhosphoSitePlus - A site "devoted to commonly studied protein post-translational modifications."
- SiC: The Silicon Cells - Computer
simulations of biochemical networks in specific cells based on experimentally
determined rate laws and parameter values.
- Virtual Cell - "The
National Resource for Cell Analysis and Modeling, NRCAM, has created a remote
user modeling and simulation environment where users can create biological
models of various types and run simulations." (University of Connecticut
Health Center)
See also the Scientific Databases and Tools page
for genomics and proteomics databases and the Metabolic
Pathway Databases and Signal
Transduction Databases sections of the relevant pages.
Specialized Software and Computer Languages
- BioTapestry
Editor - A Java-based "interactive tool for building, visualizing,
and simulating genetic regulatory networks." (Bolouri Group, Institute
for Systems Biology, Davidson Lab, California Institute of Technology)
- CellDesigner - A "a
modeling tool of biochemical networks with graphical user interface. It is
designed to be SBW (Systems Biology Workbench) compliant, and support SBML
(Systems Biology Markup Language) format."
- Cell Markup Language (CellML) - An
XML markup language which, along with MathML and RDF, "will provide
a complete vocabulary for describing biological information at a range of
resolutions from the subcellular to organism level."
- Cytoscape - "[O]pen source
bioinformatics software platform for visualizing molecular interaction networks
and integrating these interactions with gene expression profiles and other
state data."
- E-CELL Project - "[I]nternational
research project aiming to model and reconstruct biological phenomena in silico,
and developing necessary theoretical supports, technologies and software platforms
to allow precise whole cell simulation." (Institute for Advanced Biosciences,
Keio University, Japan)
- Gene Ontology Consortium - "The
goal of the Gene OntologyTM (GO) Consortium is to produce a controlled
vocabulary that can be applied to all organisms even as knowledge of gene
and protein roles in cells is accumulating and changing."
- Languages for Systems
Biology (Luca Cardelli, Microsoft Research Cambridge, UK)
- Open Biological Ontologies - "[U]mbrella
web address for well-structured controlled vocabularies for shared use across
different biological domains."
- Pathway Hunter Tool - Metabolic
pathway analysis web service, including shortest, alternate path, Load points,
Choke points and network analysis. (Cologne University Bioinformatics
Center, Germany)
- PathwayLab -
A commercial software tool for modeling, computational analysis and information
management of biochemical pathways. (InNetics)
- Systems Biology Toolbox 2 (SBtoolbox2) for MATLAB - A modeling, simulation and analysis tool for biochemical systems. (Henning Schmidt, University of Rostock, Germany)
- Software and
Databases for Computational Biology on the Internet (Steven Salzberg,
Johns Hopkins University)
- Systems Biology Markup Language (SBML) -
A "computer-readable format for representing models of biochemical reaction
networks. SBML is applicable to metabolic networks, cell-signaling pathways,
regulatory networks, and many others."
- Systems Biology Workbench
(SBW) - A "modular, broker-based, message-passing framework for
communication between applications that aid in research in systems biology."
See also the Scientific Software page.
(Data
Collections on Metabolic Pathways)
(Data Collections on Regulatory Pathways)
Discussion Groups
See also the Discussion
Groups section of the General
Resources and Tutorials page.
Labs Studying