Systems Biology

General

• What is Systems Biology?

• 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)
  • Bioinformatics
  • Genomics
  • Proteomics
    • Glycoproteomics
    • Phosphoproteomics
  • Systems Biology
• 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."
• Biomolecular Interaction Network Database (BIND) - "[BIND] is a collection of records documenting molecular interactions. The contents of BIND include high-throughput data submissions and hand-curated information gathered from the scientific literature." This site also has links to interaction, genome, pathway, enzyme, protein, small molecule and other databases (BIND Related Databases).
• 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).
• SynaSuite Bioinformatics Applications (Malaysian Genomics Resource Centre)
• PathBlast - Tool for aligning two protein interaction networks to elucidate conserved pathways.
• 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 Ontology^TM (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)
• 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.

Nucleic Acid, Gene and Genomics Databases

Protein and Proteomics Databases

Metabolic Pathway Databases (Data Collections on Metabolic Pathways)

Signal Transduction Databases (Data Collections on Regulatory Pathways)

Discussion Groups

• BioChemWeb.org Discussion Board - Discussions and questions/answers for scientists and students.

• Usenet newsgroup archives from BIOSCI/bionet (can also be accessed through Google Groups: bionet):
  • BIOLOGICAL-INFORMATION-THEORY/bionet.information-theory - Biological information theory.
  • BIOMATRX/bionet.molbio.bio-matrix - Computer applications to biological databases.
  • COMPUTATIONAL-BIOLOGY/bionet.biology.computational - Computer and mathematical applications.

See also the Discussion Groups section of the General Biochemistry and Cell Biology page.

Labs Studying Systems Biology