Jun10 Annual Schedule
Schedule for the iSEEM Jun10_Annual meeting.
Thursday June 24
9:00 - 9:30 Introductions, etc.
9:30 - 10:45 Protein Family (Guillaume, Morgan, Tom)
- Discussion will center around the recent creation of protein families for all completed genomes led by Guillaume.
10:45 - 11:00 Break
11:00 - 12:00 Ecotype Simulation (Alex Koeppel)
If there are no objections I'd like to use this session to discuss the results of our Ecotype Simulation analysis of the GOS Prochlorococcus sequences. I don't think I will necessarily need the full hour (maybe 20-30 minutes).
Presentation Slides. File:ISEEM Talk 2010.pdf
12:00 - 13:00 Lunch
13:00 - 14:00 Taxonomic Diversity Discussion (Tom)
Audio (includes audio for Aaron's presentation as well)
I'd like to have a session about characterizing microbial taxonomic diversity. At the very least:
- PHYLOTU presentation (brief)
- Where we can take PHYLOTU with future work (Discussion)
- What improvements can we make to more accurately describe taxonomic diversity (strict PD, maybe something here by Steve?)
- How can we incorporate Alex's work on the ecotype model of speciation for this purpose (something here by Alex)
- Microbial biodiversity map (with Josh?)
14:00 - 15:00 Phylogenetic cobinning (Aaron Darling)
Recent progress on binning and linkage estimation in next-generation metagenomes (30 minutes + 15-30 minutes discussion)
15:00 - 15:15 Break
15:15 - 16:15 Characterization of unknown genes (Morgan Langille)
- Planning on about 20 minute presentation leaving 25 minutes for questions/discussion
- Will discuss some of the ranking metrics and results for gene families with unknown function (universality, pathogen, habitat, etc.)for completed genomes.
- Discuss expansion of characterization metrics to metagenomic datasets.
- Discuss methods for using metagenomic datasets to predict function for families of unknown function.
16:15 - 17:00 Paper discussions
- PHYLOTU
Friday June 25
9:00 - 11:00 Diversity and Distance-Decay Relationships (Josh & James)
Audio (includes audio for Sam's presentation as well)
- Update on range estimation
- The Minkowski-Steiner formula
- Alpha diversity estimates from distance-decay?
- I will present some slides briefly summarizing the theoretical models we've developed
- I would like to extend these models to take into account environmental heterogeneity (see also here)
- These ideas are at very early stages, so I will plan to talk for about 15-20 minutes. After that I'd appreciate feedback/discussion about what people consider most interesting questions/best directions to proceed in
11:00-11:15 Break
11:15 - 12:30 Impact of simulation studies on our phylogenetic analyses (Sam Riesenfeld)
- Effect of read length, reference sequences, choice in phylogenetic inference method.
- Doing round 2 simulations now -- what should we include?
12:30 - 14:00 Lunch (ordered in) + Paper discussions
- Josh's papers
- Steve's resubmission to PLoS
- ZORRO revisions?
14:00 - 14:45 Measuring phylogenetic diversity with multiple marker genes (Steve)
- Discussion of results from analysis of GOS data based on multiple bacterial and archaeal marker genes (with Dongying & Guillaume)
- How to choose and compare marker genes, identify organisms from different clades (i.e. what's an 'archaeal marker gene', how do we make sure it's capturing the groups we want?).
- Guidelines for quality control (which sequences can we throw out - Sam, Tom, others have suggestions?)
- How could this approach to measure diversity be combined with taxonomic, functional gene analyses by others?
14:45 - 15:45 Bioinformatics Discussion (Guillaume)
- Current projects
- Future: Supporting bioinformatics needs for different projects
15:45 - 16:00 Break
16:00 - 16:45 Grants and Funding (Josh)
CHALLENGES
1) finding funding for research that does not involve data collection
2) finding funding for development of general methods -- specific systems wanted
POTENTIAL SOLUTIONS
1) add a data collection element -- but preliminary data needed
2) add human/biomedical aspect
3) software development
SOURCES
1) NIH
2) NSF -- ecology, may be willing to fund pure theory (+)
3) NSF -- oceanography, oil spill
4) NSF -- statistics
5) NSF -- mathematical biology (+)
6) private sources
7) Joint NSF/NIH -- mathematical biology (+)
8) DARPA -- may be a stretch, funding less pure science recently
9) NSF -- bioinformatics postdoctoral fellowship (+)
(+) = most promising
NOTES
- may need to break into smaller groups for new grants
- talk to SFI people about doing pure theory
- grant proposal should reflect future plans, anticipated future directions
- want to appear on job market as an expert in one field, even if interdisciplinary
- non-faculty jobs: jobs at centers (e.g., SFI, Davis Genome Center, informaticist at cancer centers)
- faculty jobs: group size highly dependent on location
