Simulators for Bioinformatics and systems biology Cell simulation

Kinetikit A graphical simulator for chemical signaling. It runs with GENESIS, the general neuronal simulator http://www.ncbs.res.in/%7Ebhalla/kkit/index.html Biospice A biological data analysis and modeling workspace and database http://genomics.lbl.gov/%7Eaparkin/Group/Codebase/BioSpice/BioSpice.html E-Cell A simulation platform for the modelling of cells at a molecular level http://www.e-cell.org/ MCell A general Monte Carlo simulator of cellular microphysiology http://www.mcell.cnl.salk.edu/ Virtual Cell A general computational framework for modeling cell biological processes http://www.nrcam.uchc.edu/ Genome Object Net http://www.genomicobject.net/member3/index.html CellDesigner http://celldesigner.org/ Copasi http://www.copasi.org/tiki-index.php SBML (Systems Biology Markup Language) http://sbml.org/index.psp

Neuron Simulation

GENESIS http://www.genesis-sim.org/GENESIS/ NEURON http://neuron.duke.edu/

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Institution

Japanese national academic institutions http://www.mext.go.jp/b_menu/link/main_b12.htm Mitsuo Kawato lab http://www.cns.atr.jp/~kawato/ Kozo Kaibuchi lab http://www.med.nagoya-u.ac.jp/Yakuri/ Shin Ishii lab http://hawaii.aist-nara.ac.jp/%7Eishii/ Upi Bhalla lab http://www.ncbs.res.in/~bhalla/index.html Lab of Bioinformactis, Keio University http://www.bioinfo.sfc.keio.ac.jp/ Bioinformatics http://bioinformatics.org/ Systems biology institute http://www.symbio.jst.go.jp/systemsbiology/index.html Institute for systems biology http://www.systemsbiology.org/

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DataBase

National Center for Biotechnology Information (NCBI) http://www.ncbi.nlm.nih.gov/ PubMed http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed Entrez http://www.ncbi.nlm.nih.gov/Entrez/ BLAST http://www.ncbi.nlm.nih.gov/BLAST/ DOQCS: database of signal transduction pathways http://doqcs.ncbs.res.in/

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Tools

Sites for the Molecular Biology http://www.yk.rim.or.jp/%7Eaisoai/molbio-j.html BOXSHADE http://www.ch.embnet.org/software/BOX_form.html WWW Primer Picking (Primer3) http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi Biology Workbench http://www.bi.s.u-tokyo.ac.jp/kuroda-lab/links.ja.html Welcome to the BioToolKit http://www.biosupplynet.com/biotoolkit/ NCBI/Cn3D http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml DBGET/LinkDB Integrated Database Retrieval System http://www.genome.ad.jp/dbget/dbget.html 4D Microscopy http://www.bocklabs.wisc.edu/imr/facility/4D/4d.htm

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Vendors

Cell signaling http://www.cellsignal.com/retail/ Sigma-Aldrich http://www.sigmaaldrich.com/Local/SA_Splash.html Applied Biosystems Japan http://www2.appliedbiosystems.com/404.cfm?requested_url=jp/ Wako http://www.wako-chem.co.jp/ Nakalai http://www.nacalai.co.jp/ TaKaRa http://www.takara.co.jp/ TOYOBO BIO http://www.toyobo.co.jp/seihin/xr/index.htm ASTEC http://www.astec-bio.com/ Promega http://www.promega.co.jp/ TOMY http://bio.tomys.co.jp/ OLYMPUS http://www.olympus.co.jp/jp/ ZEISS http://www.zeiss.co.jp/ NIKON http://www.nikon.co.jp/main/jpn/index.htm SANYO http://www.sanyo.co.jp/ Hitachi Instruments Service http://www.hisco.co.jp/

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Meetings

The Molecular Biology Society of Japan http://wwwsoc.nii.ac.jp/mbsj/index-e.html The Japanese Biochemical Society http://www.jbsoc.or.jp/jbs_eng/index.html Japanese Society for Bioinformatics http://www.jsbi.org/jsbi_en/index.html Japanese Neural Network Society http://www.jnns.org/english.html Society for Neuroscience http://www.sfn.org/

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Search Engine

Google http://www.google.co.jp/ Yahoo! Japan http://www.yahoo.co.jp/ Yahoo! http://www.yahoo.com/ excite Japan http://www.excite.co.jp/ excite http://www.excite.com/

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