Bioinformatics at UCLA

• UCLA Bioinformatics main site

• UCLA Bioinformatics Faculty

  
  

• Events at UCLA in Molecular Biology

• UCLA IPAM

• UCLA Human Genetics Seminar Series
  (weekly: Monday 11:30-1:00pm, Gonda Conference room)

• UCLA Computational Biology Methods Seminar
  (weekly: Wednesday 2-3pm, 2033 Young Hall)

• IGERT Seminar

• UCLA Computational Biology Seminar Series

• UCLA NanoSystems Seminar Series

General Bioinformatics Resources

• NCBI, ExPASy, EBI

• NCBI Data Mining Tools, including BLAST

• Bioinformatics.org's friendly Bioinformatics FAQ

Roadmaps for Bioinformatics Research

• The 2003 NIH Roadmap

  • NIH Roadmap: Bioinformatics

  • NIH Roadmap: Interdisciplinary Research

  • NIH Roadmap: Clinical Research Networks

  • Survey: Zerouni, E., "The NIH Roadmap", Science 302:3, 63-65 (2003).

  • Survey: NIH 9/30/2003 press release

  • Recommendations of BISTI (Biomedical Information Science and Technology Initiative Implementation Group), 2000

• A Vision for the Future of Genomics Research (Francis Collins, Eric Green, Alan Gutmacher, Mark Guyer, Nature 422:6934, April 24, 2003, pp. 835-847)

• DOE Office of Science 20-year Strategic Plan:

  • Facilities for the Future of Science: A Twenty-Year Outlook (Nov.2003)

  • Strategic Plan for the Future of Science (Feb.2004)

• Jim Gray's talks about Online Science.

Online Books

• Bioinformatics in practice

  • O'Reilly ("Nutshell") books on bioinformatics:

    • Developing Bioinformatics Computer Skills, with a sample chapter on Biology in the Computer Age.

    • Sequence Analysis, with a sample chapter on BLAST.

    • BLAST, with a sample chapter on sequence similarity.

    • Mastering Perl for Bioinformatics, with a sample chapter on BioPerl, and downloadable sample Perl code. (For more on BioPerl, see http://www.bioperl.org.)

    • There is also a central page for access to sample chapters from O'Reilly bioinformatics books, including a sample chapter on GenBank.

    • the O'Reilly Safari ebook service (UCLA has a license for open online access to O'Reilly books)
      

• Bioinformatics in theory

  • online version of Pavel Pevzner's book on Computational Molecular Biology (for theoretically-inclined Computer Scientists)

• Biology

  • NCBI's Bookshelf -- great online book library, which includes for example Koonin and Galperin's book on Computational Approaches in Comparative Genomics

  • Ergito Virtual Texts for the life sciences (some free)

Database Tools and Bioinformatics Databases

• open-source database tools

  • PostgreSQL

  • MySQL

  • UPenn Bioinformatics K2 (Kleisli v.2 information integration system)

• commercial database tools

  • DiscoveryLink (DB2) from IBM Life Sciences

  • SRS (Sequence Retrieval System) from Lion Bioscience

  • Gene Express (formerly OPM) from Gene Logic

• "Relationalized SwissProt database" (from UCSC Genome Bioinformatics downloads)

• GOLD (Genomes OnLine Database) -- a list of genome sequencing projects

• list of Bioinformatics databases and analysis services.

Bioinformatics Tutorials, Courses, and Curricula

• The S* ("S star") alliance, which offers excellent online lectures (with video/slides downloads).

• O'Reilly's 2003 Biotechnology Conference provided downloadable PowerPoint slides for most talks, giving a great perspective on issues of interest to the biotech industry. They also had a 2002 Biotechnology Conference, again with PowerPoint slides for most talks.

• NCBI Primer covering Bioinformatics, Genome mapping, SNPs, ESTs, Microarrays, etc.

• NCBI online tutorials, including a BLAST tutorial and Entrez tutorial.

• a long list of online Bioinformatics courses

• Ron Shamir's list of CS-oriented online Computational Biology/Bioinformatics courses

• Mark Craven's course: Introduction to Bioinformatics

• BioPerl online tutorial

• Major Bioinformatics programs at U.S. Universities (2004 Summary)

Other Useful Links

• Nice set of links on Bioinformatics Databases and Tools

• Links: XML for Molecular Biology