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Oliver's Bioinformatics Research Resources

(Note: This site is not actively updated. - Oliver He)


  1. Bioinformatics Sources
    1. Research Agencies and Organizations
    2. Portals of Bioinformatics 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. Research Agencies and Organizations:

    1. NCBI - National Center for Biotechnology Information
    2. EBI - European Bioinformatics Institute
    3. BDGP - Berkeley Drosophila Genome Project
    4. JCVI - J. Craig Venter Institute
    5. Institute of Microbiology, Chinese Academy of Sciences
    6. Whitehead Institute for Biomedical Research
    7. NLM-- National Library of Medicine
    8. ISCB - International Society for Computational Biology
    9. ExPASy Proteomics tools
    10. CBI - Peking Center of Bioinformatics; Chinese EMBnet node
    11. HKBIC - Hong Kong Bioinformatics Center
    12. BIC - BioInformatics center of the National University of Singapore

  2. Portals of Bioinformatics Sources:

    1. Amos' WWW links exclusively pointers to information sources for life scientists with an interest in biological macromolecules
    2. Pedro's BioMolecular Research Tool.
    3. OBRC: Online Bioinformatics Resources Collection
    4. Bioinformatics Resources at Cincinnati Children's

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II. Bioinformatics Knowledge:

  1. Pathogen Resources:

    1. Brucella spp.:

  2. Host Resources:

    1. General Information:

    2. Human:

    3. Animals:

    4. Laboratory Animals:

    5. Others:

  3. Genomics:

    1. NCBI Genome Resources
    2. BLAST: Resources for determining sequence similarities.
    3. COG (Clusters of Orthologous Groups): Phylogenetic classification of proteins encoded in complete genomes
    4. KEGG (Kyoto Encyclopedia of Genes and Genomee)
    5. MBGD (Microbial Genome Database)

  4. Transcriptomics:

    1. GEO - Gene Expression Omnibus
    2. ArrayExpress
    3. Agilent
    4. Microarray Informatics Resource Page, a collection of literature and web links.
    5. Biodiscovery
    6. Spotfire various analysis tools
    7. RNA-seq

  5. Proteomics:

    1. ExPASy Proteomics tools
    2. Protein Data Bank (http://www.rcsb.org/pdb) The main source for protein structure data.
    3. Cn3D NCBI's Cn3D software for viewing protein structure data from NCBI. 
    4. RasMol
    5. SWISS-3DIMAGE - 3D images of proteins and other biological macromolecules

  6. Metabolomics:

    1. BioCyc
    2. Biochemical pathways (ExPASy) - very useful on-line version of the classic maps

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III. Software:

  1. Programming Languages:

    1. Python.org
    2. PHP
    3. C/C++ Users Group
    4. Microsoft Visual C++ Home Page
    5. Java: Programming for the Internet - Sun's Java Page
    6. Oracle's Java Tutorial, The - practical, example-basedguide.
    7. JavaScript.com - resource for tutorials, scripts, and more.
    8. JavaScript Search - contains scripts, tutorials, books, and more.
    9. Perl.com - central resource for Perl developers. It contains the Perl Language, edited by Tom Christiansen, and the Perl Reference, edited by Clay Irving.
    10. http://www.perl.org/ - non-profit organization, established to support the Perl community.
    11. Perl Mongers http://www.pm.org/
    12. ActiveState - Perl for Win32 - offers information on tools for windows.
    13. Advanced Perl Programming
    14. XML.com - information and services for the XML community
    15. XML.org - provides information about the application of XML in industrial and commercial settings
    16. GNU's Homepage
    17. GNU Manuals Online
    18. CVS
    19. CVS Home
    20. LaTeX online help 1.1
    21. BioJava Project - International association of developers of Java tools for bioinformatics
    22. Bioperl Project - International association of developers of Perl tools for bioinformatics
    23. Biopython Project - International association of developers of Python tools for bioinformatics
    24. Bioxml Project - International association of developers of XML tools for bioinformatics

  2. Operating Systems:

    1. Linux.com
    2. RedHat home
    3. FreeBSD
    4. Active Windows

  3. Databases:

    1. MySQL
    2. Postgres SQL
    3. Oracle Document
    4. NAR Database of databases

  4. Software Download:

    1. GitHub.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. Bioinformatics.org - 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. University of Michigan Libraries http://www.lib.umich.edu
    5. Virginia Tech Libraries
    6. WWW Virtual Library - catalog of the web run by a confederation of volunteers. http://www.vlib.org/
    7. Association for Computing Machinery (ACM) - the world's first educational and scientific computing society for professionals and students. http://www.acm.org/
    8. Welcome to the ACM Digital Library
    9. ACM SIGGRAPH http://www.siggraph.org/
    10. 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/
    11. IEEE Software - covers useful advances in software technology, design, development and implementation techniques. http://computer.org/software/
    12. SIAM- Society for Industrial and Applied Mathematics http://www.siam.org/
    13. 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. Infection and Immunity http://iai.asm.org/
    5. Nucleic Acids Research
    6. The Scientist

  3. Dictionaries:

    1. FOLDOC: computing dictionary
    2. Life Science Dictionary
    3. Biological Dictionary: Cell Biology 

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V. Miscellaneous:

  1. U.S. News and World Report College Rankings - Updated annually
  2. World University Rankings | Times Higher Education (THE)
  3. World Science - http://www.world-science.net/
  4. United States Patent and Trademark Office - http://www.uspto.gov/
  5. FPO: http://www.freepatentsonline.com/
  6. PatentDatabase.com - free search tool for searching the USPTO patent database. Created through Nuestel Law Offices, Ltd. http://www.patentdatabase.com/
  7. The Nobel Prize https://www.nobelprize.org/
  8. Nobel Prize in Physiology or Medicine https://www.nobelprize.org/prizes/medicine/
  9. Nobel Prize in Chemistry https://www.nobelprize.org/prizes/chemistry
  10. Nobel Prize in Physics https://www.nobelprize.org/prizes/physics
  11. http://www.ucsf.edu/news/2014/02/111956/science-policy-team-wins-national-video-content (4 minutes long)
  12. Cellular Visions: The Inner Life of a Cell

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He Group
University of Michigan Medical School
Ann Arbor, MI 48109