Bioinformatics Websites

Table of Contents

• Resources
• Calendar
• Conference Series
• Introductory Courses and Papers
• Useful Skillsets
• University Courses
• Advanced Courses and Papers
• Journals

Resources

• 2can Bioinformatics Educational Resource     (European Bioinformatics Institute)
• BBSRC Bioinformatics Initiative    (Biotechnology and Biological Sciences Research Council, UK)
• BII    (BioInformatics Institute, Singapore)
• BIMAS    (NIH BioInformatics & Molecular Analysis Section)
• The Barton Group    (University of Dundee, Scotland)
• Bioinformatics Research Centre, University of Glasgow    (Scotland)
• Blueprint (Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Toronto)
• CBCB    (Center for Bioinformatics and Computational Biology)
• Community Sequencing Program (Department of Energy / Joint Genome Institute)
• Computational Biology Research Center    (National Institute of Advanced Industrial Science and Technology, Japan)
• Computational Molecular Biology at NIH    (Bethesda, Maryland)
• EBI    (European Bioinformatics Institute, UK)
• ERCIM    (European Research Consortium for Informatics and Mathematics)
• Gene Ontology Consortium
• Genome Institute of Singapore
• Genome Sciences Centre    (BC Cancer Agency, Vancouver)
• Gerstein Group    (Yale University)
• Harvard Institute of Proteomics    
• Harvard - Lipper Center for Computational Genomics    (Harvard Medical School)
• Helmholtz Network for Bioinformatics    (Germany)
• Human Genome Center    (Institute of Medical Science, University of Tokyo)
• IGB    (University of California Institute for Genomics and Bioinformatics)
• ISREC    (Swiss Institute for Experimental Cancer Research)
• Insititute of Medical Technology Bioinformatics Group    (University of Tampere, Finland)
• JCSG    (Joint Center for Structural Genomics - Stanford, UCSD and Scripps Institute)
• The Jackson Laboratory    (Maine)
• Japanese Society for Bioinformatics    (Kyoto University, Japan)
• Leeds Bioinformatics Group    (University of Leeds, UK)
• Linnaeus Centre for Bioinformatics    (Uppsala, Sweden)
• MRC Laboratory of Molecular Biology     (Cambridge, UK)
• NASA Ames Genome Research Facility
• OGMP Informatics Division     (Organelle Megasequencing Program, Canada)
• Oak Ridge National Laboratory - Computational Biosciences Section     (Oak Ridge, Tennessee)
• Phylofacts -    (UC Berkeley)
• PRC    (Proteomics Research Center, University of Toronto)
• Poxvirus Bioinformatics Resource Center
• Programs for Genomic Applications    
• Protein Structure Prediction Center    (Lawrence Livermore Laboratory, CA)
• QB3     (California Institute for Quantitative Biomedical Research)
• SANBI - South African National Bioinformatics Institute    (University of the Western Cape)
• SIB - Swiss Institute for Bioinformatics    (Geneva, Switzerland)
• Sequence Analysis on Zeon     (Wellcome Trust Center for Human Genetics, Oxford, UK)
• SocBiN    (Society for Bioinformatics in the Nordic Countries)
• Sonnhammer Bioinformatics Group    (Karolinska Institute, Sweden)
• TBR (Human Genome Mapping Project Resource Centre, UK)
• UCL Bioinformatics Unit    (University College London)
• UCLA Bioinformatics Institute
• UCSC Bioinformatics    (Santa Cruz, CA)
• UC Center for Genomics and Bioinformatics    (University of Cincinnati, Ohio)
• UMBER    (University of Manchester, UK)
• VISTA     (LBNL)
• The Virtual Institute of Bioinformatics (Eire)    (Ireland)
• WEHI Genetics and Bioinformatics Group    (The Walter and Eliza Hill Institute, Australia)
• WIS Bioinformatics and Biological Computing    (Weizmann Institute)

Calendar

• HGM 2006     HUGO's 11th Human Genome Meeting
  May 31 - June 3, 2006
  Helsinki, Finland
  

• 7th International Meeting on Zebrafish Development & Genetics    
  June 14-18, 2006
  Madison, WI
  

• Beyond Genome 2006     Cambridge Healthtech Institute
  June 19-21, 2006
  San Francisco, CA
  

• RNA 2006 Annual Meeting     The RNA Society
  June 20-25, 2006
  Seattle, WA
  

• 2006 Yeast Genetics and Molecular Biology Meeting    
  July 25-30, 2006
  Princeton, NJ
  

• ISMB 2006     14th Annual International Conference on Intelligent Systems for Molecular Biology
  Aug 6-10, 2006
  Fortaleza, Brazil
  

• 2006 LSS Computational Systems Bioinformatics Conference     Life Sciences Society
  Aug 14-18, 2006
  Stanford University, CA
  

• AFP 2006     2nd Automated Function Prediction Meeting
  Aug 30 - Sept 1, 2006
  UC San Diego
  

• ECCB 2006     5th European Conference on Computational Biology
  September 10-13, 2006
  Eilat, Israel
  

• 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology
  Sept 28-29, 2006
  Toronto, Canada
  

• Genomes, Medicine, and the Environment Conference     J. Craig Venter Institute
  Oct 16-18, 2006
  Hilton Head Island, SC
  

• PSB 2007     Pacific Symposium on Biocomputing
  Jan 3-7, 2007
  Wailea, Maui
  

Conference Series

• The Association of Biomolecular Resource Facilities
• Cambridge Healthtech Institute - Genome Series
• Canadian Bioinformatics Workshops
• Cold Spring Harbor Laboratory
• DIMACS/BioMaPS/MB Center 2004-2008 Special Focus on Information Processing in Biology
• HGP - Human Genome Project (Genome and Biotechnology Meetings Calendar)
• HUM-MOLGEN: Events in Bioscience and Medicine (Meeting list from the International Communication Forum in Human Molecular Genetics)
• ISCB - International Society for Computational Biology (List of conferences)
• Penn Bioinformatics Forum (University of Pennsylvania)
• TIGR - The Institute for Genomic Research (Conferences, Education and Training)

Introductory Courses, Papers and Tutorials

• BayGenomics Tutorial    (UCSF)
• BioComputing Hypertext Coursebook    (University of Bielefeld)
• Biology Student Workbench    (University of Indiana at Urbana-Champaign)
• Biophysical Society Educational Resources
• DNA From the Beginning    (Dolan DNA Learning Center, Cold Spring Harbor Laboratory)
• EMBnet Biocomputing Tutorials    (European Molecular Biology Computing Network)
• Forsdyke's Bioinformatics Background Papers    (Queen's University, Ontario)
• Gene Expression Data Analysis and Modeling (PDF tutorial)    (D'haeseleer, Liang & Somogyi - Pacific Symposium on Biocomputing, 1999)
• Gene Network Inference from Large-Scale Gene Expression Data    (Patrik D'haeseleer, University of New Mexico)
• Goteborg University Molecular Biology Quiz
• Introduction to Sequence Comparison    (Keith Robison, Harvard)
• KISAC Bioinformatics Guide    (Karolinska Institute, Stockholm, Sweden)
• MIT Biology Hypertextbook
• Molecular Biology Software Manuals, Course Notes and Tutorials from the New York University School of Medicine Computing Resource
• Pedestrian guide to analysing sequence databases    (Burkhard Rost and Reinhard Schneider, EMBL)
• Programming Course in Bioinformatics for Computer and Information Science Students    (Altman & Koza, Stanford University)
• Representations and Algorithms for Computational Molecular Biology    (Altman, Stanford University)
• Ribosomal Database Project Tutorial    (Michigan State University Center for Microbial Ecology)
• Science Magazine: Special Genomics Issue    (October 5, 2001)
• Sequence-Evolution-Function: Computational Approaches in Comparative Genomics (Eugene V. Koonin and Michael Y. Galperin)
• Sequence Analysis with Distributed Resources    (University of Bielefeld, Germany)
• Sequence Analysis Tutorials    (Pittsburgh Supercomputing Center)
• Structure Finder Tutorials    (Nucleic Acid Database Project)
• University of Cincinnati Help Files and Tutorials
• Virtual Bacterial ID Lab    (Howard Hughes Medical Institute - requires shockwave plugin)
• Virtual Bioinformatics - Distance Learning    (IMT Bioinformatics - University of Tampere, Finland)

Useful Bioinformatics Skillsets

• BioJava
  • BioJava Tutorial

• BioLisp
  • Lisp Tutorial

• BioPerl
  • BioPerl 1.4 Tutorial

• BioPython
  • Python Tutorial
  • Python for Structural Bioinformatics (Notes for talk at PSB 2001 - Sanner & Coon, Scripps Institute)
  • PySAT: Python Sequence Analysis Tools (Ramu Chenna, EMBL)

• BSML (Bioinformatic Sequence Markup Language)

• Open BSA - Biomolecular Sequence Analysis
  • CORBA Tutorial (Alan J. Robinson, EBI)

University Courses

• BioMedical Informatics Program    (Stanford)
• Boston University    (Bioinformatics graduate program)
• Brutlag Bioinformatics Group, Stanford University    (Courses at all levels)
• Carnegie Mellon University    (Programs at all levels)
• Center for Biophysics and Computational Biology (Undergraduate and Graduate Programs)
• Georgia Institute of Technology    (Masters of Science in Bioinformatics)
• Harvard Medical School    (Course in genomics and computational biology)
• New York University School of Medicine     (Using Computers in Molecular Biology - Online lecture notes)
• San Diego Supercomputer Center    (Using Internet Resources in Molecular Biology - Graduate course)
• Stanford University    (Computational molecular biology course, internet-only)
• UCLA    (Courses at all levels)
• UC San Diego    (Introductory courses)
• UC Santa Cruz    (BS in bioinformatics)
• Yale Bioinformatics - Gerstein Group    (Courses and lectures)

• Training Program in Bioinformatics for Health Research    (M.Sc. and Ph.D.)
• University of Toronto    (Program in Proteomics and BioInformatics)

• Birkbeck College, University of London    (MSc Bioinformatics)
• Manchester University    (MSc in bioinformatics)
• SLU - Swedish University of Agricultural Sciences    (Bioinformatics)
• Swiss Institute of Bioinformatics    (Masters program)
• Technical University of Denmark    (Elementary and advanced courses)
• University of Bergen, Norway    (Masters-level courses)
• University of Bielefeld, Germany    (Graduate program)
• Uppsala University, Sweden (Basic courses)

• Weizmann Institute    (Online course materials)

• La Trobe University    (Basic course)
• University of Melbourne    (Bioinformatics stream in Computer Science)
• University of Otago - Dunedin, New Zealand    (Basic courses)
• University of Queensland    (3rd-year course)
• University of Sydney    (BSc program)

• BioInformatics Institute, Singapore    (Ph.D program)
• Moscow State University, Russia    (GCG courses)
• National Tsing Hua University, Taiwan    (Undergraduate course)
• National University of Singapore    (Training and workshops)

Advanced Courses and Papers

• Bibliography on Computational Gene Recognition    (Wentian Li)
• Evaluating Regularizers for Estimating Distributions of Amino Acids    (Paper by Kevin Karplus, UC Santa Cruz)
• Iowa State University, PhD Program in Bioinformatics and Computatinal Biology    (Ames, Iowa)
• Perl Programing Course for Bioinformatics and Internet    (Weizmann Institute of Science, Israel)
• Rutgers University, PhD Program in Computational Biology    (Newark, New Jersey)
• Sequence Alignment and Modeling System    (Documentation for SAM)
• Technical University of Denmark, PhD Course in Biological Sequence Analysis and Protein Modeling
• Training Program for Bioinformaticians in Health Research - Vancouver     (M.Sc. and Ph.D. Programs)
• University of Pennsylvania    (Doctoral Program and Postdoctoral Program )
• USC    (PhD Program)
• Virtual School of Natural Sciences    (Online Courses)

Journals

• Bioinform    (Published by GenomeWeb)
• Bioinformatics Magazine    (Oxford Journals Online)
• Briefings in Bioinformatics     (Henry Stewart Publications)
• Genome Biology Journal    (Published by BioMed Central)
• Genome Gateway    (Nature Magazine)
• In Silico Biology    (Published by BIS - Bioinformation Systems e.V.)
• NCBI news    (National Center for Biotechnology Information)
• Online Journal of Bioinformatics    
• Swiss-Flash Bulletins    (News of databases, software and services developments from the Geneva groups of the Swiss Institute of Bioinformatics)

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