Useful links

2Can Support Portal – Bioinformatics educational resource
3DID – 3D interacting domains
Accelrys Discovery Studio
Accelrys Discovery Studio Visualizer (free version)
ActiveState – ActivePerl Downloads
Advanced PubMed Search
Affymetrix – NetAffx TM Analysis Center
AFGN Arabidopsis Functional Genomics Network
aiSee – commercial Graph layout software
AMB Algorithms for Molecular Biology
AmiGO – GO Browser
Analysis of Affymetrix data using Excel
AraCyc – Pathway Database of Arabidopsis thaliana
Arrayexpress at the EBI
AsiDesigner siRNA design pipeline
Babelomics – Systems biology microarray data mining
BALL and BALLView Visualization and Modelling Tools
Basis Gillespie Stochastic Simulator
Baylor College of Medicine HGSC
BBID-Biological Biochemical Image Database
BCM Gene Feature Searches
BCM Search Launcher
BCM Search Launcher: Multiple Sequence Alignments
BCM Sequence Utilities
BCM Structure Prediction Tools
BioBike (LISP)
BioConductor Project – Open Source Software for Bioinformatics
Bioconductor Workshops
BioCyc Database Collection
BioData Mining
Biodesigner Molecular Modeling and Visualization
BioEdit Sequence Alignment Editor for Windows 95/98/NT/XP
BioGRID – General Repository for Interaction Datasets
Bioinformatics – Online Courses and Tutorials
Bioinformatics Links Directory UBiC
Bioinformatics Open Source Conference BOSC 2011 Vienna
Bioinformatics Open Source Conference BOSC 2012 Long Beach
Bioinformatics Software Server Lille
Bioinformatics.Org – The Open-Access Institute
BioLinux – Wikipedia
Biological Networks
BioMed Central – Systems Biology Gateway
BioMed Central Bioinformatics
BioPAX – data exchange for biological pathway data
BioPAX – data exchange for biologicaql pathway data
Biotech Europe Link Base
BLAST FASTA databases download
BLAST setup procedure for Windows
BLAST standalone documentation
BLAST standalone setup for Windows PC
BLAST Wikipedia
Block Search
Blocks WWW Server
BMC Systems Biology
BOND – Biomolecular Object Network Database
Boston University Biology Proteomics Resource
BotDB DSSP analysis
Briefings in Bioinformatics
Briefings in Functional Genomics and Proteomics
Broad Institute Center for Genome Research
Broad Institute Genecluster 2.0
C.elegans Blast server (Sanger Centre)
CADLIVE – network construction system
CaliBayes – Bayesian calibration of biological simulators
Catalytic Site Atlas – CSA (EBI)
CATH database of structural domains
CATH Protein Structure Classification Database
CATMA – A complete Arabidopsis Transcriptome MicroArray
CAVER protein analysis and visulaization – pockets and tunnels
CBS Bioinformatics Courses
CBS Genome Atlas
CBS Genome atlas database
CBS HMMgene server
CBS NetGene2 server
CBS NetPlantGene server
CBS NetStart 1.0 server Translation Start
CBS Promoter 2.0 server
CCMS XtalView
CCP4 Molecular Graphics
CCP4 Molrep – automated program for molecular replacement
CCP4 Scala – scale together multiple observations of reflections
CCP4 Software for Molecular X-ray crystallography
CCP4 SOLOMON – density modification (phase improvement) by solvent flipping
CDD Conserved domains database NCBI
CellDesigner – a modeling tool for biochemical networks
Cellware – Modeling and Simulation Tool
ChEBI – Chemical Entities of Biological Interest
CHEMINFO: Chemical Information Sources from Indiana University
CiteULike – online reference management sharing service
Clinical Proteomics
CMBI Courses for protein structure
CMS Molecular Biology Resource
Cn3D Home Page
CNSsolve Crystallography and NMR system
Comparison of WAMPs
Connotea – online reference and link sharing
Conserved Domain Database NCBI
Conserved Domains Database NCBI
ConTra – identification of conserved transcription factor binding sites
COPASI – Complex Pathway Simulator
CoPub Mapper Gene Co-Publication Text Mining
CPAN PERL Script Archiv
CPHmodels – Homology modeling
Crossref Search – commercial publishers worldwide common paper service
Current Proteomics
CUSI – Suchmoeglichkeiten im Internet
Cytoscape – open source software for interaction visualization and integration
DAS – Distributed Annotation System
DAS registry server at Sanger – available DAS servers
Dasty – DAS client
DBGET/LinkDB Integrated Database Retrieval System
dChip Software: Gene Expression Microarray and SNP Microarray Analysis
Debian Linux
DeepView Swiss-PdbViewer social bookmarking
Delta Mass PTM database (ABFR)
Deutsche Gesellschaft f�r Proteomforschung
DIALIGN – multiple sequence alignments to find conserved regulatory elements
DIP – Database of Interacting Proteins
DIP DLRP Database of Interactiong Proteins
DiRE identification of DIstant Regulatory Elements of co-regulated genes
Dizzy stochastic simulations tool
DOAJ – Directory of open access journals
Documentation for Expression Profiler
DomCut prediction of linker regions between functional domains
DOMINE Database of Protein Domain Interactions
Domino Domain peptide interaction database
Dotter dot-matrix sequence comparison program
DSSP Kabsch Sander PDB secondary structure assignment
DSSPCont Rostlab
Dynetica – a simulator of dynamic networks
EBI European Bioinformatics Institute
EBI IntAct Project
EBI Wise2 matches protein to genomic DNA
EBI: The BioCatalogue
EBIMed Medline information retrieval and extraction
E-Cell project
eFamily Project – Grid integrating of protein database annotations
ELM Eukaryotic Linear Motif Functional Site Prediction
EMAN 3D single particle image reconstruction
EMBL Dali protein structure comparison server
EMBNet – A Quick Guide to Expasy
EMBNet – A Quick Guide to Swiss-Model
EMBNet A Quick Guide to PHYLIP
EMBNet A QuickGuide to UNIX
EMBNet Bioinformatics Network
EMBNet Courses
EmbNet EMBOSS and wEMBOSS Quick Guides
EMBNet QickGuides PERL and Regular Expressions
EMBNet Quick Guides
EMBNet Quick Guides to phred and phrap
EMBNet QuickGuide BLAST
EMBNet QuickGuide Swissprot Trembl Databases
EMBOSS Administrators Guide
EMBOSS application wiki
EMBOSS applications
EMBOSS applications program groups
EMBOSS Developers Guide
EMBOSS for Windows
EMBOSS mailing lists
EMBOSS Main Tutorial
EMBOSS user documentation
EMBOSS Users Guide
EMBRACE Network of Excellence
Ensembl Genome Browser
EnsEMBL Genome Browser DAS client
Entrez Browser NCBI
Entrez-Genome NCBI
Enzyme Database – BRENDA
EPD Eukaryotic promotor database
Espacenet – Europe’s network of patent databases
ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences
eTBlast – related articles to any text
Eukaryotic WebGeneMark
European Molecular Biology Open Software Suite EMBOSS
ExPASy – Biochemical Pathways
ExPASy – FindMod tool
ExPASy – QuickMod – MS/MS modified peptide search tool
ExPASy – ScanProsite tool
ExPASy – Sulfinator tool Tyr sulfination sites predictor
Expasy Life Science Directory
ExPASy Mass Search
ExPASy MultIdent Peptide Mass Fingerprinting Tool
ExPASy Peptide Mass Tool
Expasy Proteomics Server
ExPASy Swiss 2Dpage
Expression Profiler at EBI
FAF-Drugs: Free ADME/tox Filtering
Fasta3 Database Searches at the EBI
Fedora Project
FlyBase Drosophila
foldit – The Protein folding game
FORESTER phylogenomics software libraries
Frog2 format conversion tool for drugs
Fugu Fish Genome Project
Fungal Genetics Stock Center
gabi Arabidopsis Proteomics Data
GABI Primary Database ( GabiPD ) – Genomanalyse Pflanze
Galaxy bioinformatics framework
GBM Gesellschaft fuer Biochemie und Molekularbiologie
GCB 2011 German Conference on Bioinformatics – Weihenstephan
GCB 2012 German Conference on Bioinformatics – Jena
Gene Expression Atlas – Large Scale Meta-Analysis of Public Microarray Data
Gene Ontology (GO) Consortium
Gene Ontology Tools for Gene Expression Analysis
Gene3D Structural and Functional Annotation
GeneCards Weizmann
GeneCAT – Gene Co-expression Analysis Toolbox
GeneDoc Homepage
GeneInfinity’s Protein Interaction Analysis page
Genetic Association Database
GenMAPP Gene Map Annotator and Pathway Profiler
GENO3D : Automatic Modeling of Protein Structure
Genome assembly by phred and phrap
Genome Matrix databases information integration
GenomeNet WWW server Japan
GENSCAN (C. Burge)
GEO Gene Expression Omnibus at NCBI
Gepasi – Biochemical Kinetics Simulator
Gesellschaft fuer Informatik – Fachgruppe Bioinformatik
Glimmer Microbial Gene-Finding System
GNP Genome Network Platform
GOA – Gene Ontology Annotation Project at EBI
GOLD: Genomes On Line Database v 3.0
Google Scholar
GoPubMed – Ontology based literature search
GOStat – find statistically overrepresented GO terms
GPMDB proteomics database
GrailExp Grail Experimental Gene Discovery Suite
Graphviz – Open Source Graph Visualization Software
GraphWeb: analysis of biological networks
Harvard Dept of MCB – Biology Links
HepatoSys – Network Systems Biology
HGP – Human genome project information
HKL X-ray crystallography package
HMMTOP Prediction of transmembrane helices and topology
HomoMINT predicted human interaction network
HPRD Human Protein Reference Database
HSLS: Microarray, SAGE and other gene expression data analysis tools
HSLS: OBRC: Online Bioinformatics Resources Collection
HubMed pubmed rewired
Human Gene and Protein Database (HGPD)
Human Genome Resources NCBI
Human Genomics
Human Metabolome Database
Human Protein Atlas
Human Protein Reference Database
HUPO – Human Proteome Organisation
HUPO 2011 10th World Congress Geneva
HUPO 2012 11th World Congress Boston
HUPO Proteomics Standards Initiative
HUPO PSI Protein Modification Documentation
Hypertree large tree displaying tool
IET Synthetic Biology
IET Systems Biology
iHOP – Information Hyperlinked over Proteins
In Silico Biology
Installing Bioperl on Windows – BioPerl
Integr8 Proteome Analysis at EBI
Integrated DNA Technologies Oligo SciTools
Integrated DNA Technologies Unafold server
IntEnz EBI Enzyme Database
International Rice Genome Sequencing Project
Interpro Domain and Profile Database
IonSource Proteomics Resource Links
IPI – International Protein Index EBI
iPSORT N-terminal protein sorting signals
ISB NHLBI Seattle Proteome Center
ISCB – International Society for Computational Biology
ISMB ECCB 2011 Vienna
ISMB ECCB 2012 Long Beach
ISPIDER MS meta protein database search
ISREC TMpred Server
IUPHAR receptor database
J. Craig Venter Institute (ex TIGR) MD USA
Jalview – Java alignment editor
Jarnac biochemical simulation package
JASPAR Transcription factor database
JASPAR Transcription factor database paper
Java Molecular Editor at RPBS
JCV Institute Genomics
JDesigner: A Biochemical Network Layout Tool
J-Express microarray analysis free version
JME Molecular Editor by Peter Ertl
Journal of Computational Biology
Journal of Medical Internet Research
Journal of Proteome Research
Journal of Proteomics and Bioinformatics
JPRED Secondary structure prediction
JSim – a Java based simulation system
JUFO neuronal network prediction server
JWS Online – Online Cellular Systems Modelling
KDBI – Kinetic Data of Biomolecular Interactions
KEGG Drug Database
KEGG Ligand Database
KEGG: Kyoto Encyclopedia of Genes and Genomes Global kinome analysis
LGICD Ligand-gated ion-channel database
Linnea Pathways
Linux Community (German)
Linux Kernel Archives
LipoP 1.0 server gram negative lipoprotein prediction
Lowe Lab tRNAscan-SE Search Server
MacClade Home Page
MAGNOLIA advanced RNA sequence and structural alignment
Maize Genetics and Genomic Database
MapMan – integrative view of microarray data and metabolic maps
MaRe Microarray Retriever
MASC Arabidopsis Proteomics Standards Subcommittee
MASCOT Peptide Mass Fingerprint
Mass spectrometry data formats – Wikipedia
MassTRIX Metabolomics mass to pathway mapper
MEGA phylogeny software
MEME MAST motif discovery and search
MetaCyc Encyclopedia of Metabolic Pathways
Microarray Bioinformatics at EBI
MicroArray Explorer tool for Data Mining Gene Expression Patterns
Microarray Gene Expression Data Society
Microarray Tools at NCI A resource for predicted microRNA targets and expression
MINT – Molecular Interactions database
MIPS Mammalian Protein-Protein Interaction Databank
MIPS MPact Protein Interaction and Complex DB
MIPS Yeast Protein-Protein-Interaction and Complex Viewer
MIPS: Munich Information Centre for Protein Sequences
miRBASE microRNA database Sanger Institute
mMass – Open Source Mass Spectrometry Tool
ModBase – Comparative protein structure models
Molecular and Cellular Proteomics
Molecular Systems Biology
Mosflm diffraction data processing
MotifMogul – Multiple Transcription Factor Binding Sites Algorithms
Mouse Genome Resources NCBI
MPsrch at EBI
mreps DNA tandem repeat identifier
MSD Ligand Chemistry in PDB
MyNCBI PubMed updating and alerting
mzML Specification | HUPO Proteomics Standards Initiative
NASC Affymetrix Service: Analysis hints
Nature Omics Gateway
Nature web focus: Systems biology: a user’s guide
NAViGaTOR – Network Analysis, Visualization, & Graphing TORonto
NCBI BLAST download
NCBI Esearch Entrez Utility
NCBI Glimmer3
NCBI HIV Human protein interaction database
NCBI Journal database
NCBI PubChem Compound
NCBI PubChem Substance
NCBI Sequence Read Archive
NCBI Structure
NCBI Taxonomy Browser
NCBI UniVec and VecScreen Vector contamination search
NCBI US National Center for Biotechnology Information
NCBI VAST structural alignments
NCI BioCarta – Pathways
NCI Nature Pathway Interaction Database
NCI-3D Search
ncRNA tools for sequence/structure analyses of non-conding RNAs
NetNGlyc Server
NetOGlyc server
NetPath human signal transduction pathways
NetPhos 2.0 Server STY phosphorylation site predictor
Network Analysis Tools (NeAT)
NetworKIN kinase substrate relationship prediction
Neurospora crassa Database (Broad)
Neurospora crassa Database (MIPS)
NGFN German National Functional Genomics Network
NIH – DAVID Annotation tools
NIH – Guide to Microarray Data analysis
NIH ENCODE Project: ENCyclopedia Of DNA Elements
NIH Histone Sequence Database
NLM SIS Chemical Information
NPS : coiled-coils prediction
NPS: Consensus secondary structure prediction
NPS: Network Protein Sequence Analysis
Nucleic Acids Research
Nucleic Acids Research Database Issue 2011
Nucleic Acids Research Database Issue 2012
Nucleic Acids Research Database Summary Paper List
Nucleic Acids Research Webserver Issue 2010
Nucleic Acids Research Webserver Issue 2011
O (Alwyn Jones)
Oligo Heat Map hybridization analysis
OligoWalk Web Server for siRNA design
Omics: A Journal of Integrative Biology
OMSSA ms/ms search engine
Online Mendelian Inheritance in Man
Ontology Lookup Service (OLS)
Open Bioinformatics Foundation
Open Rasmol
Open Source Initiative OSI
Open SUSE Linux
OpenMS / TOPP open source MS proteomics pipeline
OPHID Interologous interaction database
ORegAnno: Open Regulatory Annotation
Osprey – protein interaction molecular modeling
Osprey – protein interaction viewer
PaLS Pathway and Literature Strainer (gene set annotation tool)
PANDIT Protein and Associated NucleotideDomains with Inferred Trees
PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System
Panther Classification Systems – Panther Pathways
Pasadena Twain ODE solver of the SWB package
PathBlast – Comparison of interaction networks between organisms
pDraw32 Acaclone Plasmid drawing
PeCoP Psi-Blast to find persistently conserved positions
PeptideMass – Expasy
PeptideProphet MS proteomics prediction tool
Perl documentation
Perl Download
Phaser crystallographic software
Phenyx MS protein search engine (GeneBio/SIB)
Phobius – combined TM and signal peptide prediction
Phospho.ELM Database of phosphorylation sites
PhosphoMotif Finder
PhosphoPep Phosphopeptide systems biology database
PHP Labware Project
Phylip Online Help
PHYLIP Phylogeny Programs
Phylip Tutorial (Jarno Tuimala)
Phylogeny Web Servers List – robust phylogenetic analysis for the non-specialist
pI/Mw tool – Expasy
PIPs Human Protein Interaction Prediction Database
PIR – Protein Information Resource
PIR iProClass Protein Classification
Plant genomes (MIPS)
PLoS Computational Biology
PLoS Public Library of Science
Polyview 3D web server for animated images
Potato Genome Sequencing Consortium
PRED-TMBB transmembrane beta barrel prediction
PRIDE – Proteomics Identifications Database
PRIDE modification ontology lookup service (OLS)
PRIDE Modification Search
Primer 3
PrimerX – mutagenic primer design
PRINTS protein fingerprints
ProDom conserved protein domains
ProdoNet Prokaryotic gene list pathway annotator
PROF – Secondary Structure Prediction System
Professional SUSE Linux
Protein Databank in Europe (PDBe)
Protein Identifier Cross-Reference Service
Protein Kinase Resource
ProteinProphet MS proteomics prediction tool
Proteome commons
Proteome Science
Proteomics – Clinical Applications
ProtParam tool – Expasy
ProtScale – Expasy
PROWL protein and MS tools
PSI-MI HUPO Standard for interactions
PSIPRED Protein Structure Prediction Server
Pub Med Central
PubCrawler PubMed GenBank Update Service
Public SRS installations | Biowisdom
PubMed Single Citation Matcher
PubMed/Medline NLM Mesh Browser
PVS: Protein Variability Server – conserved epitope discovery
PyBioS – web server for modeling and simulation of cellular systems
PyMOL molecular visualization system
QuickGO – GO Browser at EBI
R and Bioconductor Manual (Thomas Girke)
RasTop – Rasmol Graphical Interface
Rat Genome resources NCBI
RCSB PDB Protein Data Bank – PDB
RCSB Protein Data Bank
Reactome Project
REBASE The Restriction Enzyme Database
RedHat Linux
REDI Databases of Baden-Wuerttemberg
RefSeq Reference Sequence NCBI
Regulatory Sequence Analysis Tools (RSAT)
RESID Database of protein modifications
Ressource Parisienne en Bioinformatique Structurale (RPBS)
Reverse Complement of Sequence
Rfam RNA families database of alignments and CMs Sanger Institute
Ribosomal Database Project
RNA Molecular Biology Tuschl Lab
RNA-Seq software ERANGE
Rod Page Software
SARSA Structural Alignment of RNA Using a Structural Alphabet
SASHIMI MS proteomics pipeline
Savvy Plasmid Maps
SBGN Systems Biology Graphical Notation Standardization
SBML Systems Biology Markup Language
SBMLsqueezer: A CellDesigner plug-in to generate kinetic rate equations for biochemical networks
Scaffold protein identification framework (by Proteome Software)
Schizosaccharomyces pombe genome (Sanger Centre)
SCOP: Structural Classification of Proteins
Sequence Analysis with distributed Resources
Sequence Extractor cloning toolbox
Sequence Manipulation Suite 2
Sequence Ontology Project
Sequence similarity searches at the EBI
SEQUEST MS proteomics search engine
SeWeR – Sequence Analysis using Web Resources
SIB myHits motif scan
Signal Transduction – virtual library
Signaling Gateway – Cell Signaling Resource Nature
SignalP server
SMART – Simple Modular Architecture Research Tool
SOSUI Structure prediction of membrane proteins Open Source Resource
SPICE – DAS Client
SPIDER and WEB EM 3D single particle image reconstruction
Standalone BLAST
Stanford Functional Genomics Facility
Stanford Microarray Database
STOCKS – Stochastic kinetic simulations
STRAP Interactive Structure based Alignment Program
Strawberry Perl for Windows
String: functional protein association networks
Structures by electron microscopy at MSD
Superfamily HMM models SCOP
SuperPred Drug Target Prediction Server
Swiss Proteomics Society
SWISS Proteomics Society Proteomics Links
Synthetic Biology 5.0 Conference Stanford, CA, USA
Systems Biology at UC San Diego
Systems Biology in Germany
Systems Biology Portal
Systems Biology Wikipedia
Systems Biology WorkBench SBW package
SystemsX – The Swiss Initiative in Systems Biology
tair – The Arabidopsis Information Resource
TarFisDock identifying drug targets by docking
Tcoffee DNA, RNA, Protein alignment tools
TFM Explorer
TFSEARCH – Transcription Factor Search
The Arabidopsis Information Resource – TAIR
The Comprehensive R archive network
The DALI database
The DALI database Dali Fold Classification
The Gibbs Motif Sampler
The International Society for Systems Biology
The JCB Protein-Protein Interaction Website
The Perl directory at
The R project for statistical computing
The Reactome Project
The Sanger Centre
The Sanger Centre HMM Pfam Searcher
The Sanger Centre Pfam Server
The siRNA user guide – Tuschl Lab
The Systems Biology Institute – Tokyo
The Tree of Life Home Page
The Vim Editor
TIGR Microarray Software
TIGRFAMs protein families HMM
TMAP multiple sequence alignment protein prediction
TMHMM Server 2.0
Tools from the Eisen Lab
TopPred – Topology prediction of membrane helices
TPP Trans-Proteomic Pipeline
Tranche – Secure P2P for Scientific Data Dissemination
Tree of Life Links
Tutorial Protein Structures (EXPASY) SwissModel
Ubuntu Linux
UCSF Chimera
UCSF Mass Spectrometry Facility Protein Prospector
Unafold RNA folding services
Unigene NCBI
Unimod – Modification naming guidelines
Unimod database – protein modifications for MS
Unipro UGENE: Integrated Bioinformatics Tools
UniProt Chordata protein annotation program
Uniprot Universal Protein Resource Swiss-Prot/TREMBL/PIR
US National Centers for System Biology
useR! 2011 R user conference Warwick, UK
useR! 2012 R user conference Nashville, TN
USF Uppsala software factory
Vienna RNA secondary structure servers
Virtual Cell Internet simulation server at NRCAM
visANT – Visual Analysis Tool for Biological Networks and Pathways
VMD – Visual Molecular Dynamics
W3 Search Engines FU Berlin
Web of Science
Webcutter 2.0
WebLogo Server
Weizmann Institute Bioinformatics and Biological Computing
WETLAB: an open source electronic lab notebook
Whitehead Institute
Wolfram alpha
WORLD-2DPAGE Index to 2D-PAGE databases and services
Wormbase C. elegans
WWW BLAST Database Searches at NCBI
WWW Promotor Scan Pol II
X! Tandem MS search engine
XDS diffraction data processing
Yale Microarray Database
YASS genomic DNA local alignment similarity search tool
Yeast Genome Database MIPS
Yeast Protein complex database
YSBN The Yeast Systems Biology Network
ZFIN – Zebrafish information network