Networks and Centers International
NCBI US National Center for Biotechnology Information http://www.ncbi.nlm.nih.gov/
Kyoto University Bioinformatics Center Japan http://www.bic.kyoto-u.ac.jp/
UBC Bioinformatics Centre UBiC Canada http://bioinformatics.ubc.ca/
Bioinformatics.Org - The Open-Access Institute http://bioinformatics.org/
Weizmann Institute Bioinformatics and Biological Computing Israel http://bip.weizmann.ac.il/index.html
Baylor College of Medicine HGSC Houston Texas http://www.hgsc.bcm.tmc.edu/HGSC_home.html
San Diego Supercomputer Center Biological Projects CA USA http://scirad.sdsc.edu/soap/bio.html
TIGR The Institute for Genomic Research Rockville MD USA http://www.tigr.org/
Whitehead Institute MIT MA USA http://www.wi.mit.edu/
Broad Institute Center for Genome Research MIT MA USA http://www.broad.mit.edu/seq/
Stanford Genomic Resources CA USA http://genome-www.stanford.edu/
The Genomics and Bioinformatics Group National Cancer Institute USA http://discover.nci.nih.gov/index.jsp
Systems Biology Germany
HepatoSys - Network Systems Biology http://www.systembiologie.de/de/index.html
SFB 495 - Topologie und Dynamik von Signalprozessen (Stuttgart/Hohenheim) http://www.uni-stuttgart.de/izi/sfb495/
ZBSA - Center for Systems Biology Freiburg http://www.zbsa.uni-freiburg.de/
FDM - Freiburg Center for Data Analysis and Modeling http://www.fdm.uni-freiburg.de/groups/timeseries/biocs/ index.php
System Biology and Bioinformatics Wolkenhauer Univ. Rostock http://www.sbi.uni-rostock.de/
BIOMS - Center for Modelling and Simulation in the Biosciences Heidelberg http://www.bioms.de/index.shtml
Systems Biology at the IST and ISYS at University of Stuttgart http://www.sysbio.de/
MPI Dynamik komplexer Systeme - Magdeburg System Biology http://www.mpi-magdeburg.mpg.de/research/groups/sb/
EML Research gGmbH Heidelberg http://www.eml-r.org/english/research/index.php
Theoretical Biophysics Humboldt University Berlin http://www2.hu-berlin.de/biologie/theorybp/
Bork Group at EMBL - Comparative Systems Analysis http://www.bork.embl.de/j/
Systems Biology Europe
SystemsX - The Swiss Initiative in Systems Biology http://www.systemsx.ch/
YSBN The Yeast Systems Biology Network http://www.gmm.gu.se/YSBN/
SYSBIO Systems Biology and Bioinformatics Finland http://www.aka.fi/sysbio
SCMBB Bruxelles http://www.ucmb.ulb.ac.be/
Systems Biology International
The International Society for Systems Biology http://www.symbio.jst.go.jp/issb/
Systems Biology Portal www.systems-biology.org http://www.systems-biology.org/
Systems Biology at UC San Diego http://systemsbiology.ucsd.edu/
Institute for Systems Biology Seattle - USA http://www.systemsbiology.org/
The Systems Biology Institute - Tokyo http://sbi.jp/

 

Organizations Conferences
Bioinformatik.de http://www.bioinformatik.de
Bioinformatics.Org - The Open-Access Institute http://bioinformatics.org/
EMBNet Bioinformatics Network http://www.embnet.org/
Gesellschaft fuer Informatik - Fachgruppe Bioinformatik http://www.cebitec.uni-bielefeld.de/groups/fg402/
GBM Gesellschaft fuer Biochemie und Molekularbiologie http://www.gbm-online.de/
ISCB - International Society for Computational Biology http://www.iscb.org/
GCB 2006 German Conference on Bioinformatics - Tuebingen http://www.gcb2006.de/
ECCB 2006 European Conference on Computational Biology - Eilat, Israel http://www.eccb06.org/
ISMB 2006 Intelligent Systems for Molecular Biology - Fortaleza, Brazil http://ismb2006.cbi.cnptia.embrapa.br/
3rd International Workshop on Data Integration in the Life Sciences 2006 http://www2.informatik.hu-berlin.de/dils2006/index.html
SBMC Conference on Systems Biology of Mammalian Cells 2006 http://www.sbmc06.de/
Bioinformation Systems e.V. http://www.bioinfo.de/
Upcoming Proteomics Meetings (Univ Louisville Proteomics Lab) http://kdpnw.kdp-baptist.louisville.edu/proteomelab/ meetings.html

 

Journals
Applied Bioinformatics http://bioinformatics.adisonline.com/pt/re/abi/home.htm
Bioinformatics http://bioinformatics.oxfordjournals.org/
BioMed Central Bioinformatics http://www.biomedcentral.com/bmcbioinformatics
Briefings in Bioinformatics http://bib.oxfordjournals.org/
Human Genomics http://www.henrystewart.com/human_genomics/
In Silico Biology http://www.bioinfo.de/isb/
Journal of Computational Biology http://www.liebertpub.com/publication.aspx?pub_id=31
Journal of Medical Internet Research http://www.jmir.org/
Nucleic Acids Research http://www.oxfordjournals.org/nar/about.html
Omics: A Journal of Integrative Biology http://www.liebertpub.com/publication.aspx?pub_id=43
PLoS Computational Biology http://compbiol.plosjournals.org/perlserv/ ?request=index-html&issn=1553-7358
Nature Omics Gateway http://www.nature.com/omics/index.html
Proteomics http://www.wiley-vch.de/publish/en/journals/alphabeticIndex/ 2120/
Molecular and Cellular Proteomics http://www.mcponline.org/
Journal of Proteome Research http://pubs.acs.org/journals/jprobs/
Electrophoresis http://www.wiley-vch.de/publish/en/journals/alphabeticIndex/ 2027/
BioMed Central - Systems Biology Gateway http://www.biomedcentral.com/gateways/systemsbiology
Molecular Systems Biology http://www.nature.com/msb/index.html
BioSystems http://www.sciencedirect.com/science/journal/03032647
Systems Biology Journal - IEE Proceedings Systems Biology - The IET http://www.iee.org/Publish/Journals/ProfJourn/Proc/SYB/

 

Bioinformatics server
EBI European Bioinformatics Institute http://www.ebi.ac.uk/index.html
NCBI US National Center for Biotechnology Information http://www.ncbi.nlm.nih.gov/
GenomeNet WWW server Japan http://www.genome.ad.jp/
Expasy Proteomics Server http://www.expasy.org/
EMBNet - A Quick Guide to Expasy http://www.embnet.org/download/guides.html
Pôle Bio-Informatique Lyonnais http://pbil.univ-lyon1.fr/
Weizmann Institute Bioinformatics and Biological Computing http://bip.weizmann.ac.il/index.html
Baylor College of Medicine HGSC http://www.hgsc.bcm.tmc.edu/HGSC_home.html
San Diego Supercomputer Center Biological Projects http://www.sdsc.edu/research/ResearchOverview.html
Bielefeld University Bioinformatics Server http://bibiserv.techfak.uni-bielefeld.de/
HUSAR Bioinformatics Lab - Biocomputing Services at DKFZ http://genome.dkfz-heidelberg.de/
The Genomics and Bioinformatics Group NCI http://discover.nci.nih.gov/index.jsp

 

Databases
Sequences
Entrez Browser NCBI http://www.ncbi.nlm.nih.gov/Entrez/
SRSWWW EMBL-EBI http://srs.ebi.ac.uk/
DBGET/LinkDB Integrated Database Retrieval System http://www.genome.ad.jp/dbget/dbget2.html
SRSWWW at Expasy http://www.expasy.org/srs5/
BCM Search Launcher http://searchlauncher.bcm.tmc.edu/
GeneCards Weizmann http://www.genecards.org/index.shtml
Genome Matrix databases information integration http://genomematrix.rzpd.de/
RefSeq Reference Sequence NCBI http://www.ncbi.nlm.nih.gov/RefSeq/
Unigene NCBI http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene
Uniprot Universal Protein Resource Swiss-Prot/TREMBL/PIR http://www.expasy.uniprot.org/
EMBNet QuickGuide Swissprot Trembl Databases http://www.embnet.org/download/guides.html
PIR - Protein Information Resource http://pir.georgetown.edu/
IPI - International Protein Index EBI http://www.ebi.ac.uk/IPI/IPIhelp.html
Vector Database http://genome-www2.stanford.edu/vectordb/
Genomes
Ensembl Genome Browser http://www.ensembl.org/
Entrez-Genome NCBI http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Genome
Integr8 Proteome Analysis at EBI http://www.ebi.ac.uk/integr8/
GOLD: Genomes On Line Database v 2.0 http://www.genomesonline.org/
CBS Genome atlas database http://www.cbs.dtu.dk/services/GenomeAtlas/
MIPS: Munich Information Centre for Protein Sequences http://mips.gsf.de/
The Institute for Genomic Research http://www.tigr.org/
The Sanger Centre http://www.sanger.ac.uk/
Whitehead Institute http://www.wi.mit.edu/
Broad Institute Center for Genome Research http://www.broad.mit.edu/seq/
GeneCards Weizmann http://bioinformatics.weizmann.ac.il/cards/
HGP - Human genome project information http://www.ornl.gov/sci/techresources/Human_Genome/ home.shtml
DHGP - German human genome project http://www.dhgp.de/
Human Genome Resources NCBI http://www.ncbi.nlm.nih.gov/genome/guide/human/
Mouse Genome Resources NCBI http://www.ncbi.nlm.nih.gov/genome/guide/mouse/
Rat Genome resources NCBI http://www.ncbi.nlm.nih.gov/genome/guide/rat/
Fugu Fish Genomics Project QMUL http://fugu.biology.qmul.ac.uk/
ZFIN - Zebrafish information network http://zfin.org/
Wormbase C. elegans http://www.wormbase.org/
C.elegans Blast server (Sanger Centre) http://www.sanger.ac.uk/cgi-bin/blast/submitblast/c_elegans
FlyBase Drosophila http://flybase.net/
Yeast Genome Database MIPS http://mips.gsf.de/genre/proj/yeast/index.jsp
Schizosaccharomyces pombe genome (Sanger Centre) http://www.sanger.ac.uk/Projects/S_pombe/
Neurospora crassa Database (Broad) http://www.broad.mit.edu/annotation/fungi/neurospora/
Neurospora crassa Database (MIPS) http://mips.gsf.de/proj/neurospora/
Fungal Genetics Stock Center http://www.fgsc.net/
tair - The Arabidopsis Information Resource http://www.arabidopsis.org/
GABI Primary Database ( GabiPD ) - Genomanalyse Pflanze http://gabi.rzpd.de/
Plant genomes (MIPS) http://mips.gsf.de/projects/plants/
Maize Genetics and Genomic Database http://www.maizegdb.org/
International Rice Genome Sequencing Project http://rgp.dna.affrc.go.jp/E/IRGSP/
Protein structures
RCSB Protein Data Bank http://www.rcsb.org/pdb/
Entrez-Structure http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Structure
MSD Macromolecular Structure Database at EBI http://www.ebi.ac.uk/msd/index.html
Structures by electron microscopy at MSD http://www.ebi.ac.uk/msd-srv/emsearch/index.html
SWISS-MODEL http://swissmodel.expasy.org/SWISS-MODEL.html
EMBNet - A Quick Guide to Swiss-Model http://www.embnet.org/download/guides.html
SCOP: Structural Classification of Proteins http://scop.mrc-lmb.cam.ac.uk/scop/
Superfamily HMM models SCOP http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/
CATH database of structural domains http://cathwww.biochem.ucl.ac.uk/
Gene3D Structural and Functional Annotation http://cathwww.biochem.ucl.ac.uk:8080/Gene3D/
The DALI database http://ekhidna.biocenter.helsinki.fi/dali/start
Domain Structure Database NCBI http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Domains
ModBase - Comparative protein structure models http://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi
BALL and BALLView Visualization and Modelling Tools http://www.ball-project.org/
Motifs Profiles Domains
Interpro Domain and Profile Database http://www.ebi.ac.uk/interpro/
ExPASy - PROSITE http://www.expasy.org/prosite/
ExPASy - ScanProsite tool http://www.expasy.org/tools/scanprosite/
SIB myHits motif scan http://hits.isb-sib.ch/cgi-bin/motif_scan
PRINTS protein fingerprints http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/
SMART - Simple Modular Architecture Research Tool http://smart.embl-heidelberg.de/
Blocks WWW Server http://blocks.fhcrc.org/blocks/
Block Search http://blocks.fhcrc.org/blocks/blocks_search.html
The Sanger Centre Pfam Server http://www.sanger.ac.uk/Software/Pfam/
The Sanger Centre HMM Pfam Searcher http://www.sanger.ac.uk/Software/Pfam/search.shtml
TIGRFAMs protein families HMM http://www.tigr.org/TIGRFAMs/index.shtml
ProDom conserved protein domains http://prodes.toulouse.inra.fr/prodom/current/html/home.php
CDD Conserved domains database NCBI http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd
PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System http://www.pantherdb.org/
PIR iProClass Protein Classification http://pir.georgetown.edu/iproclass/
Superfamily HMM models SCOP http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/
Gene3D Structural and Functional Annotation http://cathwww.biochem.ucl.ac.uk:8080/Gene3D/
ModBase - Comparative protein structure models http://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi
Interproscan - Standalone Interpro Search (Linux) Perl Script Interproscan (also Windows) http://www.ebi.ac.uk/Tools/webservices/services/interproscan
Pathways
KEGG: Kyoto Encyclopedia of Genes and Genomes http://www.genome.ad.jp/kegg/
ExPASy - Biochemical Pathways http://www.expasy.org/cgi-bin/search-biochem-index
BioCarta - Pathways http://www.biocarta.com/genes/index.asp
PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System http://www.pantherdb.org/
Signaling Gateway - Cell Signaling Resource Nature http://www.signaling-gateway.org/
Reactome Project http://www.reactome.org/
Pathway Knowledge Base http://pkb.stanford.edu/pkbdev/
BioCyc Database Collection http://www.biocyc.org/
MetaCyc Encyclopedia of Metabolic Pathways http://metacyc.org/
MIM Molecular Interaction Maps at NCI http://discover.nci.nih.gov/mim/
IUPHAR receptor database http://www.iuphar-db.org/
LGICD Ligand-gated ion-channel database http://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php
SPAD: Signaling PAthways Database http://www.grt.kyushu-u.ac.jp/spad/
AraCyc - Pathway Database of Arabidopsis thaliana http://www.arabidopsis.org/biocyc/
DRASTIC- Database resource for analysis of signal transduction in plant cells http://www.drastic.org.uk/
Invitrogen iPath Human Biological Pathways http://escience.invitrogen.com/iPath/
BBID-Biological Biochemical Image Database http://bbid.grc.nia.nih.gov/
biodirectory - biochemical and metabolic pathways http://www.biodirectory.com/directory/Biochemistry/ Biochemical_and_metabolic_pathways_434.html
Signal Transduction - Biochemweb.org virtual library http://www.biochemweb.org/signaling.shtml
BioPAX - data exchange for biological pathway data http://www.biopax.org/
visANT - Visual Analysis Tool for Biological Networks and Pathways http://visant.bu.edu/
MapMan - integrative view of microarray data and metabolic maps http://gabi.rzpd.de/projects/MapMan/
GenMAPP Gene Map Annotator and Pathway Profiler http://www.genmapp.org/introduction.asp
Biological Networks http://biologicalnetworks.net/index.php
Enzymes
Enzyme Database - BRENDA http://brenda.bc.uni-koeln.de/
REBASE The Restriction Enzyme Database http://rebase.neb.com/rebase/rebase.html
Protein Kinase Resource http://www.kinasenet.org/pkr/
Kinase.com Global kinome analysis http://www.kinase.com/
IntEnz EBI Enzyme Database http://www.ebi.ac.uk/intenz/index.html
Catalytic Site Atlas - CSA (EBI) http://www.ebi.ac.uk/thornton-srv/databases/CSA/
Software
EBI: The BioCatalog http://www.ebi.ac.uk/biocat/
Bioperl http://bio.perl.org/
Open Source Initiative OSI http://www.opensource.org/
SourceForge.net Open Source Resource http://sourceforge.net/
Bioinformatics.Org - The Open-Access Institute http://bioinformatics.org/
Literature
Pub Med Central http://www.pubmedcentral.nih.gov/
Advanced PubMed Search http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed
PubMed/Medline NLM Mesh Browser http://www.nlm.nih.gov/mesh/MBrowser.html
PubMed Single Citation Matcher http://www.ncbi.nlm.nih.gov/entrez/query/static/ citmatch.html
NCBI Journal database http://www.ncbi.nlm.nih.gov/entrez/ query.fcgi?db=journals&term=
List of Journals Indexed for Medline http://www.nlm.nih.gov/tsd/serials/lji.html
Scopus http://www.scopus.com/scopus/home.url
Web of Science http://scientific.thomson.com/products/wos/
Google Scholar http://scholar.google.com/
CiteSeer (Computer and Information Sciences) http://citeseer.ist.psu.edu/
Scirus http://www.scirus.com/srsapp/
Espacenet - Europe's network of patent databases http://ep.espacenet.com/
REDI Databases of Baden-Wuerttemberg http://www-fr.redi-bw.de/
BIOSIS Previews http://scientific.thomson.com/products/bp/
Medline http://medline.cos.com/
OVID - Journals http://www.ovid.com/site/catalog/journals_landing.jsp
DOAJ - Directory of open access journals http://www.doaj.org/
PLoS Public Library of Science http://www.plos.org/
HighWire Press - Stanford University free full papers http://highwire.stanford.edu/
WorldSciNet Search Engine - World Scientific http://www.worldscinet.com/
JSTOR - The Scholarly Journal Archive http://www.jstor.org/
Electronic Journals Library http://rzblx1.uni-regensburg.de/ezeit/
Subito - German libraries combined paper delivery service http://www.subito-doc.com/
Crossref Search - commercial publishers worldwide common paper service http://www.crossref.org/
Wiley Interscience http://www3.interscience.wiley.com/
Springer Link http://www.springerlink.com/
IngentaConnect http://www.ingentaconnect.com/

 

Literature and Data Mining
Compendia
PubMed tools - The Edu Web http://www.kib.ki.se/student/pubmed_tools_en.html
Arrowsmith text mining tool compendium http://arrowsmith.psych.uic.edu/arrowsmith_uic/tools.html
Literature mining for the biologist - Review http://www.nature.com/nrg/journal/v7/n2/abs/nrg1768.html
Text-mining and information-retrieval services for molecular biology - Review http://genomebiology.com/2005/6/7/224/abstract
Text mining in Biology - Martin Krallinger http://www.pdg.cnb.uam.es/martink/
PDG Course Text mining in Biomedical Literature March 2006 http://www.pdg.cnb.uam.es/martink/LINKS/ tm_master_barc2006.html
BioCreAtIvE Text mining challenge http://biocreative.sourceforge.net/
Information retrieval and clustering
EBIMed Medline information retrieval and extraction http://www.ebi.ac.uk/Rebholz-srv/ebimed/index.jsp
GoPubMed - Ontology based literature search http://www.gopubmed.org/
HubMed pubmed rewired http://www.hubmed.org/
MyNCBI PubMed updating and alerting http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed
BioMail Pubmed Mail Update Service http://www.biomail.org/
PubCrawler PubMed GenBank Update Service http://pubcrawler.gen.tcd.ie/
E-BioSci literature search for life sciences http://www.e-biosci.org/
PubFinder - finds related articles in PubMed http://www.glycosciences.de/tools/PubFinder/
eTBlast - related articles to any text http://invention.swmed.edu/etblast/index.shtml
MedBlast - sequence-based literature retrieval http://medblast.sibsnet.org/
CoPub Mapper Gene Co-Publication Text Mining http://copub.gatcplatform.nl/
PubMatrix http://pubmatrix.grc.nia.nih.gov/
Vivisimo PubMed Clustering Search http://vivisimo.com/
Clusty the Clustering Engine http://clusty.com/
Information Extraction and Mining
The Arrowsmith Project http://arrowsmith.psych.uic.edu/arrowsmith_uic/index.html
BioIE - Extracting informative sentences http://umber.sbs.man.ac.uk/dbbrowser/bioie/
PubGene http://www.pubgene.org/
XplorMed: eXploring Medline abstracts http://www.ogic.ca/projects/xplormed/
iProLink integrated Protein Literature INformation and Knowledge http://pir.georgetown.edu/pirwww/iprolink/iprolink.shtml
RLIMS-P Rule-based LIterature Mining System for Protein Phosphorylation http://pir.georgetown.edu/iprolink/rlimsp/
iHOP - Information Hyperlinked over Proteins http://www.ihop-net.org/UniPub/iHOP/
MedMiner gene-based text mining http://discover.nci.nih.gov/textmining/main.jsp
String: functional protein association networks http://string.embl.de/
SPIES - Scientific-literature-based protein interaction extraction system http://spies.cs.tsinghua.edu.cn/spies/
PreBIND literature protein interaction extractor http://prebind.bind.ca/
BITOLA - Biomedical Discovery Support System http://www.mf.uni-lj.si/bitola/
ONDEX - Open Source Data Mining and Integration tool http://ondex.sourceforge.net/index.php
Text entity recognition tools
AliasServer Protein synonym search http://cbi.labri.fr/outils/alias/index.php
Biomedical Abbreviation Server http://bionlp.stanford.edu/abbreviation
ARGH Biomedical Acronym Database http://invention.swmed.edu/argh/index.shtml
Text2Knowledge - Acronym, Gene Name, Synonym, Interaction Database http://bioinformatics.org/textknowledge/
ABNER: A Biomedical Named Entity Recognizer http://www.cs.wisc.edu/~bsettles/abner/
GAPSCORE Gene and Protein Name Server http://bionlp.stanford.edu/gapscore/
Literature mining software
RefViz http://www.refviz.com/
TRANSINSIGHT http://www.transinsight.com/
InforSense http://www.inforsense.com/
BioLT Literature Mining Tool (Biomax Informatics AG) http://www.biomax.com/BIOMAX.COM/products/biolt.php
Attenex Patterns Document Mapper http://www.attenex.com/products/documentMapper/visual/

 

Alignment and database searches
WWW BLAST Database Searches at NCBI http://www.ncbi.nlm.nih.gov/BLAST/
EMBNet QuickGuide BLAST http://www.embnet.org/download/guides.html
Fasta3 Database Searches at the EBI http://www.ebi.ac.uk/fasta33/
BLITZ searches at the EBI http://www.ebi.ac.uk/searches/blitz_input.html
MPsrch at EBI http://www.ebi.ac.uk/MPsrch/
BCM Search Launcher: Multiple Sequence Alignments http://searchlauncher.bcm.tmc.edu/multi-align/ multi-align.html
The Sequence and Structure Searching Site Berkeley http://sss.berkeley.edu/
PeCoP Psi-Blast to find persistently conserved positions http://bioinformatics.org/pecop/
Directory of /pub/ClustalX http://bips.u-strasbg.fr/fr/Documentation/ClustalX/
GeneDoc Homepage http://www.psc.edu/biomed/genedoc/
Standalone BLAST (also for Windows) http://searchlauncher.bcm.tmc.edu/seq-util/Options/ readseq.html
BLAST standalone setup for Windows PC http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/pc_setup.html

 

Sequence tools
BCM Sequence Utilities http://searchlauncher.bcm.tmc.edu/seq-util/seq-util.html
SeWeR - Sequence Analysis using Web Resources http://bioinformatics.org/sewer/
Sequence Manipulation Suite 2 http://bioinformatics.org/sms2/
Sequence Extractor cloning toolbox http://bioinformatics.org/seqext/
ReadSeq http://searchlauncher.bcm.tmc.edu/seq-util/Options/ readseq.html
Webcutter 2.0 http://www.firstmarket.com/cutter/cut2.html
Reverse Complement of Sequence http://searchlauncher.bcm.tmc.edu/seq-util/Options/ revcomp.html
Primer 3 http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi
PrimerX - mutagenic primer design http://bioinformatics.org/primerx/
pDraw32 (Acaclone) Plasmid drawing http://www.acaclone.com/
Savvy Plasmid Maps http://bioinformatics.org/savvy/
European Molecular Biology Open Software Suite EMBOSS http://emboss.sourceforge.net/
Genome assembly by phred and phrap http://www.phrap.org/
EMBNet Quick Guides to phred and phrap http://www.embnet.org/download/guides.html

 

 

Phylogenetics
PHYLIP http://evolution.genetics.washington.edu/phylip.html
BIOBOX / Phylip Online Server http://pore.csc.fi/molbio/progs/phylip/
Phylip Online Help http://portal.litbio.org/Registered/Help/phylip/phylip.html
EMBNet A Quick Guide to PHYLIP http://www.embnet.org/download/guides.html
MacClade Home Page http://macclade.org/macclade.html
PAUP http://paup.csit.fsu.edu/index.html
METREE http://iubio.bio.indiana.edu:7780/archive/00000068/
TreeView http://taxonomy.zoology.gla.ac.uk/rod/treeview.html
Rod Page Software http://taxonomy.zoology.gla.ac.uk/rod/rod.html
PANDIT Protein and Associated NucleotideDomains with Inferred Trees http://www.ebi.ac.uk/goldman-srv/pandit/
PeCoP Psi-Blast to find persistently conserved positions http://bioinformatics.org/pecop/
Ribosomal Database Project II http://wdcm.nig.ac.jp/RDP/html/index.html
Phylogeny Web Servers List http://evolution.genetics.washington.edu/phylip/ software.serv.html
PHYLIP Phylogeny Programs http://evolution.genetics.washington.edu/phylip/ software.html
The Tree of Life Home Page http://tolweb.org/tree/phylogeny.html
Tree of Life Links http://tolweb.org/tree/home.pages/links.html
NCBI Taxonomy Browser http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Taxonomy
The Mathematical Basis of Molecular Phylogenetics http://www.techfak.uni-bielefeld.de/bcd/Curric/MathAn/ mathan.html

 

Annotation
Gene Function Resources
Gene Ontology (GO) Consortium http://www.geneontology.org/
QuickGO - GO Browser at EBI http://www.ebi.ac.uk/ego/QuickGO
AmiGO - GO Browser http://www.godatabase.org/
GOA - Gene Ontology Annotation Project at EBI http://www.ebi.ac.uk/GOA/index.html
GOStat - find statistically overrepresented GO terms http://gostat.wehi.edu.au/
Online Mendelian Inheritance in Man http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM
GeneCards Weizmann http://www.genecards.org/index.shtml
Genetic Association Database http://geneticassociationdb.nih.gov/
Integrated annotation services
NIH - DAVID 2006 Annotation tools http://david.abcc.ncifcrf.gov/home.jsp
eFamily Project - Grid integrating of protein database annotations http://www.efamily.org.uk/
DAS - Distributed Annotation System http://biodas.org/
DAS registry server at Sanger - available DAS servers http://das.sanger.ac.uk/registry/listServices.jsp
SPICE - DAS Client http://www.efamily.org.uk/software/dasclients/spice/
EnsEMBL Genome Browser DAS client http://www.ensembl.org/
Dasty - DAS client http://www.ebi.ac.uk/das-srv/uniprot/dasty/
Gene prediction services
AAT Server - Analysis and Annotation Tool http://genome.cs.mtu.edu/aat.html
Glimmer Microbial Gene-Finding System http://cbcb.umd.edu/software/glimmer/
GrailExp Grail Experimental Gene Discovery Suite http://compbio.ornl.gov/Grail-1.3/
BCM Gene Feature Searches http://searchlauncher.bcm.tmc.edu/seq-search/ gene-search.html
CBS HMMgene server http://www.cbs.dtu.dk/services/HMMgene/
CBS NetGene2 server http://www.cbs.dtu.dk/services/NetGene2/
CBS NetPlantGene server http://www.cbs.dtu.dk/services/NetPGene/
CBS Genome Atlas http://www.cbs.dtu.dk/services/GenomeAtlas/
GeneMark http://opal.biology.gatech.edu/GeneMark/
WebGeneMark http://opal.biology.gatech.edu/GeneMark/genemark24.cgi
Eukaryotic WebGeneMark http://opal.biology.gatech.edu/GeneMark/eukhmm.cgi
GENSCAN (C. Burge) http://bioweb.pasteur.fr/seqanal/interfaces/ genscan-simple.html
SplicePredictor http://deepc2.psi.iastate.edu/cgi-bin/sp.cgi
Lowe Lab tRNAscan-SE Search Server http://lowelab.ucsc.edu/tRNAscan-SE/
Rat Genome Database METAGENE Annotation Tool http://rgd.mcw.edu/METAGENE/
Promotor prediction services
CBS NetStart 1.0 server Translation Start http://www.cbs.dtu.dk/services/NetStart/
CBS Promoter 2.0 server http://www.cbs.dtu.dk/services/promoter/
WWW Promotor Scan Pol II http://bimas.dcrt.nih.gov/molbio/proscan/
EPD Eukaryotic promotor database http://www.epd.isb-sib.ch/
TRADAT Transcription Databases and Analysis Tool http://www.epd.isb-sib.ch/TRADAT.html
TFSEARCH - Transcription Factor Search http://www.cbrc.jp/research/db/TFSEARCH.html
TRANSFAC database at Biobase Biological Databases http://www.gene-regulation.com/pub/databases.html
ORegAnno: Open Regulatory Annotation http://www.oreganno.org/oregano/Index.jsp
cisRED: cis-regulatory element database http://www.cisred.org/
MotifMogul - Multiple Transcription Factor Bindin Sites Algorithms http://labs.systemsbiology.net/bolouri/Mogul/

 

Structures
Transmembrane features
TMHMM Server 2.0 http://www.cbs.dtu.dk/services/TMHMM-2.0/
ISREC TMpred Server http://www.ch.embnet.org/software/TMPRED_form.html
SOSUI Structure prediction of membrane proteins http://bp.nuap.nagoya-u.ac.jp/sosui/
HMMTOP Prediction of transmembrane helices and topology http://www.enzim.hu/hmmtop/
TMAP multiple sequence alignment protein prediction http://bioweb.pasteur.fr/seqanal/interfaces/tmap.html
TMPred - Prediction of transmembrane regions and orientation http://www.ch.embnet.org/software/TMPRED_form.html
TopPred - Topology prediction of membrane helices http://bioweb.pasteur.fr/seqanal/interfaces/toppred.html
3D structures
RCSB PDB Protein Data Bank - PDB http://www.rcsb.org/pdb/
NCBI Structure http://www.ncbi.nlm.nih.gov/Structure/
MSD Macromolecular Structure Database at EBI http://www.ebi.ac.uk/msd/index.html
Domain Structure Database NCBI http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Domains
NCBI VAST structural alignments http://www.ncbi.nlm.nih.gov/Structure/VAST/vast.shtml
SWISS-MODEL http://swissmodel.expasy.org//SWISS-MODEL.html
EMBNet - A Quick Guide to Swiss-Model http://www.embnet.org/download/guides.html
EMBL Dali protein structure comparison server http://www.ebi.ac.uk/dali/
The DALI database Dali Fold Classification http://ekhidna.biocenter.helsinki.fi/dali/start
GENO3D : Automatic Modeling of Protein Structure http://geno3d-pbil.ibcp.fr/cgi-bin/geno3d_automat.pl?page=/ GENO3D/geno3d_home.html
CPHmodels - Homology modeling http://www.cbs.dtu.dk/services/CPHmodels/index.html
ModBase - Comparative protein structure models http://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi
SCOP: Structural Classification of Proteins http://scop.mrc-lmb.cam.ac.uk/scop/
Superfamily HMM models SCOP http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/
CATH Protein Structure Classification Database http://cathwww.biochem.ucl.ac.uk/latest/index.html
Gene3D Structural and Functional Annotation http://cathwww.biochem.ucl.ac.uk:8080/Gene3D/
PredictProtein http://www.predictprotein.org/
Cn3D Home Page http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml
BALL and BALLView Visualization and Modelling Tools http://www.ball-project.org/
DeepView Swiss-PdbViewer http://www.expasy.org/spdbv/mainpage.html
Protein Explorer http://www.umass.edu/microbio/chime/pe/protexpl/frntdoor.htm
RasMol http://www.umass.edu/microbio/rasmol/
RasTop - Rasmol Graphical Interface http://www.geneinfinity.org/rastop/
Chime http://www.umass.edu/microbio/chime/
Simulation Dynamischer Molekuele (DKFZ) http://www.md-simulations.de/
Biodesigner Molecular Modeling and Visualization http://www.pirx.com/biodesigner/overview.html
VMD - Visual Molecular Dynamics http://www.ks.uiuc.edu/Research/vmd/
Accelrys Discovery Studio Visualizer (free version) http://www.accelrys.com/products/downloads/ds_visualizer/ index.html
Principals of protein structure http://www.expasy.org/swissmod/course/course-index.htm
Genetic algorithms on proteins http://www.techfak.uni-bielefeld.de/bcd/Curric/ProtEn/ contents.html
Signal peptides and glycosylation sites
SignalP server http://www.cbs.dtu.dk/services/SignalP/
PSORT WWW Server http://psort.ims.u-tokyo.ac.jp/
NetOGlyc server http://www.cbs.dtu.dk/services/NetOGlyc/
ExPASy - ScanProsite tool http://www.expasy.org/tools/scanprosite/
Secondary structures
NNPredict http://www.cmpharm.ucsf.edu/~nomi/nnpredict.html
PredictProtein http://www.predictprotein.org/
PredictProtein Help http://predictprotein.org/newwebsite/docs/help_entry.htm
JPRED Secondary structure prediction http://www.compbio.dundee.ac.uk/~www-jpred/
JUFO neuronal network prediction server http://carbon.structbio.vanderbilt.edu/ view.php?section=0&page=6
PSIPRED Protein Structure Prediction Server http://bioinf.cs.ucl.ac.uk/psipred/
NIH: GOR4 secondary structure prediction http://abs.cit.nih.gov/gor/
PROF - Secondary Structure Prediction System http://www.aber.ac.uk/~phiwww/prof/
ISREC COILS Server http://www.ch.embnet.org/software/COILS_form.html
NPS: Consensus secondary structure prediction http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/ npsa_seccons.html
NPS : coiled-coils prediction http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/ npsa_lupas.html
NPS: MLRC http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/ npsa_mlrc.html
NPS: HNN http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/ npsa_hnn.html
NPS: SOPMA http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/ npsa_sopma.html
NPS: GOR4 http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/ npsa_gor4.html
RNA
BiC RNA folding services http://www.bioinfo.rpi.edu/applications/
Vienna RNA secondary structure servers http://rna.tbi.univie.ac.at/

 

Small molecules
Human Metabolome Database http://www.hmdb.ca
KEGG Drug Database http://www.genome.ad.jp/kegg/drug/
KEGG Ligand Database http://www.genome.ad.jp/kegg/ligand.html
ChEBI - Chemical Entities of Biological Interest http://www.ebi.ac.uk/chebi/
MSD Ligand Chemistry in PDB http://www.ebi.ac.uk/msd-srv/msdchem/cgi-bin/cgi.pl
NCBI PubChem Compound http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pccompound
NCBI PubChem Substance http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pcsubstance
NLM SIS Chemical Information http://sis.nlm.nih.gov/chemical.html
NCI-3D Search http://chem.sis.nlm.nih.gov/nci3d/
ChemIDplus http://chem.sis.nlm.nih.gov/chemidplus/
ChemFinder Searching http://chemfinder.cambridgesoft.com/
CHEMINFO: Chemical Information Sources from Indiana University http://www.indiana.edu/~cheminfo/
Acronymfinder http://www.acronymfinder.com/
Functional genomics
Microarrays
Microarray Bioinformatics at EBI http://www.ebi.ac.uk/microarray/index.html
Arrayexpress at the EBI http://www.ebi.ac.uk/arrayexpress/
Expression Profiler at EBI http://www.ebi.ac.uk/expressionprofiler/
Documentation for Expression Profiler http://ep.ebi.ac.uk/Docs/
GEO Gene Expression Omnibus at NCBI http://www.ncbi.nlm.nih.gov/geo/
Stanford Microarray Database http://genome-www5.stanford.edu/
Yale Microarray Database http://info.med.yale.edu/microarray/
TIGR functional genomics http://www.tigr.org/microarray
NGFN German National Functional Genomics Network http://www.ngfn.de/
Genevestigator https://www.genevestigator.ethz.ch/
CATMA - A complete Arabidopsis Transcriptome MicroArray http://www.catma.org/
The Arabidopsis Information Resource - TAIR http://www.arabidopsis.org/
AFGN Arabidopsis Functional Genomics Network http://www.uni-tuebingen.de/plantphys/AFGN/
Microarray Gene Expression Data Society http://www.mged.org/
Microarray.Org - Microarray protocols and software http://microarray.org/sfgf/
NIH - Guide to Microarray Data analysis http://discover.nci.nih.gov/microarrayAnalysis/ Microarray.Home.jsp
Microarray Tools at NCI http://discover.nci.nih.gov/tools.jsp
Mesher - TIGR MeSH terms overrepresented in microarray data http://pga.tigr.org/pubminer/mesher.html
J-Express microarray analysis free version http://www.ii.uib.no/%7Ebjarted/jexpress/main.html
MicroArray Explorer tool for Data Mining Gene Expression Patterns http://maexplorer.sourceforge.net/
Cluster and Treeview from the Eisen Lab http://rana.lbl.gov/EisenSoftware.htm
BioConductor Project - Open Source Software for Bioinformatics http://www.bioconductor.org/
R and Bioconductor Manual (Thomas Girke) http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/ R_BioCondManual.html
TIGR TM4 Microarray Software Suite http://www.tm4.org/
Broad Institute Genecluster 2.0 http://www.broad.mit.edu/cancer/software/genecluster2/ gc_license.html
dChip Software: Gene Expression Microarray and SNP Microarray Analysis http://biosun1.harvard.edu/complab/dchip/
NASC Affymetrix Service: Analysis hints http://affymetrix.arabidopsis.info/analysis/index.html
Analysis of Affymetrix data using Excel http://affymetrix.arabidopsis.info/analysis/ AffyAnalysisWithExcel.html
Affymetrix - NetAffxTM Analysis Center http://www.affymetrix.com/analysis/index.affx
MapMan - integrative view of microarray data and metabolic maps http://gabi.rzpd.de/projects/MapMan/
GenMAPP Gene Map Annotator and Pathway Profiler http://www.genmapp.org/introduction.asp
Proteomics
EXPASY Swiss 2Dpage http://www.expasy.org/ch2d/
WORLD-2DPAGE Index to 2D-PAGE databases and services http://www.expasy.org/ch2d/2d-index.html
EXPASY Peptide Mass Tool http://www.expasy.org/tools/peptide-mass.html
EXPASY Aldente Tool http://www.expasy.org/tools/aldente/
MASCOT Peptide Mass Fingerprint http://www.matrixscience.com/search_form_select.html
UCSF Protein Prospector http://prospector.ucsf.edu/
PROWL protein and MS tools http://prowl.rockefeller.edu/
PRIDE - Proteomics Identifications Database http://www.ebi.ac.uk/pride/
RESID Database of protein modifications http://www.ebi.ac.uk/RESID/
Scaffold protein identification framework (by Proteome Software) http://www.proteomesoftware.com/ Proteome_software_prod_Scaffold.html
Proteomics Society http://www.proteome.org/
HUPO - Human Proteome Organisation http://www.hupo.org/
HPI - Human Proteomics Initiative http://www.ebi.ac.uk/swissprot/hpi/hpi.html
gabi Arabidopsis Proteomics Data http://gabi.rzpd.de/projects/Arabidopsis_Proteomics/
Proteomics from Angelika Görg http://www.weihenstephan.de/blm/deg/
Boston University Biology Proteomics Resource http://genomics10.bu.edu/jtullai/proteomics_resources/
Deutsche Gesellschaft für Proteomforschung http://www.dgpf.org/
SWISS Proteomics Society Proteomics Links http://www.swissproteomicsociety.org/links.html
IonSource Proteomics Resource Links http://www.ionsource.com/links/proteolinks.htm
Protein-Protein Interactions
EBI IntAct Project http://www.ebi.ac.uk/intact/index.jsp
DIP - Database of Interacting Proteins http://dip.doe-mbi.ucla.edu/
BOND - Biomolecular Object Network Database http://bond.unleashedinformatics.com/
MIPS Mammalian Protein-Protein Interaction Databank http://mips.gsf.de/proj/ppi/
BioGRID - General Repository for Interaction Datasets http://www.thebiogrid.org/
HPID Human Protein Interaction Database http://wilab.inha.ac.kr/hpid/
The JCB Protein-Protein Interaction Website http://www.imb-jena.de/jcb/ppi/
MIPS Yeast Protein-Protein-Interaction and Complex Viewer http://mips.gsf.de/proj/yeast/CYGD/interaction/
Yeast Protein complex database http://yeast.cellzome.com/
MINT - Molecular Interactions database http://mint.bio.uniroma2.it/mint/
Complexpander - Predicting protein complexes http://llama.med.harvard.edu/cgi/Complexpander/ Complexpander.pl
PathBlast - Comparison of interaction networks between organisms http://www.pathblast.org/
iHOP - Information Hyperlinked over Proteins http://www.ihop-net.org/UniPub/iHOP/
String: functional protein association networks http://string.embl.de/
SPIES - Scientific-literature-based protein interaction extraction system http://spies.cs.tsinghua.edu.cn/spies/
PreBIND literature protein interaction extractor http://prebind.bind.ca/
BioPAX - data exchange for biologicaql pathway data http://www.biopax.org/
Graphviz - Open Source Graph Visualization Software http://www.graphviz.org/
Cytoscape - open source software for interaction visualization and integration http://www.cytoscape.org/
visANT - Visual Analysis Tool for Biological Networks and Pathways http://visant.bu.edu/
aiSee - commercial Graph layout software http://www.aisee.com/
Stratagene PathwayArchitect Software http://www.stratagene.com/tradeshows/feature.aspx?fpId=90
miRNA
RNA Molecular Biology Tuschl Lab http://www.rockefeller.edu/labheads/tuschl/
miRBASE microRNA database Sanger Institute http://microrna.sanger.ac.uk/
Rfam RNA families database of alignments and CMs Sanger Institute http://www.sanger.ac.uk/Software/Rfam/
The siRNA user guide - Tuschl Lab http://www.rockefeller.edu/labheads/tuschl/sirna.html

 

Systems Biology
System Biology Information Resources
BioModels.NET http://www.biomodels.net/
The Reactome Project http://www.reactome.org/
Panther Classification Systems - Panther Pathways http://www.pantherdb.org/pathway/
Human Metabolome Database http://www.hmdb.ca
KDBI - Kinetic Data of Biomolecular Interactions http://xin.cz3.nus.edu.sg/group/kdbi/kdbi.asp
SBML Systems Biology Markup Language http://sbml.org/index.psp
The International Society for Systems Biology http://www.symbio.jst.go.jp/issb/
Systems Biology Portal www.systems-biology.org http://www.systems-biology.org/
The Systems Biology Institute - Tokyo http://sbi.jp/
Systems Biology at UC San Diego http://systemsbiology.ucsd.edu/
HepatoSys - Network Systems Biology http://www.systembiologie.de/de/index.html
SystemsX - The Swiss Initiative in Systems Biology http://www.systemsx.ch/
YSBN The Yeast Systems Biology Network http://www.gmm.gu.se/YSBN/
Systems Biology Modeling Tools
Systems Biology WorkBench SWB package http://sbw.kgi.edu/research/sbwIntro.htm
JDesigner: A Biochemical Network Layout Tool http://sbw.kgi.edu/software/jdesigner.htm
Jarnac biochemical simulation package http://sbw.kgi.edu/software/jarnac.htm
Pasadena Twain ODE solver of the SWB package http://sbw.sourceforge.net/sbw/software/
CADLIVE - network construction system http://kurata21.bse.kyutech.ac.jp/cadlive/
Dizzy stochastic simulations tool http://magnet.systemsbiology.net/software/Dizzy/
CellDesigner - a modeling tool for biochemical networks http://www.celldesigner.org/
CellWare - building computational chassis for systems and synthetic biology http://www.cellware.org/
E-Cell project http://www.e-cell.org/
COPASI - Complex Pathway Simulator http://www.copasi.org/
Gepasi - Biochemical Kinetics Simulator http://www.gepasi.org/
Dynetica - a simulator of dynamic networks http://www.duke.edu/~you/Dynetica_page.htm
PLAS Power Law Analysis and Simulation tool http://www.dqb.fc.ul.pt/docentes/aferreira/plas.html
JSim - a Java based simulation system http://nsr.bioeng.washington.edu/PLN/Software/
STOCKS - Stochastic kinetic simulations http://www.sysbio.pl/stocks/index.html
Basis Gillespie Stochastic Simulator http://www.basis.ncl.ac.uk/software.html
CaliBayes - Bayesian calibration of biological simulators http://www.calibayes.ncl.ac.uk/
JWS Online - Online Cellular Systems Modelling http://jjj.biochem.sun.ac.za/
PyBioS - web server for modeling and simulation of cellular systems http://pybios.molgen.mpg.de/
Virtual Cell Internet simulation server at NRCAM http://www.nrcam.uchc.edu/

 

Internet search
Search engines
Google http://www.google.com
Clusty the Clustering Engine http://clusty.com/
AltaVista http://de.altavista.com/
Yahoo! http://de.yahoo.com/
Overture http://www.content.overture.com/d/
WebCrawler http://webcrawler.com/
HotBot http://www.hotbot.com/
search.com http://www.search.com/search
Lycos http://www.lycos.com/
MetaGer http://meta.rrzn.uni-hannover.de/
CUSI - Suchmoeglichkeiten im Internet http://www.tu-chemnitz.de/misc/cusi.html
W3 Search Engines FU Berlin http://www.chemie.fu-berlin.de/outerspace/meta-index.html
Google Hacks http://hacks.oreilly.com/pub/ht/2
Link lists
Expasy http://www.expasy.org/
Expasy Life Science Directory http://www.expasy.org/links.html
Bioinformatics Links Directory UBiC http://bioinformatics.ubc.ca/resources/links_directory/
Nucleic Acids Research Database Summary Paper List http://www3.oup.co.uk/nar/database/a/
Nucleic Acids Research Database Issue 2006 http://nar.oxfordjournals.org/content/vol34/suppl_1/ index.dtl
Nucleic Acids Research Webserver Issue 2006 http://nar.oxfordjournals.org/content/vol34/suppl_2/ index.dtl
CMS Molecular Biology Resource http://restools.sdsc.edu/
Harvard Dept of MCB - Biology Links http://mcb.harvard.edu/BioLinks.html
Institute Pasteur Bio NetBook http://www.pasteur.fr/recherche/BNB/bnb-en.html
Biotech Europe Link Base http://www.biotech-europe.de/rubric/linkbase/index.html
Internet Directory for Botany http://www.bgbm.fu-berlin.de/idb/bio/botany.html
Botanisches Webportal http://www.botanik.ch/
CiteULike - online reference management sharing service http://www.citeulike.org/
Connotea - online reference and link sharing http://www.connotea.org/
Internet
Connected: An Internet Encyclopedia http://freesoft.org/CIE/index.htm
RSS Tutorial for Content Publishers and Webmasters http://www.mnot.net/rss/tutorial/

 

 

Books
Bioinformatics (Mount) CSHL Press http://www.bioinformaticsonline.org/
Bioinformatics (Baxevanis Ouellette Francis) Wiley-VCH http://www.wiley-vch.de/publish/en/books/bySubjectLS00/ bySubSubjectLS70/0-471-47878-4/?sID=84cf81f051c597d68adf6531e2062326
Beginning Perl for Bioinformatics (Tisdall) O'Reilly http://www.oreilly.com/catalog/begperlbio/
Mastering Perl for Bioinformatics (Tisdall) O'Reilly http://www.oreilly.com/catalog/mperlbio/
Angewandte Bioinformatik (Selzer Marhoefer Rohwer) - Springer http://www.springer.com/west/home/generic/ order?SGWID=4-40110-22-2317982-0
Bioanalytik (Lottspeich Engels Joachim) Elsevier http://www.elsevier.de/artikel/1036327
Systems Biology in Practice (Klipp Herwig Kowald Wierling Lehrach) Wiley-VCH http://www.wiley-vch.de/publish/en/books/bySubjectLS00/ bySubSubjectLS70/3-527-31078-9/?sID=d05b
Bioinformatics and Computational Biology Solutions Using R and Bioconductor http://www.springerlink.com/content/u014612g263032jk/
BLAST - (Korf, Yandell, Bedell) O'Reilly http://www.oreilly.com/catalog/blast/
Sequence Analysis in a Nutshell (Markel Leon) O'Reilly http://www.oreilly.com/catalog/seqanalyian/

 

The bioinformatics bench
Linux
Novell SUSE Linux http://www.novell.com/linux/
Linux Online http://www.linux.org/
RedHat Linux http://www.redhat.com/
Debian Linux http://www.debian.org/
Ubuntu Linux http://www.ubuntu.com/
Linux Kernel Archives http://www.kernel.org/
Knoppix http://www.knopper.net/knoppix/index-en.html
BioKnoppix http://bioknoppix.hpcf.upr.edu/
BioLinux http://www.biolinux.org/
EMBNet A QuickGuide to UNIX http://www.embnet.org/download/guides.html
Linux Community (German) http://www.linux-community.de/
linux.de http://www.linux.de/
Linux user group Tuebingen http://tuebingen.linux.de/
Apache + HTML
Apache http://www.apache.org/
SELFHTML http://selfhtml.org/
MySQL
MySQL http://www.mysql.com/
PHP
PHP http://www.php.net/
SELFPHP http://www.selfphp.info/
PHP FAQ http://www.faqts.com/knowledge_base/index.phtml/fid/51/
phpMyAdmin http://sourceforge.net/projects/phpmyadmin/
php-homepage.de - Resource fuer PHP und MySQL http://www.php-homepage.de/
PHP-Archiv - PHP Scripts http://www.phparchiv.de/
phpwelt http://www.phpwelt.de/
Perl and R
PERL http://www.perl.com/
The Perl directory at perl.org http://www.perl.org/
Perl documentation http://perldoc.perl.org/
ActiveState - ActivePerl Downloads http://www.activestate.com/Products/ActivePerl/
CPAN PERL Script Archiv http://www.cpan.org/
Bioperl http://bio.perl.org/
BioConductor Project - Open Source Software for Bioinformatics http://www.bioconductor.org/
EMBNet QickGuides PERL and Regular Expressions http://www.embnet.org/download/guides.html
The R project for statistical computing http://www.r-project.org/
The Comprehensive R archive network http://cran.r-project.org/
BioConductor Project - Open Source Software for Bioinformatics http://www.bioconductor.org/
R and Bioconductor Manual (Thomas Girke) http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/ R_BioCondManual.html
Open Source Initiative OSI http://www.opensource.org/
SourceForge.net Open Source Resource http://sourceforge.net/
Editors
The Vim Editor http://www.vim.org/
Proton http://www.meybohm.de/download.html
Enote
DOE 2000 Electronic Notebook Project ORNL http://www.csm.ornl.gov/~geist/java/applets/enote/
DOE 2000 Electronic Notebook Project Main http://www.epm.ornl.gov/enote/
WETLAB: an open source electronic lab notebook http://128.248.65.210/arrowsmith_uic/wetlab.html
EMBOSS
European Molecular Biology Open Software Suite EMBOSS http://emboss.sourceforge.net/
EMBNet Quick Guides EMBOSS and wEMBOSS http://www.embnet.org/download/guides.html
Ready-to-install EMBOSS at BioLinux http://www.biolinux.org/emboss.html
wEMBOSS http://bigben.vub.ac.be:6080/wEMBOSS/
BioKNOPPIX with JEMBOSS and EMBOSS http://bioknoppix.hpcf.upr.edu/
Bioinformatic System Management Workshop 2005 http://www.be.embnet.org/tutorials/BSMW05
EMBOSS for Windows (Interactive Biosoftware) http://www.interactive-biosoftware.com/embosswin/ embosswin.html
EMBOSS For Windows (EBI) (alpha release) ftp://emboss.open-bio.org/pub/EMBOSS/windows
Open Source Bioinformatics Platforms
myGRID - Open Source Middleware Environment for Bioinformatics Workflows http://www.mygrid.org.uk/
TAVERNA Open Source Bioinformatics Workbench http://taverna.sourceforge.net/
eFamily Project - Grid integrating of protein database annotations http://www.efamily.org.uk/
Bioclipse - visual platform for structural chemo- and bioinformatics http://www.bioclipse.net/
Systems Biology WorkBench SWB package http://sbw.kgi.edu/research/sbwIntro.htm
Bioinformatics Web APIs (nodalpoint wiki) http://wiki.nodalpoint.org/bioinformatics_web_apis