Free Workshop on Comparative Genomics – Register Now

We are pleased to announce a free workshop on Comparative Genomics on December 6-7, 2010 on the UC Davis campus. It will be given by Prof. Andrew Hanson, Univ of Florida. All the material it covers is on line at http://www.hos.ufl.edu/meteng/HansonWebpagecontents/workshop/workshop.html

In order to ensure ample interaction among the participants, there are only 11 slots available. If you want to be considered for participation in the workshop, please have the above information to Dr. Dawei Lin by the end of business on 11/23/2010.

Day 1 classroom sessions:

  • Outline phylogenomics approaches, giving selected case-histories
  • Briefly review public on-line resources (SEED, STRING)

Day 1 hands-on computer sessions:

  • Use STRING to recapitulate historic gene discoveries made via clustering and co-distribution
  • Introduce the SEED database – its genomes, how to navigate, clustering tools, essentiality data
  • Teach SEED annotation tools using selected target genes that participants annotate themselves

Day 2 hands-on computer sessions:

  • Creation and curation of a SEED subsystem incorporating the above novel genes
  • Using the subsystem to develop hypotheses about novel genes’ function using the subsystem

We have a few left due to people’s schedule change. This course format is designed by Dr. Andrew Hanson. The decision will be based on the need of this course and not your research program. Faculty members are encouraged to participate. For selection, we need the following information:

  1. Your name
  2. Lab Name
  3. Your position
  4. Research focus, such as Human, Animal Sciences, Plant Sciences or Microbiology
  5. Will you bring a problem of your own to the course? This problem could be, for example:
    • A plant gene of unknown function that has good homologs in prokaryotes
    • An enzyme that is known to exist but for which a gene has not yet been found.
    • In case (1) we can try to predict a function for the gene; in case (2) we can try to find the gene corresponding to the enzyme.
  6. Do you have the basic knowledge of the following:
    • Some familiarity with the basics of GenBank entries, Blast searches, sequence alignment and phylogenetic analysis, prediction programs for organellar targeting etc, and microarray databases
    • Elementary microbiology (e.g. that bacteria and archaea are different, that prokaryotic lifestyles and metabolic capacities differ enormously, and what operons are). Some acquaintance with KEGG pathways is helpful but few will have this.
  7. DaFIS account number

The workshop will be free if completed in its entirety. However, if you cannot stay for the entire two days it will affect the course, and a participant from the wait list will be selected to fill your spot. To cover the cost of personnel effort in making these special arrangements, a $100 fee will be charged to your account.

If you want to be considered for participation in the workshop, please have the above information to me by the end of business on next Tuesday (11/23/2010).
Dawei Lin by  :  Email Dawei Lin

Dr. Dawei Lin received his PhD from Peking University, China in Computational and Structural Biology. He started his career at the Protein Data Bank (PDB) at Brookhaven National Laboratory, a worldwide repository for macromolecular structures. He is currently the Bioinformatics Core Director at the UC Davis Genome Center. In his current position, he is leading his team to provide expertise and infrastructure to carry out acquisition curation, and distribution of complex data sets as well as to develop and perform computations, analyses and simulations addressing a wide variety of biological questions from genomics to network biology.