ISEEM:For Team
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Conference Call Notes
The notes from conference calls are here.
Conference calls are currently scheduled for Wednesdays at 10:00am and usually lasts an hour. From time to time the call will be a journal club. Occasionally the call will be PIs only. Other calls with be group research updates and discussions.
Projects
See also the list of personal wiki pages, which have notes about what each person is doing and links to related wiki pages.
- Tara Oceans Analysis Plans
- Oil Spill Brainstorm
- hmmbuild
- GeneFamilies
- Searching for Novelty
- Workflows
- Survey of existing metagenomic data
- Simulations of metagenomic data
- Phylogenetic Metagenomics
- Species-area relationships
- Tree building from metagenomic reads + reference phylogeny
- Community assembly
- Phylogenetic diversity and community structure
- Global Ocean Survey Analysis
- Convergent Gene Family Evolution between Communities
- OTU Identification
- CAMERA DATA
- rRNA and metagenomic databases with spatial metadata
- GOS Range Map
- Amphora-2
Resources
Bioinformatics Requests
- Post Data requests and wishlists here OR using trac.
- Post computing and database tasks that you would like to do at CAMERA here.
Meetings
iSEEM1
iSEEM2
Products
Outreach/Education
- Conference calendar
- Courses we might take
- Course materials we are developing
- Slides and other materials from presentations
Papers in Progress
iSEEM1
iSEEM2
- MicrobeCensus
- Shotmap
- Variable gene families
- Niche modeling
- Tibetan soils
- N American soils
- American Gut
Bibliography
An iSEEM bibliography is being created on an ongoing basis using citeulike. This citation application is described here. We have set up an iSEEM Group, which is visible to the public. You can access the cited articles and sort/filter them using the tags listed on the right hand side. In order to post articles or to edit the library, you need to create a user account. It is possible to keep different articles in your personal library or the same articles with different tags. Articles can be copied between libraries (your own, iSEEM, or others). If you post an article, be sure to enter some tags.
People involved
See the list of personal wiki pages.
E-mail addresses
iSEEM1
- Jessica Green, mailto:jlgreen@uoregon.edu
- Steven Kembel, PostDoc, mailto:steve.kembel@gmail.com, skype: stevekembel, iChat: stevekembel (AIM)
- James O' Dwyer, PostDoc, mailto:jodwyer@uoregon.edu, skype: jamesodwyer
- Liz Perry, PhD Student, mailto:eperry1@uoregon.edu
- Jess Bryant, Research Assistant, mailto:JessAwBryant@gmail.com, skype: jessbxctf
- Katie Pollard, mailto:kpollard@gladstone.ucsf.edu, skype: djkt604, iChat: djkt604 (AIM)
- Josh Ladau, PostDoc, mailto:jladau@gmail.com, skype: jladau
- Sam Riesenfeld, PostDoc, mailto:sriesenfeld@gmail.com, skype: sriesenfeld
- Thomas Sharpton, PostDoc, mailto:thomas.sharpton@gmail.com, skype: thomas.sharpton
- Jonathan Eisen, mailto:jonathan.eisen@gmail.com; skype: jonathan_eisen
- Morgan Langille, PostDoc, mailto:mlangille@ucdavis.edu skype:morgan_langille
- Dongying Wu, Staff Scientist, mailto:dongyingwu1@gmail.com; skype: dongyingwu2005
- Srijak Bhatnagar, Bioinformatics Engineer, mailto:sbhatnagar@ucdavis.edu, skype: srijak.bhatnagar
- Guillaume Jospin, Bioinformatics Engineer, mailto:gjospin@ucdavis.edu, skype: guillaumeJ_work
- Sarah Hird, PostDoc, mailto:sarah.hird@gmail.com; skype: smhird
- Martin Wu, mailto:mwu2000@gmail.com; skype: mwu2000
- Alex Koeppel, PostDoc, mailto:afk2s@virginia.edu, skype: afkoeppel
- Eisen lab minor roles
- Marisano James, PhD student, Population Biology Graduate Group, mailto:marisano@yahoo.com; skype: marisano
- Amber Hartman, PhD student, Johns Hopkins University (but in Eisen lab at Davis), mailto:alhartman@ucdavis.edu,
- Jenna Morgan, PhD student, Microbiology Graduate Group, UCD, mailto:jlmorgan@lbl.gov
- Aaron Darling, PostDoc, mailto:aarondarling@ucdavis.edu
- EisenLab past members
- Sourav Chatterji, PostDoc, mailto:schatterji@ucdavis.edu, skype: souravchat
Send Mail to Everyone
iSEEM2
- Katie Pollard, PI, mailto:kpollard@gladstone.ucsf.edu, skype: djkt604, iChat: djkt604 (AIM)
- Patrick Bradley, PostDoc, mailto:patrick.bradley@gladstone.ucsf.edu
- Josh Ladau, PostDoc, mailto:jladau@gmail.com, skype: jladau
- Stephen Nayfach-Battilana, Grad Student, mailto:snayfach@gmail.com
- Stacia Wyman, Bioinformatician, mailto:stacia.wyman@gladstone.ucsf.edu
- Thomas Sharpton, Co-Investigator, mailto:thomas.sharpton@gmail.com, skype: thomas.sharpton
- Jonathan Eisen, Co-Investigator, mailto:jonathan.eisen@gmail.com; skype: jonathan_eisen
- Ladan Doroud, Grad Student, mailto:ladan.doroud@gmail.com
- Sarah Hird, PostDoc, mailto:sarah.hird@gmail.com; skype: smhird
- Guillaume Jospin, Bioinformatics Engineer, mailto:gjospin@ucdavis.edu, skype: guillaumeJ_work
- Dongying Wu, Staff Scientist, mailto:dongyingwu1@gmail.com; skype: dongyingwu2005
Grant Proposals
iSEEM2
- Deadlines and deliverables
- Note: Use these deadlines not the task assignments to years in the Aims document
iSEEM1
- Future work proposal (to Kelly in July 2010)
Progress Reports
iSEEM1
- Progress Report March 2008
- Progress Report June 2008
- Progress Report September 2008
- Annual Report 2008
- Progress Report March 2009
- Progress Report June 2009
- Progress Report September 2009
- Annual Report Template Feb 2010 - word document*
- Annual Report Feb 2010 - wiki version
- Progress Report March 2010
- Progress Report June 2010
- Progress Report September 2010
- Final Progress Report 2011
iSEEM2
- Progress Report January 2013
- Progress Report June 2013
- Progress Report June 2014
- Software and data release report 2015
