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Oliver's Bioinformatics Research Tools

Contents:

  1. Bioinformatics Sources
    1. Government Agencies and Organizations
    2. Academic Institutes
    3. Research Groups and Individuals
    4. Commercial Sources
  2. Bioinformatics Knowledge:
    1. Pathogen Resources
    2. Host Resources
    3. Genomics
    4. Transcriptomics
    5. Proteomics
    6. Metabolomics
  3. Software
    1. Programming Languages
    2. Operating Systems
    3. Databases
    4. Software Download
  4. References
    1. Literature Search Tools
    2. Journals
    3. Dictionaries
  5. Miscellaneous

I. Bioinformatics Sources:

  1. Government Agencies and Organizations:

    1. NCBI - National Center for Biotechnology Information
    2. EBI - European Bioinformatics Institute
    3. ABCC - Advanced Biomedical Computing Center at the NCI
    4. BDGP - Berkeley Drosophila Genome Project
    5. TIGR - The Institute for Genome Research
    6. LANL - Los Alamos National Laboratory (LANL) center for human genome studies
    7. MICRO-NET - Microbial Information Network of China
    8. APBioNet - Asia-Pacific Bioinformatics network
    9. NLM-- National Library of Medicine
    10. ISCB - International Society for Computational Biology
    11. CBR - Canadian Bioinformatics Resource
    12. BiSC - Canada Bioinformatics Supercomputing Center

  2. Academic Institutes:

    1. U of M Bioinformatics Program
    2. Virginia Bioinformatics Institute
    3. University of Pennsylvania Center for Bioinformatics
    4. CBIL - Computational Biology and Informatics Laboratory at the University of Pennsylvania
    5. ACGT - Advanced Center for Genome Technology at the University of Oklahoma
    6. BMERC - Biomolecular Engineering Research Center
    7. CBI - Peking Center of Bioinformatics; Chinese EMBnet node
    8. HKBIC - Hong Kong Bioinformatics Center
    9. UCSC Computational Biology.
    10. Bioinformatics and Computational Biology at George Mason Univ.
    11. Computational Biology USC, University of Southern California.
    12. UCLA - UCLA Bioinformatics Institute
    13. MBCR - Molecular Biology Computational Resource at Baylor College of Medicine
    14. BIC - BioInformatics center of the National University of Singapore
    15. MBCR - Molecular Biology Computational Resource at Baylor College of Medicine
    16. Web Resources for Protein Scientists, Protein Science.
    17. Motif Bioinformatics Server, Stanford.
    18. The World-Wide Web Virtual Library: Biosciences, Harvard.
    19. Survey of Molecular Biology Databases and Servers, R. Smith.
    20. ExPASy Proteomics tools
    21. Database searches, EBI (Fasta, Blitz,...).
    23. UCLA Advanced Research Computing

  3. Research Groups and Individuals:

    1. The EMBL Sander Group
    2. Amos' WWW links exclusively pointers to information sources for life scientists with an interest in biological macromolecules
    3. Jeff's biolinks, Yale University.
    4. Molecular ToolBox, by Dr. Sidney M. Morris, University of Pittsburgh.
    5. Pedro's BioMolecular Research Tool.

  4. Commercial Sources:
    1. Celera
    2. Biolinks from Bioplanet
    3. Bioexchange.com


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II. Bioinformatics Knowledge:

  1. Pathogen Resources:

    1. Brucella spp.:

  2. Host Resources:

    1. General Information:

      1. NCBI Genomic Biology
      2. Animal Genomics Research Links
      3. The WWW Virtual Library: Model Organisms

    2. Human:

      1. NCBI Human Genome Resources
      2. DOE Human Genome Program, Human Genome Project Publications
      3. National Human Genome Research Institute
      4. Human Genome Project
      5. Human Affymetrix Microarray:
        1. GeneChip Human Genome U133 Plus 2.0 Array
        2. GeneChip Human Genome U133 Set
        3. GeneChip Human Genome U95 Set

    3. Animals:

      1. NCBI Cow Genome Resources
      2. Cattle Genome Database
      3. NCBI Pig Genome Resources
      4. U.S. Pig Genome Project
      5. France Goat Genome Project
      6. NCBI Sheep Genome Resources

    4. Laboratory Animals:

      1. NCBI Mouse Genome Resources
      2. Mouse Genome Informatics
      3. Mouse Affymetrix Microarray:
        1. GeneChip Mouse Genome 430 2.0 Array
        2. GeneChip Murine Genome U74v2 Set

    5. Others:

      1. TAIR: The Arabidopsis Information Resource
      2. C. elegans (worm): C. elegans recources
      3. Drosophila (fly): Drosophila recources

  3. Genomics:

    1. NCBI Genome Resources
    2. Unigene
    3. Microbesonline.org - Facilitate comparative studies on prokaryotic genomes.
    4. HGP Columbia - Human Genome Project at Columbia University
    5. National Human Genome Research Institute Multiple Image Analysis Image analysis (gene clustering)
    6. BLAST: Resources for determining sequence similarities.
    7. COG (Clusters of Orthologous Groups): Phylogenetic classification of proteins encoded in complete genomes
    8. KEGG (Kyoto Encyclopedia of Genes and Genomee)
    9. MBGD (Microbial Genome Database)
    10. WIT ("What Is There")

  4. Transcriptomics:

    1. GEO - Gene Expression Omnibus
    2. ArrayExpress
    3. SMD - Stanford microarray db
    4. MicroArray informatics at the EBI
    5. Microarray Informatics Resource Page, a collection of literature and web links.
    6. ChipDB - Gene expression db
    7. GeneX - Gene Expression project
    8. ExpressDB - Yeast and E. coli RNA expression db
    9. RAD - RNA abundance db
    10. ChipDB - Gene expression db
    11. Biodiscovery
    12. GeneSpring
    13. LION Bioscience AG arraySCOUT data analysis software
    14. Partek Incorporated
    15. Spotfire various analysis tools
    16. Dr. Leming Shi's Introduction to DNA microarray
    17. Introduction to Microarrays (Alscher and Sederoff)
    18. MIT/Whitehead Institute self-organizing maps
    19. Rockefeller bibliography, includes data analysis references
    20. Stanford Determining changing DNA copy number on microarrays, Botstein, Brown, Eisen et al.

  5. Proteomics:

    1. Proteome Commons
    2. ExPASy Proteomics tools
    3. PEDANT (Protein Extraction, Description, and ANalysis Tool)
    4. Protein Data Bank (http://www.rcsb.org/pdb) The main source for protein structure data.
    5. Cn3D NCBI's Cn3D software for viewing protein structure data from NCBI. 
    6. RasMol
    7. CATH Database CATH protein structure classification database (University College of London)
    8. Enzyme Nomenclature Database A searchable database of enzymes organized by function.
    9. SCOP (Structural Classification of Proteins) Database
    10. CE server Combinatorial Extension/Compound Likeness server at SDSC
    11. CHIME Plug-in (http://www.mdlchime.com)
    12. CAST-P Compute solvent accessibility using alpha-shapes method.
    13. GRASS server Compute electrostatics and surface properties of proteins online.
    14. SWISS-MODEL Repository - Automatically generated protein models db
    15. PredictProtein, Heidelberg.
    16. BioMagResBank - Repository for data on proteins, peptides, and nucleic acids from NMR spectroscopy
    17. ModBase - Db of comparative protein structure models
    18. Mol_R_Us - Molecules R Us, browser for PDB
    19. BMM Domain Server - Biomolecular Modelling Laboratory (ICRF) protein domain server
    20. PRESAGE - Collaborative resource for structural genomics
    21. ReLiBase - Receptor/ligand complexes db [Mirror in USA]
    22. TOPS - Protein topology atlas
    23. CCDC - Cambridge Crystallographic Data Center (Cambridge Stuctural Db (CSD))
    24. HSSP - Homology-derived secondary structure of proteins db
    25. MutaProt - Comparison of PDB files which differ by point mutations
    26. BioImage - Biological image database
    27. SWISS-3DIMAGE - 3D images of proteins and other biological macromolecules
    28. INTERACT - Protein-Protein interaction db

  6. Metabolomics:

    1. KEGG (Kyoto Encyclopedia of Genes and Genomee)
    2. BioCyc
    3. Biochemical pathways (ExPASy) - very useful on-line version of the classic maps

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III. Software:

  1. Programming Languages:

    1. C And C++ Standards
    2. Microsoft Visual C++ Home Page
    3. C/C++ Users Group
    4. Java: Programming for the Internet - Sun's Java Page
    5. Sun's Java Tutorial, The - practical, example-basedguide.
    6. Java Programming Resources
    7. JavaScript.com - resource for tutorials, scripts, and more.
    8. Nic's JavaScript Page - with a variety of javascript examples.
    9. JavaScript Source, The - cut and paste JavaScript library with source.
    10. JavaScript Search - contains scripts, tutorials, books, and more.
    11. JavaScript Guide
    12. Javascript Tip of the Day - tips and tricks.
    13. Perl.com - central resource for Perl developers. It contains the Perl Language, edited by Tom Christiansen, and the Perl Reference, edited by Clay Irving.
    14. Perl Institute http://bioinformatics.oupjournals.org/
    15. http://www.perl.org/ - non-profit organization, established to support the Perl community.
    16. Perl Mongers http://www.pm.org/
    17. ActiveState - Perl for Win32 - offers information on tools for windows.
    18. Advanced Perl Programming
    19. XML.com - information and services for the XML community
    20. XML.org - provides information about the application of XML in industrial and commercial settings
    21. Directory of XML Resources - includes applications, xml browsers, books, technology, and more.
    22. XML Version 1.0 Specification
    23. Apache XML Project - to provide commercial-quality standards-based XML developed in an open and cooperative fashion and to provide feedback to standards bodies.
    24. GNU's Homepage
    25. GNU Manuals Online
    26. CVS
    27. CVS Home
    28. LaTeX online help 1.1
    29. PHP
    30. Biology Software and Data (Indiana Univ.)
    31. NCBI FTP server
    32. NIH Software
    33. BRASS, Bioinformatics Resource for Algorithms, Software and Sequences.
    34. BioJava Project - International association of developers of Java tools for bioinformatics
    35. Bioperl Project - International association of developers of Perl tools for bioinformatics
    36. Biopython Project - International association of developers of Python tools for bioinformatics
    37. Bioxml Project - International association of developers of XML tools for bioinformatics
    38. The Open lab - International collaboratory for open-sources bioinformatics R&D

  2. Operating Systems:

    1. Linux.com
    2. RedHat home
    3. Linux Journal - monthly publication serving the Linux community.
    4. Linux Help Line
    5. Linux FAQ list
    6. Some Useful Linux Commands
    7. Linux Document
    8. Sun Documents
    9. FreeBSD
    10. Active Windows
    11. MSDN Online Library
    12. Microsoft Developer Network
    13. Windows Utilities

  3. Databases:

    1. MySQL
    2. Postgres SQL
    3. Oracle Document
    4. NetResources in Bioinformatics
    5. Links to Databases for Molecular Biologists

  4. Software Download:
    1. Download Freeware - directory of freeware programs submitted by their developers. http://www.download-freeware.com/
    2. download.com - a shareware directory from CNET. http://www.download.com/
    3. sourceforge.net - the world's largest Open Source software development website. http://sourceforge.net
    4. The R Project - an open source language for data, statictics and graphics. http://www.r-project.org/
    5. The BioConductor Project - an open source and open development software project for the analysis and comprehension of genomic data. http://www.bioconductor.org/
    6. The R Project - an open bioinformatics source repository and projects. http://bioinformatics.org/
    7. hotscripts.com - the net’s largest PHP, CGI, Perl, JavaScript and ASP script collection and resource web portal. http://www.hotscripts.com
    8. Planet Source Code - the largest public source code database on the Internet. http://www.planet-source-code.com/


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IV. References:

  1. Literature Search Tools:

    1. National Library of Medicine
    2. Entrez-PubMed http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed/
    3. PubMed Search Field Descriptions and Tags
    4. BioMedNet- collection of resources for biological medical researchers, including databases, reviews, news, links, and journals. http://www.bmn.com/
    5. University of Michigan Libraries http://www.lib.umich.edu
    6. Virginia Tech Libraries
    7. VMRCVM Library - VA-MD Regional College of Veterinary Medicine
    8. Cambridge Sci Abs Cambridge Scientific Abstracts.
    9. Ingenta: http://www.ingenta.com/
    10. WWW Virtual Library - catalog of the web run by a confederation of volunteers. http://www.vlib.org/
    11. Association for Computing Machinery (ACM) - the world's first educational and scientific computing society for professionals and students. http://www.acm.org/
    12. Welcome to the ACM Digital Library
    13. ACM SIGGRAPH http://www.siggraph.org/
    14. IEEE: Institute of Electrical and Electronics Engineers technical objectives center on advancing the theory and practice of electrical, electronics, and computer engineering and science. http://www.ieee.org/
    15. IEEE Software - covers useful advances in software technology, design, development and implementation techniques. http://computer.org/software/
    16. SIAM- Society for Industrial and Applied Mathematics http://www.siam.org/
    17. IDEAL, International Digital Electronic Access Library - online abstracts.
    18. Collection of Computer Science Bibliography

  2. Journals:

    1. Science http://www.sciencemag.org/
    2. Nature http://www.nature.com/nature/
    3. Proc Natl Acad Sci USA http://www.pnas.org/
    4. Bioinformatics, Bioinformatics Online
    5. Journal of Computational Biology
    6. Journal of Molecular Biology
    7. Proteins: Structure, Function and Genetics
    8. Infection and Immunity http://iai.asm.org/
    9. Protein Science
    10. Nature, Genome Gateway
    11. Nucleic Acids Research
    12. Genome Research
    13. The Scientist
    14. Bioinform
    15. The Bioinformer, published by EBI.
    16. In Silico Biology, online journal
    17. Hottest Journals in the Millenium (so far)
    18. bioinformatics journal list

  3. Dictionaries:

    1. Dictionary of Computing
    2. Free On-line Dictionary of Computing
    3. Internet and Unix Dictionary
    4. BioTech's Biotechnology Dictionary  - free, searchable online dictionary of biology, chemistry and biotechnology terms.
    5. Dictionary of Cell Biology - provides quick access to easily-understood and cross-referenced definitions. 


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V. Miscellaneous:

  1. U.S. News and World Report College Rankings - Updated annually
  2. World Science - http://www.world-science.net/
  3. United States Patent and Trademark Office - http://www.uspto.gov/
  4. Patent Cafe - patent, trademark, and intellectual property resource for inventors, attorneys, and entrepreneurs. Features patent search, forums, and more. http://www.patentcafe.com/
  5. PatentDatabase.com - free search tool for searching the USPTO patent database. Created through Nuestel Law Offices, Ltd. http://www.patentdatabase.com/
  6. Nobel e-Museum http://www.nobel.se/
  7. Nobel Prize in Physiology or Medicine http://www.nobel.se/medicine/index.html
  8. Nobel Prize in Chemistry http://www.nobel.se/chemistry/index.html
  9. Nobel Prize in Physics http://www.nobel.se/physics/index.html


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