Selected Internet Resources for Systems Biology

E. Mjolsness, Winter 2003

Data

Pathway databases:

KEGG pathway database

Enzyme reaction database Brenda

Enzyme Metabolic Pathways EMP

What Is There WIT

Species-specific genomes:

Yeast: Saccharomyces Genome Database

Fly: FlyBase

Worm: WormBase

Human/Mouse comparison for human chromosome 19

 Regulatory interactions

General Repository for Interaction Datasets

Biomolecular Interaction Network Database BIND

Transfac

Yeast ChIP-chip gene regulatory network data (October 2002).

Gene Ontology

Literature

http://www.ics.uci.edu/~emj/classes/280_03/, subdirectory papers/

http://thornvalley.caltech.edu/bioinformatics/ , files literature.html and references.html
Software

Cellerator biological model generation system

SIGMOID pathway modeling database project

Software category	Name	Web site	Reference
Pathway database	Sigmoid	http://sigmoid.sourceforge.net/
	KEGG	www.genome.ad.jp/kegg/kegg2.html
	Brenda	http://www.brenda.uni-koeln.de/
	Enzymes and Metabolic Pathways -EMP	http://emp.mcs.anl.gov/
	What Is There?	http://wit.mcs.anl.gov/WIT2/
	Transpath/Transfac	http://transfac.gbf.de/	[Wingender 00]
	Ecocyc,Biocyc	http://www.ecocyc.org/, http://biocyc.org/	[Karp 02]
	Pathway Prism	www.physiome.com (commercial)
	Genenet	http://wwwmgs.bionet.nsc.ru/mgs/systems/genenet/
	Monod, soon Alpha project	http://monod.molsci.org/ , http://molsci.org/
	Gene Microarray Pathway Profiler - GenMAPP	http://www.genmapp.org/	[Dahlquist 02]
	Biomolecular Interaction Network Database BIND	www.bind.ca
	BM (Roche) Biochemical Pathways Wall Chart	http://www.expasy.org/cgi-bin/search-biochem-index
	Science Signal Transduction Knowledge Environment	http://stke.sciencemag.org/ (membership required)
Cell simulation	Cellerator	http://www-aig.jpl.nasa.gov/public/mls/cellerator/ ; www.ics.uci.edu/~emj/cellerator.htm	[Shapiro et al. 01]
	Gepasi	www.gepasi.org	[Mendes 01]
	Virtual cell	www.nrcam.uchc.edu	[Schaff 97]
	Jarnac	www.cds.caltech.edu/~hsauro	[Sauro 00]
	E-cell	www.e-cell.org	[Tomita 99]

Table I. Existing pathway databases and cell simulation software is proliferating, to the likely benefit of biological users. SIGMOID when fully developed will share data with other pathway databases, put it into a form suitable for modeling, and through Cellerator create pathway models in SBML which can be shared with other cell simulation programs.

Software: Cell model repositories

SBML: http://www.sbw-sbml.org/ModelsWebPages/ModelRepository.htm

Cellerator: http://www-aig.jpl.nasa.gov/public/mls/cellerator/nb.html

Software: Machine Learning

WEKA: http://www.cs.waikato.ac.nz/~ml/publications.html

Lush (Y. LeCun - announced at NIPS): http://lush.sourceforge.net/

PDP++ (McClelland et al.): http://www.cnbc.cmu.edu/Resources/PDP++//PDP++.html

MLX: http://woldlab.caltech.edu/docs/MLX/

Research Groups and Institutions

Scientific Inference Systems Laboratory, UCI Institute for Genomics and Bioinformatics

Machine Learning Systems Group, Jet Propulsion Laboratory, California Institute of Technology

Wold Laboratory, California Institute of Technology

Meyerowitz Laboratory, California Institute of Technology

Signal Transduction and Cell-Cell Communication Laboratory, Johns Hopkins University

Center for Cell Mimetic Space Exploration, University of California, Los Angeles

Systems Biology Software at Keck Graduate Institute

Collaborators

Dennis Decoste, Jet Propulsion Laboratory

Andre Levchenko, Johns Hopkins University

Elliot Meyerowitz, California Institute of Technology

John Reinitz, SUNY Stony Brook

Bruce Shapiro, Jet Propulsion Laboratory

Barbara Wold, California Institute of Technology