Old Lab Meeting Info

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Past lab meetings


  • 28 Jan - Soeren - Biolog: Probabilistic Logic Programming for Bioinformatics
  • 4 Feb - Ian - recent enhancements to phylocomposer/handalign
  • 11 Feb - Peter Schattner - Implementation of xrate on parallel compute-clusters and application to RNA structure prediction
  • 18 Feb - Mitch - JBrowse
  • 25 Feb - Oscar - Examining viral quasispecies evolution using microarrays: technical, experimental, and statistical perspectives.
  • 4 Mar - CANCELED (Ian @Duke)
  • 11 Mar - CANCELED (Ian @Pythium workshop)
  • 18 Mar (relocated to 381 Stanley) - Benedict - Evolutionary chains and genomic cacti: a recursive method for homology mapping based upon chains of evolutionary conserved homology.
  • 25 Mar - CANCELED (Spring break)
  • 1 Apr - Oscar - Quasispecies array progress
  • 8 Apr - Alexandre Bouchard-Cфtй
  • 15 Apr - Oscar/everyone: discuss this paper: link
  • 27 May Erick Matsen



Spring 2007 lab meetings are held on alternate Wednesdays, from 12-1:30pm, in 381 Stanley Hall. Each lab meeting will focus on a particular topic in bioinformatics algorithms or software. One goal of this format is to work out ideas for new projects.

Prior to the meeting, one or two related papers will be assigned to each group member. Each person will present a quick summary of their assigned paper(s) and will then lead a short discussion of the work. These paper summaries will lead into an ad hoc summary of the state of the field in this area & a discussion of open questions and possible future projects.

The style is very informal; no powerpoint presentations or any of that rubbish; just "whiteboards, banter and the occasional URL". [tm]

To give people time to read & prepare I suggest we meet every 2-4 weeks.

When we're not holding a formal lab meeting we will try to meet at the same time/place for some kind of mini-jamboree, Wikipedia:Hackathon or other collective activity, or just to chat. Guests are always welcome.

Please note that dates marked "provisional" are subject to change!

Date Time Topic
3/7/2007 noon Gene species tree reconciliation lab meeting
4/4/2007 noon Makefile lab meeting
4/18/2007 noon Gene family evolution lab meeting
5/2/2007 noon Ontology modeling lab meeting
5/23/2007 noon Metagenomics clustering lab meeting
6/13/2007 noon Genome assembly lab meeting
6/27/2007 noon HIV fitness landscape lab meeting

Future meeting dates...

 ? noon Fungal genome mini-hackathon
 ? (provisional) noon Metagenomics workshop review lab meeting - take 2
 ? (provisional) noon Automated ortholog database lab meeting
 ? (provisional) noon Pathway evolution lab meeting

Suggested future topics:

Some other ideas we might consider covering

Population genetics is of course a huge beast of a topic but a few semi-manageable entry points might include


For reference, presentation titles & other notes for previous lab meetings are preserved below.

Fall 2006:

Date Speaker Topic Snacks
09/08 Andrew Uzilov, Gabriel Wu, Yuri Bendana, Robert Bradley, Ian Holmes Overview of ongoing projects and opportunities Yuri Bendana
09/22 Andreas Heger Fruitfly CDS alignments and resources Andrew Uzilov
10/13 Andrew Uzilov Javascript genome browser (see PowerPoint) Robert Bradley
10/20 Gabriel Wu Protein structure annotation with xrate Yuri Bendana
11/03 Robert Bradley Phylogenetic SCFG composition Gabriel Wu
11/10 Yuri Bendana Genome annotation with xrate Andrew Uzilov
11/17 Ian Holmes String transducers TBA

Possible future speakers to invite for Fall 2006 - Spring 2007:

Ideas for future lab meetings

  • Tree-adjoining grammars
  • Langevin equations and Markov models for ion channels

Other notes

  • A journal club is now in full effect
  • See Teaching.CompbioTeaching for lecture and lab times


Spring 2006 speakers:

Date Speaker Topic Lunch
02/24 Ian Holmes Overview of fruitfly comparative genomics Andrew Uzilov
03/03 Andrew Uzilov Sixty Four Bit Cluster Ian Holmes
03/10 Ian Holmes Evolutionary grammars and xgram (ppt) Sharon Chao
03/17 Andrew Uzilov Generic Genome Browser Yuri Bendana
03/24 Yuri Bendana Drosophila noncoding RNA genes Sharon Chao
03/31 n/a (adjourned for Drosophila Research Conference, 2006) n/a
04/07 Ian Holmes Fly genome annotation Robert Bradley
04/14 Robert Bradley Drosophila transposons Andrew Uzilov
04/21 Ian Holmes informal wiki review (posted at lab news) Robert Bradley
04/28 n/a (adjourned for QB3/Designated Emphasis in Compbio Seminar, UCSF) n/a
05/05 n/a (adjourned for CSHL Biology of Genomes Meeting) n/a
05/12 n/a (adjourned for CSHL Biology of Genomes Meeting) n/a
05/19 Chris Smith Drosophila heterochromatin Ian Holmes
05/26 Chris Mungall BioMake and skam Cancelled YuriBendana
06/02 Ian Holmes Multiple RNA alignment and stemloc Postponed and replaced by short "general lab stuff" meeting Yuri Bendana


-- Created by: Ian Holmes on 04 Dec 2005

Moved from Lab Meeting -- Ian Holmes - 29 Sep 2008