====== Link collection ======

**The collected links will be included as browser bookmarks in future versions of SB.OS.**


===== General =====

Systems Biology Graphical Notation (SBGN) Templates (use this to standardize your graphical network models)
http://sbgn.org/Documents/Templates

Wikipedia
http://www.wikipedia.org/

Social Network: myExperiment makes it easy to find, use and share scientific workflows and other Research Objects
http://www.myexperiment.org/

OpenHelix On-demand, multimedia, narrated tutorials on a large number of the most popular and powerful free web-based bioinformatics tools. You get the web tutorial, PowerPoint slides, handouts, and exercises.
http://openhelix.com/

Minimum Information Checklists for Biologial Data: MIBBI Minimum Information for Biological and Biomedical Investigations
http://mibbi.sourceforge.net/

Insert your title and/or abstract and get suggestion in which journal you should publish
http://www.biosemantics.org/jane/

Open source SOPs 
http://openwetware.org/

Links to Bioinformatics/Systems Biology tools and resources
http://www.bioinfowiki.mpg.de/

===== Literature =====

Systems Biology - A Textbook
http://eu.wiley.com/WileyCDA/WileyTitle/productCd-3527318747.html


===== SBML infrastructure and model databases =====

SBML
www.sbml.org

MIRIAM resources
http://www.ebi.ac.uk/miriam/

BioModels Database
http://www.ebi.ac.uk/biomodels-main/

JWS model database
http://jjj.biochem.sun.ac.za/database/

===== Software =====

E-cell
http://www.e-cell.org/ecell/

Zotero is a free, easy-to-use Firefox extension to help you collect, manage, and cite your research sources. It lives right where you do your work—in the web browser itself.
http://www.zotero.org/

Ubuntu Science Software
https://help.ubuntu.com/community/UbuntuScience

===== Databases =====

Pathguide contains information about 299 biological pathway resources (hinting SBML/BioPAX/CellML export capability )
http://www.pathguide.org/

Sacharomyces Genome Database
http://www.yeastgenome.org/

Thermodynamics of Enzyme-Catalyzed Reactions
http://xpdb.nist.gov/enzyme_thermodynamics/

EMBL Nucleotide Sequence Database
http://www.ebi.ac.uk/embl

Fly View - Drosophila development and genetics
http://pbio07.uni-muenster.de/

GenBank - all known nucleotide and protein sequences
http://www.ncbi.nlm.nih.gov/Genbank/GenbankOverview.html

Kyoto Encyclopedia of Genes and Genomes (KEGG)
http://www.genome.ad.jp/kegg

PDB - Structure data determined by X-ray crystallography and NMR
http://www.rcsb.org/pdb

WikiPathways In the new tradition of Wikipedia, WikiPathways is an open, public platform dedicated to the curation of biological pathways by and for the scientific community.
http://www.wikipathways.org/

Reactome - a curated knowledgebase of biological pathways
http://www.reactome.org/

BioCyc is a collection of 507 Pathway/Genome Databases.
http://biocyc.org/

Ontology Lookup Service
http://www.ebi.ac.uk/ontology-lookup/

BioCatalogue: providing a curated catalogue of Life Science Web Services.
http://www.biocatalogue.org/

LaTeX Bibliography Styles Database
http://bst.maururu.net/

The Database of Useful Biological Numbers
http://bionumbers.hms.harvard.edu/

===== Groups =====

Innovationskolleg Theoretische Biologie (ITB) - Hanspeter Herzel, Peter Hammerstein, Andreas Herz
http://itb.biologie.hu-berlin.de/

Theoretical Biochemistry, Charité - Hermann-Georg Holzhütter
http://www.charite.de/

Göteborg Yeast Centre - Stefan Hohmann
http://www.gmm.gu.se/gyc/index.html

Metabolic Control Analysis Research Group - David Fell
http://bms-mudshark.brookes.ac.uk/

Molecular Cell Physiology - Hans Westerhoff
http://www.bio.vu.nl/vakgroepen/mcp/

Computational Physiology Hamiliton Institute - Wilhelm Huisinga
http://www.hamilton.ie/compphysiol/

Institut für Biologie, Humboldt-Universität
http://www.biologie.hu-berlin.de/

Zentrum für BioPhysik und BioInformatik der Humboldt-Universität (BPI)
http://www.biologie.hu-berlin.de/%7EBPI/

Humboldt University Research Initiative "Systems Biology"
http://bioinf.charite.de/biophys/systemsbiology/

SFB 555 Complex Nonlinear Processes
http://sfb555.physik.hu-berlin.de/

SFB 618 Theoretical Biology: Robustness, Modularity and Evolutionary Design of Living Systems
http://www.biologie.hu-berlin.de/forschung/SFB_618/

Graduate program - Dynamics and evolution of cellular and macromolecular processes
http://www.biologie.hu-berlin.de/gk

BioCentrum Amsterdam
http://www.science.uva.nl/biocentrum/

Bioinformatics Graduate Program Boston University
http://www.bu.edu/bioinformatics

Kyoto Bioinformatics Center
http://www.bic.kyoto-u.ac.jp/