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20 August 2017

       15:01 Xu lab (diff; hist) . .  (0) . . Peisheng Xu (Talk | contribs) (News: )

18 August 2017

+      15:39 Min-Ho Kim Lab‎ (2 changes) . . (+250) . . (Page history) [Min-Ho Kim‎ (2×)]
+      10:42 Xu lab‎ (3 changes) . . (+202) . . (Page history) [Peisheng Xu‎ (3×)]

17 August 2017

  N    18:27 Gos (diff; hist) . .  (+1,180) . . Katie Pollard (Talk | contribs) (New page: 31 phylogenetic markers were identified by BLAST and HMM searches from the Global Ocean Survey read peptides. The marker sequences were then aligned and trimmed. '''Peptides''': 41,146,5...)
  N    18:26 MetagenomicPhylodiversity (diff; hist) . .  (+2,392) . . Katie Pollard (Talk | contribs) (New page: = Measuring phylogenetic diversity using metagenomic data = --Steven Kembel * General question is how we can measure phylogenetic diversity using metagenomic data. ...)
  N    18:26 Mechanistic models community assembly (diff; hist) . .  (+4,036) . . Katie Pollard (Talk | contribs) (New page: (These notes added mainly by James.) ===Overview=== With Jess Green I am developing a theoretical and mathematical underpinning for certain spatial patterns in ecology. In the first inst...)
  N    18:25 ReadsOnATree (diff; hist) . .  (+3,242) . . Katie Pollard (Talk | contribs) (New page: == Placing metagenomic reads on a reference phylogeny == This is a place to discuss the method for building phylogenies from metagenomic reads that I've been trying. === Individual gene ...)
  N    18:25 SARs (diff; hist) . .  (+1,758) . . Katie Pollard (Talk | contribs) (New page: {{ISEEM}} <div style="width: 750px;padding-right: 25px; padding-left: 25px;font-family: Arial, Helvetica, sans-serif;font-size: 12px;margin-bottom: 30px;line-height: 18px;padding-top: 0px...)
  N    18:24 Simulation pipeline (diff; hist) . .  (+2,631) . . Katie Pollard (Talk | contribs) (New page: The simulation pipeline generates specific kinds of metagenomic data sets and alignments. Details about dependencies, how to use the script, what files are output, etc., are covered in th...)
  N    18:23 Developing phylogenetic methods (diff; hist) . .  (+918) . . Katie Pollard (Talk | contribs) (New page: (15 April 2009) These are notes for an ongoing project. Please let me know if you have suggestions.<br> -- Sam Riesenfeld I am working on developing a phylog...)
  N    18:23 PhyloPipeline (diff; hist) . .  (+3,580) . . Katie Pollard (Talk | contribs) (New page: == Availability and dependencies== The scripts are available as an archive. The data included with the scripts are the results of running AMPHORA on the HOT/ALOHA metagenomic data set. Do...)
  N    18:22 List of phylogenetic methods (diff; hist) . .  (+2,020) . . Katie Pollard (Talk | contribs) (New page: We are trying to compile here a list of methods, and ways to tweak methods, that we might want to compare using (at least) the simulated data. '''Methods to create alignments''' *Metagen...)
  N    18:22 Discussion on phylogenetic methods (diff; hist) . .  (+10,436) . . Katie Pollard (Talk | contribs) (New page: Major overhaul (15 April 2009): I reorganized the wiki pages on phylogenetic methods; the main page is Phylogenetic Methods, and this page is reserved for discussion. I have also bro...)
  N    18:21 Phylogenetic Methods (diff; hist) . .  (+2,167) . . Katie Pollard (Talk | contribs) (New page: Major overhaul (15 April 2009): I reorganized the wiki pages on phylogenetic methods, started a new page just for the discussion, and broke up the discussion page into several pages.<br> ...)
  N    18:21 Discussion on simulating metagenomic data (diff; hist) . .  (+9,174) . . Katie Pollard (Talk | contribs) (New page: Major overhaul (15 April 2009): I reorganized the wiki pages on simulations; the main page is Simulations of Metagenomic Data, and this page is reserved for discussion.<br> --[[User:S...)
  N    18:20 Action items for the simulations and analysis (diff; hist) . .  (+9,132) . . Katie Pollard (Talk | contribs) (New page: (Page created: Nov. 2009) ==Simulation code - Sam: I got these items== * ''Done.'' Output alignment of source seqs and ref seqs and as well as an alignment of reads and ref seqs. (Source...)
  N    18:19 Simulations of Metagenomic Data (diff; hist) . .  (+1,447) . . Katie Pollard (Talk | contribs) (New page: Major overhaul (15 April 2009): I reorganized the wiki pages on simulations of metagenomic data; all related pages should be linked to from this page.<br> --[[User:Samantha_Riesenfeld | S...)
  N    18:16 Survey of metagenomic data (diff; hist) . .  (+3,601) . . Katie Pollard (Talk | contribs) (New page: {{ISEEM}} <div style="width: 750px;padding-right: 25px; padding-left: 25px;font-family: Arial, Helvetica, sans-serif;font-size: 12px;margin-bottom: 30px;line-height: 18px;padding-top: 0px...)
  N    18:16 Workflow Notes (diff; hist) . .  (+391) . . Katie Pollard (Talk | contribs) (New page: {{ISEEM}} <div style="width: 750px;padding-right: 25px; padding-left: 25px;font-family: Arial, Helvetica, sans-serif;font-size: 12px;margin-bottom: 30px;line-height: 18px;padding-top: 0px...)
  N    18:16 Novelty Notes (diff; hist) . .  (+166) . . Katie Pollard (Talk | contribs) (New page: == Jonathan and Dongyings work on automated methods for IDing protein family novelty == Coming soon == Possible project on looking for unique pathways == Coming soon)
  N    18:15 Gene Family Notes (diff; hist) . .  (+38,156) . . Katie Pollard (Talk | contribs) (New page: == 100 genomes (Dongying Wu) == * Summary **Took 100 genomes (bacterial and archaea) ** Did all vs all blastp ** Identified protein families using MCL ** Annotated families according to e...)
  N    18:15 HMM Profile Building Notes (diff; hist) . .  (+1,824) . . Katie Pollard (Talk | contribs) (New page: <pre> 5/2/2009 I've picked 102 gene families with universality of 100, and build 102 hmm profiles. Here is the protocols: 1. get all the peptides for each family 2. use kalign to align ...)
  N    18:15 Oil Spill Brainstorm (diff; hist) . .  (+3,530) . . Katie Pollard (Talk | contribs) (New page: *Josh, May 31: I think that some of our methods and ideas could be easily adapted for investigating the effects of the Gulf of Mexico oil spill on marine microbes. There is a lot funding...)
  N    18:14 Tara Oceans Analysis Plans (diff; hist) . .  (+2,507) . . Katie Pollard (Talk | contribs) (New page: Tara Oceans Analysis Ideas * Prevalence of novel SFams (diverse families with no annotated function) across Tara sampling locations. ** Potentially correlate with annotated families and/...)
  N    18:14 Moore Notes 4 24 09-EisenCallWithCamera (diff; hist) . .  (+1,171) . . Katie Pollard (Talk | contribs) (New page: JE talked with Ilkay from Camera this PM they have been working on implementing some of our software within CAMERA, some as sort of stand alone apps and some as workflows and some apparen...)
  N    18:13 Moore Notes 11 25 08-EisenCallWithCamera (diff; hist) . .  (+337) . . Katie Pollard (Talk | contribs) (New page: Conference call to discuss CAMERA 11-25-08 2 PM CAMERA is turning software and algorithms into APIs They are using REST style services - services invoked using standard http get or other...)
  N    18:13 Moore Notes 11 19 08-EisenCallWithCamera (diff; hist) . .  (+204) . . Katie Pollard (Talk | contribs) (New page: Eisen had conversation with Gilna, et al from CAMERA at 4 PM on 11-19 Discussed two main issues * Getting iSEEM tools and products into CAMERA * Getting access to CAMERA General commitme...)
  N    18:13 Moore Notes CAMERA 4 18 08 (diff; hist) . .  (+2,754) . . Katie Pollard (Talk | contribs) (New page: {{ISEEM}} iSEEM team went to visit CAMERA on 4/18/08 This was our Quarterly Meeting as well as a chance to interact with CAMERA = Visitors were = *Green Lab - Jessica Green, Liz Perry, ...)
  N    18:12 Moore Notes 12 16 08 (diff; hist) . .  (+2,229) . . Katie Pollard (Talk | contribs) (New page: Group Skype Chat * How to build phylogenetic trees for marker gene families with complete genomes plus metagenomic reads? ** KP emailed Bret Larget (waiting response) ** SR emailed Tandy ...)
  N    18:12 Moore Notes 12 2 08 (diff; hist) . .  (+360) . . Katie Pollard (Talk | contribs) (New page: Group skype conference call * Planning quarterly meeting ** Arrival times, logistics ** Presentations on previous work first (Wednesday 2-5pm) ** Project topic discussions second (Thursda...)
  N    18:12 Moore Notes 11 25 08 (diff; hist) . .  (+1,287) . . Katie Pollard (Talk | contribs) (New page: Phone call with Katie and Jessica Discussing the new private wiki Decision to do most things in the private system and then copy stuff over to the public page when needed For some things...)
  N    18:11 Moore Notes 11 18 08 (diff; hist) . .  (+3,197) . . Katie Pollard (Talk | contribs) (New page: <div style="width: 800px;border-top-width: 4px;border-bottom-width: 4px;border-top-style: solid;border-bottom-style: solid;border-top-color: #333333;border-right-color: #333333;border-bott...)
  N    18:11 Moore Notes 11 11 08 (diff; hist) . .  (+706) . . Katie Pollard (Talk | contribs) (New page: {{ISEEM}} JG and KP Skype chat * Our lab members need UC Davis computer accounts ** Step 1: Get @ucdavis.edu emails for kerberos pwds ** Step 2: Get accounts on Genome Center clusters ...)
  N    18:11 Moore Notes 11 4 08 (diff; hist) . .  (+1,399) . . Katie Pollard (Talk | contribs) (New page: {{ISEEM}} All Group Call * New personnel: Josh, Sam and Steve all started * OWW site ** Every one should add their photo and edit their text ** Steve Green will pick some photos of micr...)
  N    18:11 Moore Notes 10 28 08 (diff; hist) . .  (+1,452) . . Katie Pollard (Talk | contribs) (New page: {{ISEEM}} PI Conference Call (JG, JE, KP) * OWW website ** calendar planning ** JE and OWW are still working on the private page * Update on Genographic project ** H. pylori papers (M....)
  N    18:11 Moore Notes 10 21 08 (diff; hist) . .  (+2,031) . . Katie Pollard (Talk | contribs) (New page: {{ISEEM}} PI skype chat (JG, JE, KP) * OWW website: ** Steve still needs to *** fix calendar *** Transfer relevant information from Jonathan's wiki over to the openwetware page rather t...)
  N    18:10 Moore Notes 10 14 08 (diff; hist) . .  (+932) . . Katie Pollard (Talk | contribs) (New page: {{ISEEM}} PI skype video chat (JG and KP) * OWW website: Steve will ** look into photo images from Dennis Kunkel ** add calendar (as a menu link) ** revise menu links: Transfer relevant...)
  N    18:10 Moore Notes 9 7 08 (diff; hist) . .  (+619) . . Katie Pollard (Talk | contribs) (New page: {{ISEEM}} Group Conference Call (Pollard & Eisen labs) * First skype conference call. After some glitches, worked great for multiple party calls. * Progress Report * Genevieve Erwin (Po...)
  N    18:10 Moore Notes 9 30 08 (diff; hist) . .  (+811) . . Katie Pollard (Talk | contribs) (New page: {{ISEEM}} Phone Conference Call (JG, JE, KP) * Website update ** Steve's html needs to be converted to media wiki (JE will send link) ** Steve will send billing info and an estimate to ...)
  N    18:09 Moore Notes 9 24 08 (diff; hist) . .  (+589) . . Katie Pollard (Talk | contribs) (New page: {{ISEEM}} Conference Call (JG, JE, KP) * Tutorial: multiple alignment, sequence processing, etc. ** Srijak will start with a simple metagenomic data set ** Then, JG's PKS and 16S data *...)
  N    18:09 Moore Notes 9 17 08 (diff; hist) . .  (+1,410) . . Katie Pollard (Talk | contribs) (New page: {{ISEEM}} PI iChat: JG, KP, JE * Openwetware website ** Pages: *** Home: logo and brief project summary *** Project: detailed project summary, links to subprojects *** People: photo of ...)
  N    18:09 Moore Notes 9 10 08 (diff; hist) . .  (+1,455) . . Katie Pollard (Talk | contribs) (New page: {{ISEEM}} Full Group Conference Call (PIs plus lab members) * Update on Kepler work flow meeting with UCD and CAMERA ** CAMERA is already working with Forest Rohwer ** Our tools would be...)
  N    18:08 Moore Notes 9 3 08 (diff; hist) . .  (+3,743) . . Katie Pollard (Talk | contribs) (New page: {{ISEEM}} PI iChat (JE, JG, KP) * review article discussion ** has served purpose of us all doing lit review, and talking about articles ** put writing the article itself on hold for now...)
  N    18:08 Moore Notes 8 20 08 (diff; hist) . .  (+377) . . Katie Pollard (Talk | contribs) (New page: {{ISEEM}} KP and JG chatted (JE at DARPA meeting this week). * Both of us have finished reading through the iSEEM bibliography * JG has updated the tables organizing methods from the lit...)
  N    18:08 Moore Notes 8 13 08 (diff; hist) . .  (+584) . . Katie Pollard (Talk | contribs) (New page: {{ISEEM}} * Technology ** Jess and Katie tested Marratech, which was not good. ** iChat is better, so we'll stick with it and phone calls for now. * Science ** Discussion of sequencing ...)
  N    18:08 Moore Notes 8 6 08 (diff; hist) . .  (+884) . . Katie Pollard (Talk | contribs) (New page: {{ISEEM}} Notes * Discussing video conferencing set up ** Jess discussed multiple options ** Maratech system is a web server based system *** NCEAS using it *** We might be able to use i...)
  N    18:08 Moore Notes 7 30 08 (diff; hist) . .  (+2,048) . . Katie Pollard (Talk | contribs) (New page: {{ISEEM}} Group Call 7-30-08 Called in to AT&T conference = Participants = * Green Lab ** Jessica Green ** James O'Dwyer ** Steve Kembel * Pollard Lab ** Katie Pollard ** Josh Ladau ** ...)
  N    18:07 Moore Notes 7 23 08 (diff; hist) . .  (+809) . . Katie Pollard (Talk | contribs) (New page: {{ISEEM}} Participating: Jessica Green, Katie Pollard Conference calls * Group call next week and bi-weekly thereafter * JE looking into video conference technology * KP will check what ...)
  N    18:07 Moore Notes 7 16 08 (diff; hist) . .  (+634) . . Katie Pollard (Talk | contribs) (New page: {{ISEEM}} conference call with Eisen and Green # JE is going to look into some type of video conferencing (not crazy high tech) that we can each buy for our weekly meetings that will ho...)
  N    18:07 Moore Notes 7 9 08 (diff; hist) . .  (+343) . . Katie Pollard (Talk | contribs) (New page: {{ISEEM}} Conference call with Jessica Green, Jonathan Eisen, Martin Wu and Steve Kembel * Discussed general outline of the iSEEM workflow that Eisen has laid out * Discussed working on ...)
  N    18:06 Moore Notes 2 13 08 Ichat Notes (diff; hist) . .  (+1,421) . . Katie Pollard (Talk | contribs) (New page: {{ISEEM}} 1. Bodega Bay phylogenetics course. JE is at BB now, is exploring the possibility of us teaching a metagenomics course there. 2. Quarterly report. Due at the end of Marc...)
  N    18:06 Moore Notes 2 1 08 Ichat Notes (diff; hist) . .  (+543) . . Katie Pollard (Talk | contribs) (New page: {{ISEEM}} * Got iChat set up * Agreed on language for the job ad with Bioinformatics Engineer terms. Katie will rewrite. * Will use genome portal for job search. Katie will check into ...)
  N    18:05 Moore Notes 1 11 08 Ichat Notes (diff; hist) . .  (+696) . . Katie Pollard (Talk | contribs) (New page: {{ISEEM}} Jessica, Katie and Jonathan had a joint meeting on 1_11_08 via Ichat It took a bit to get Ichat up and running but now it is all set up We identified a few items to work on fo...)
  N    18:05 Moore Notes 2008 (diff; hist) . .  (+1,321) . . Katie Pollard (Talk | contribs) (New page: {{ISEEM}} <div style="width: 750px;padding-right: 25px; padding-left: 25px;font-family: Arial, Helvetica, sans-serif;font-size: 12px;margin-bottom: 30px;line-height: 18px;padding-top: 0px...)
  N    18:02 Moore Notes 12 11 09 (diff; hist) . .  (+285) . . Katie Pollard (Talk | contribs) (New page: PI Call * Annual meeting schedule * Review of Moore grant outcomes ** CAMERA outcomes may be a challenge ** Population genomics - Alex? ** Trees - Guillaume? ** Main deliverables are on ...)
  N    18:02 Moore Notes 12 8 09 (diff; hist) . .  (+1,042) . . Katie Pollard (Talk | contribs) (New page: PI Call * Bioinformatics hire He started today. JE will ask if he can come to the meeting. ** projects In the long run, we need to come up with a system to figure out what he will spe...)
  N    18:01 Moore Notes 12 2 09 (diff; hist) . .  (+2,370) . . Katie Pollard (Talk | contribs) (New page: Subgroup Call * OTUs ** version 1 of pipeline is done! *** Sam's simulation results might lead to modifications *** JE will talk to CAMERA: Tom will follow up Thurs ** JE's question about...)
  N    18:01 Moore Notes 12 1 09 (diff; hist) . .  (+902) . . Katie Pollard (Talk | contribs) (New page: Group Call * Dec meeting ** hotel all set ** sessions: http://iseem.private.openwetware.org/wiki/Dec09_Annual *** each person said what they want/need from the meeting *** idea is that ea...)
  N    18:01 Moore Notes 11 11 09 (diff; hist) . .  (+3,392) . . Katie Pollard (Talk | contribs) (New page: Subgroup call about OTU pipeline * Conversion of large tree into a distance matrix ** TS: recursive calculation from leaves to root ** TS/SR: create table storing distance from a node to ...)
  N    18:01 Moore Notes 11 10 09 (diff; hist) . .  (+7,406) . . Katie Pollard (Talk | contribs) (New page: ==James' update== *Looking at neutral theory of biodiversity, makes assumptions about processes driving biodiversity (simple starting point) **Key points: ***Many species at same trophic l...)
  N    18:00 Moore Notes 10 27 09 (diff; hist) . .  (+2,722) . . Katie Pollard (Talk | contribs) (New page: Group Call * JE is making an offer to Guillaume * Simulation discussion: schedule a skype call for this topic early next week, especially who is going to do what * Annual Meeting ** Ses...)
  N    18:00 Moore Notes 10 21 09 (diff; hist) . .  (+728) . . Katie Pollard (Talk | contribs) (New page: PI Call (JG, KP, JE) * writing reference letters for postdocs * personnel ** engineer position *** JE talking to candidate today *** want some one pro-active *** hope to make a decision ...)
  N    18:00 Moore Notes 10 14 09 (diff; hist) . .  (+1,836) . . Katie Pollard (Talk | contribs) (New page: == Discussion of progress report sections == === Morgan === *MicrobeDB, database of information on organisms and their genomes. Includes characteristics of genomes plus full sequence of g...)
  N    17:59 Moore Notes 10 12 09 (diff; hist) . .  (+440) . . Katie Pollard (Talk | contribs) (New page: PI Call * Bioinformatics engineers ** JE interviewed candidate last Friday ** JE emailed second candidate last Friday and will follow up ** Hold off on others for now * Steve's paper **...)
  N    17:59 Moore Notes 9 30 09 (diff; hist) . .  (+2,794) . . Katie Pollard (Talk | contribs) (New page: Group Call * Finding a time that JE can make the call * Progress Report ** Put more stuff in Section C ** Add names to subsections ** Clean up headers with no text below * James' paper...)
  N    17:59 Moore Notes 9 23 09 (diff; hist) . .  (+321) . . Katie Pollard (Talk | contribs) (New page: PI Call (JG & KP) * Engineer hire ** JE is doing interviews and checking refs ** Will follow up later today or early next week * Quarterly report ** Steve made a template ** sent reminde...)
  N    17:59 Moore Notes 9 16 09 (diff; hist) . .  (+5,683) . . Katie Pollard (Talk | contribs) (New page: ==Science chat== *Steve asked about next step for GOS phylogenetic diversity analyses **can we add the 100 additional gene families? **additional gene family HMM data should be available f...)
  N    17:58 Moore Notes 9 9 09 (diff; hist) . .  (+309) . . Katie Pollard (Talk | contribs) (New page: PI Call * Bioinformatics engineer ** JE will make final calls, schedule interview * JG: hire some one new since James has funding ** no-cost extensions are generally acceptable, with rev...)
  N    17:58 Moore Notes 9 2 09 (diff; hist) . .  (+2,257) . . Katie Pollard (Talk | contribs) (New page: Group Call * INFERNAL/OTU analysis (Tom will post update on wiki) ** have 16S reads from GOS ** how to align? *** INFERNAL aligns reads to probabilistic model *** has an option for shotgu...)
  N    17:58 Moore Notes 8 26 09 (diff; hist) . .  (+486) . . Katie Pollard (Talk | contribs) (New page: PI Call (JG, KP) * Budget issues: in future should all discuss and approve a precise budget before changes are made * Bioinformatics Engineer ** interviews ** new candidates * Authorship:...)
  N    17:57 Moore Notes 8 19 09 (diff; hist) . .  (+1,977) . . Katie Pollard (Talk | contribs) (New page: Group Call * Sam will email questions about simulations * Update on svn or git server ** Srijak will follow up * Problems with skype ** gizmo ** google ** Gladstone teleconference syste...)
  N    17:57 Moore Notes 8 18 09 (diff; hist) . .  (+1,266) . . Katie Pollard (Talk | contribs) (New page: '''Conference Call about computing OTUs from GOS data''' 1. Tom has algorithms set up to run on genbeo. 2. Options: a) blast all genes, b) align raw reads, c) align XX 3. After blas...)
  N    17:57 Moore Notes 8 12 09 (diff; hist) . .  (+1,024) . . Katie Pollard (Talk | contribs) (New page: PI Call (JG, JE, KP) * Dec meeting ** attending *** Green lab: Steve, James, JG *** Eisen lab: let KP know ** organization *** each person will lead on a topic *** goals: conversation, fe...)
  N    17:57 Moore Notes 8 5 09 (diff; hist) . .  (+2,912) . . Katie Pollard (Talk | contribs) (New page: Group Conference Call * Martin: still waiting for subcontract ** Tom: JE worked on it Monday * Josh: update on GOS ** Met with James in Eugene ** Emailed Rusch for pooled GOS reads assig...)
  N    17:56 Moore Notes 7 29 09 (diff; hist) . .  (+820) . . Katie Pollard (Talk | contribs) (New page: PI Call (KP & JG) * Engineer position ** check JE has posted ad ** 4 applications already * Josh & James met * James' paper: submit to Ecology Letters * Samantha on PBBR grant for 9 mo...)
  N    17:56 Moore Notes 7 22 09 (diff; hist) . .  (+1,438) . . Katie Pollard (Talk | contribs) (New page: Group Call * 16S based OTUs from GOS (Josh) ** Quince got data from Rusch ** They only have them for all samples together ** Do they know which reads go into OTUs: could try to de-convolv...)
  N    17:56 Moore Notes 7 15 09 (diff; hist) . .  (+396) . . Katie Pollard (Talk | contribs) (New page: PI Call (JG & KP) * CAMERA ** Getting JG and KP direct access to people at CAMERA * Bioinformatics position ** post to: *** Science *** Personal networks *** evoldir *** others (?) ** u...)
  N    17:56 Moore Notes 7 8 09 (diff; hist) . .  (+2,256) . . Katie Pollard (Talk | contribs) (New page: = Group Call = * Steve: genome-wide trees from gene family trees ** ML works OK in HOT/ALOHA, does not work in larger data sets ** how to incorporate differences in rate between gene fami...)
  N    17:55 Moore Notes 7 1 09 (diff; hist) . .  (+221) . . Katie Pollard (Talk | contribs) (New page: PI Call (KP and JG) * Bioinformatics ad * Discussion about authorship on SAR papers * JG NSF grant application (microbial communities in dirt on mountainsides) * Date for annual meetin...)
  N    17:55 Moore Notes 6 24 09 (diff; hist) . .  (+2,956) . . Katie Pollard (Talk | contribs) (New page: 1. Steve: would be useful to be able to root trees. Is there some outgroup that is included in the AMPHORA reference sequences? Is there some easy way we could get a single archaeal ge...)
  N    17:55 Moore Notes 6 22 09 (diff; hist) . .  (+546) . . Katie Pollard (Talk | contribs) (New page: PI Call * Bioinformatics support ** Dawei's group *** Can do long or short term *** Cost is fairly high *** Could hire a 50% "virtual person" *** Request tracking system *** But might n...)
  N    17:55 Moore Notes 6 17 09 (diff; hist) . .  (+3,854) . . Katie Pollard (Talk | contribs) (New page: Group call (Katie and Jonathan missing) (Sam taking notes) * Progress report due June 30; Jessica Green has started an outline on the OWW page. ** Everyone should put a paragraph (and ...)
  N    17:54 Moore Notes 6 10 09 (diff; hist) . .  (+392) . . Katie Pollard (Talk | contribs) (New page: PI Call * Budget ** Revised now ** Have not spent computing $ yet * Equipment / Computing ** Disk space ** Db servers for Oregon, Gladstone (~$5,000 each) * Bioinformatics support ** Mo...)
  N    17:53 Moore Notes 6 03 09 (diff; hist) . .  (+3,724) . . Katie Pollard (Talk | contribs) (New page: 1. iSEEM meeting to happen September 9-10 or 10-11. Jonathan e-mailing Kelly to see what dates she prefers. 2. Steve K. going to help set up a tracker for the future. 3. For future t...)
  N    17:53 Moore Notes 5 27 09 (diff; hist) . .  (+616) . . Katie Pollard (Talk | contribs) (New page: PI Call * Budget ** Gail's budget was wrong (missing roll-over from year 1) ** Moore needs amount invoiced before 12/31/08 at Gladstone ** funds transfer to Gladstone for Tom ** enough fo...)
  N    17:53 Moore Notes 5 13 09 (diff; hist) . .  (+1,907) . . Katie Pollard (Talk | contribs) (New page: Group Call * JE just got a budget from Gail ** PIs will follow up on this later ** Also need to talk about hiring * ASM ** JE and JG will be there ** Kelly will too ** OK to talk about o...)
  N    17:53 Moore Notes 4 29 09 (diff; hist) . .  (+1,748) . . Katie Pollard (Talk | contribs) (New page: Group Chat * Differences between diversity measures for different gene families and why ** [http://www.citeulike.org/group/6072/article/3361212 Knight paper] *** Why joining gene trees at...)
  N    17:52 Moore Notes 4 22 09 (diff; hist) . .  (+1,775) . . Katie Pollard (Talk | contribs) (New page: PI Call * JE has a meeting to do the budget ** modify budget? ** Gladstone/UO transfers ** We will talk again Friday 3pm * Wiki postings ** Sam's reorganization looks good ** UO group we...)
  N    17:52 Moore Notes 4 15 09 (diff; hist) . .  (+1,459) . . Katie Pollard (Talk | contribs) (New page: Group Call * Simulation stuff ** Need the "drop box" at UCD - temporary solution: Use UO machine ** Jess & Steve paper idea: effects of different components of the pipeline on measures *...)
  N    17:52 Moore Notes 4 8 09 (diff; hist) . .  (+748) . . Katie Pollard (Talk | contribs) (New page: PIs Only * James got a UK Bioinformatics fellowship starting in Jan 2010 * JE working on budget with Davis grants people * Grant with Kimmen S. * Albert Wu * Tom Sharpton ** novelty *...)
  N    17:51 Moore Notes 4 1 09 (diff; hist) . .  (+1,130) . . Katie Pollard (Talk | contribs) (New page: Group Call * Progress Report was due Monday (now Friday) ** OK if not much to add since annual report ** JE will start wiki page ** We should all add what we're up to (~ paragraph per pos...)
  N    17:51 Moore Notes 3 25 09 (diff; hist) . .  (+419) . . Katie Pollard (Talk | contribs) (New page: PI Call - KP and JE * Challenge Grants: maybe? * Tom Sharpton ** Population genetics ** Novelty (novel protein families in metagenomic data, rates, community phylogenetic profiling w/ en...)
  N    17:51 Moore Notes 3 18 09 (diff; hist) . .  (+2,537) . . Katie Pollard (Talk | contribs) (New page: Group call 18 March 09 (Sam taking notes) Steve, James, Jess B., Josh, and Sam were the only iSEEM folks around for the call. * Steve: Preliminary results ** At a workshop last weekend...)
  N    17:50 Moore Notes 3 6 09 (diff; hist) . .  (+184) . . Katie Pollard (Talk | contribs) (New page: PI Discussion about planning * objectives ** which ones need to be re-worked (if any) ** which ones need timing changed? * budget * CAMERA/software engineer * next quarterly report)
  N    17:50 Moore Notes 3 4 09 (diff; hist) . .  (+1,262) . . Katie Pollard (Talk | contribs) (New page: Group Conference Call * Data sharing ** genbeo (behind a firewall - need to sftp, a few terrabytes) ** put a note on the wiki with readme info ** include non-metagenomic datasets, maybe i...)
  N    17:50 Moore Notes 2 25 09 (diff; hist) . .  (+1,901) . . Katie Pollard (Talk | contribs) (New page: PI Conference Call * Report approved ** budget item breakdown needs to be modified possibly * postdoc candidate (Morgan Langille) visiting Eisen lab Thursday * Robin and Erick meeting *...)
  N    17:49 Moore Notes 2 18 09 (diff; hist) . .  (+2,017) . . Katie Pollard (Talk | contribs) (New page: Group Call * GBMF needs more detail on UCSF expenditures for annual budget * Eric Matson (Berkeley) and Robin Kodner (from Ginger Armbrust's Lab, UW) are visiting Eisen lab ** they are w...)
  N    17:49 Moore Notes 2 11 09 (diff; hist) . .  (+537) . . Katie Pollard (Talk | contribs) (New page: Conference Call: JG amd KP * James is close to having closed form solutions for predicting species area relationships/turnover under neutral theory ** Might do metagenomics analysis with ...)
  N    17:48 Moore Notes 2 4 09 (diff; hist) . .  (+1,381) . . Katie Pollard (Talk | contribs) (New page: Group Call (KP and JG away) *Here are some examples of the alignment and trees for the DeLong SSU rRNA, built with a variety of methods. *At this point we're hashing out mechanics and sq...)
  N    17:47 Moore Notes 1 28 09 (diff; hist) . .  (+591) . . Katie Pollard (Talk | contribs) (New page: PI Call * Scheduling meeting with Steven Brenner et al. * Hiring ** Tom Sharpton met with JE *** has lots of genomics experience *** Thinking about projects *** Will meet with KP and JE...)
  N    17:47 Moore Notes 1 21 09 (diff; hist) . .  (+1,057) . . Katie Pollard (Talk | contribs) (New page: Group Call 1/21/09 * Annual Report ** Kelly sent a template (simpler if we don't use it - will if there is time) ** Be sure to include: *** Any collaborations with people outside project...)
  N    17:47 Moore Notes 1 14 09 (diff; hist) . .  (+1,009) . . Katie Pollard (Talk | contribs) (New page: PIs only: skype chat * JE & KP will try again to chat with Pierre Z. * JE will talk to Tom Sharpton at Davis next week * Postdocs will meet in person ~1x per month ** Eisen & Pollard la...)
  N    17:46 Moore Notes 1 7 09 (diff; hist) . .  (+1,767) . . Katie Pollard (Talk | contribs) (New page: Group Conference Call (skype) * UCD Cluster ** send logins to JE to send to Mike Lewis ** how should people do analyses (cluster, Eisen lab linux machine bobcat) * Srijak is working on d...)

16 August 2017

  N    18:32 Moore Notes 2009 (diff; hist) . .  (+2,278) . . Katie Pollard (Talk | contribs) (New page: {{ISEEM}} <div style="width: 750px;padding-right: 25px; padding-left: 25px;font-family: Arial, Helvetica, sans-serif;font-size: 12px;margin-bottom: 30px;line-height: 18px;padding-top: 0px...)
  N    18:32 Moore Notes 12 15 10 (diff; hist) . .  (+2,563) . . Katie Pollard (Talk | contribs) (New page: Group Call * Call logistics ** Will use all calls for research topics ** Announce to the group if you want to lead a discussion on a particular project ** PIs will grab the time slot if n...)
  N    18:31 Moore Notes 12 10 10 (diff; hist) . .  (+391) . . Katie Pollard (Talk | contribs) (New page: PI Call * niche mapping update ** issue with sediment samples ** James is looking at some theory using predicted locations * plan for going forward with calls ** new phase: specific proj...)
  N    18:31 Moore Notes 12 1 10 (diff; hist) . .  (+3,075) . . Katie Pollard (Talk | contribs) (New page: Group Call * PhylOTU paper accepted at PLoS Comp Bio ** Tom is handling proofs * Protein Db/AMPHORA 2 ** Guillaume is parsing results ** Pipeline is fairly stable *** Testing on GOS data...)
  N    18:30 Moore Notes 11 24 10 (diff; hist) . .  (+1,632) . . Katie Pollard (Talk | contribs) (New page: Group Call * Niche mapping ** Error checking *** Minor code errors (indices off by one, etc) found by Guillaume *** MICROBIS meta-data file errors found by Tom ** Comparing 1/2 degree sc...)
  N    18:29 Moore Notes 11 17 10 PI (diff; hist) . .  (+2,921) . . Katie Pollard (Talk | contribs) (New page: Group Call * PhylOTU manuscript is resubmitted * Niche mapping figures ** Range maps are really just for abundant organisms ** Hard limit of occurring at 10...)
  N    18:29 Moore Notes 11 10 10 PI (diff; hist) . .  (+224) . . Katie Pollard (Talk | contribs) (New page: PI Call * Niche mapping paper ** authorship issues ** JG can mentor/work with Josh on background and story * GBMF RFIs ** JG is on JEs Bodega Bay proposal ** JG is on review committee *...)
  N    18:29 Moore Notes 11 3 10 PI (diff; hist) . .  (+1,027) . . Katie Pollard (Talk | contribs) (New page: PI Call - regarding GBMF RFI * JE is working on data proposal about microbes on marine algae ** eel grass: only marine plant ** kelp as comparison ** wants one experimental system for lab...)
  N    18:28 Moore Notes 11 3 10 (diff; hist) . .  (+3,160) . . Katie Pollard (Talk | contribs) (New page: Group Call * GBMF request for information http://www.moore.org/mmi-rfi.aspx ** think tank approach, new collaborations will be made later in process ** separate, linked proposals * HOT/A...)
  N    18:28 Moore Notes 10 20 10 (diff; hist) . .  (+2,135) . . Katie Pollard (Talk | contribs) (New page: Group Call * Steve: PLoS paper has been in review for 2 months - should hear soon. * Morgan: Gerstein lab paper uses ARCGIS data - might be useful for niche mapping * PhylOTU revision *...)
  N    18:27 Moore Notes 10 6 10 (diff; hist) . .  (+4,365) . . Katie Pollard (Talk | contribs) (New page: Group Call * MaxEnt Niche Mapping Project (Josh leading discussion) General idea is to model the distribution of microbial species. We do this via MaxEnt by taking correlates of taxon pr...)
  N    18:27 Moore Notes 10 5 10 (diff; hist) . .  (+1,486) . . Katie Pollard (Talk | contribs) (New page: PI Call * Progress Report * PhylOTU paper ** Excellent reviews ** Strategy: do some new analyses, but not necessarily everything Reviewer #2 requested ** Editor will be reasonable * Dis...)
  N    18:27 Moore Notes 9 22 10 (diff; hist) . .  (+1,983) . . Katie Pollard (Talk | contribs) (New page: Group Call *No PIs on this call, by chance. ** Katie called in periodically from a poor internet connection. ** Jessica in surgery ** Jonathan teaching * Quarterly Progress Report: due O...)
  N    18:26 Moore Notes 9 8 10 (diff; hist) . .  (+2,847) . . Katie Pollard (Talk | contribs) (New page: Group Call * Quarterly report due Oct 8 ** JE should make a template * Projects using GOS data ** Steve *** Assign reads to AMPHORA gene families with HMMR/AMPHORA *** Build phylogenies ...)
  N    18:26 Moore Notes 9 1 10 (diff; hist) . .  (+2,055) . . Katie Pollard (Talk | contribs) (New page: Group Call * ISME ** Tom's notes: http://friendfeed.com/isme13 ** Josh's observations *** Neutral theory for microbial soil communities with species abundance distributions (M. Vos talk)...)
  N    18:26 Moore Notes 8 25 10 (diff; hist) . .  (+1,555) . . Katie Pollard (Talk | contribs) (New page: Group Call * Introduce Rebecca Lamb * ISME meeting ** Kelly's event ** Meeting with Kelly on Friday ** Tom's notes: http://friendfeed.com/isme13 * CAMERA 2.0 ** JE is testing workflows,...)
  N    18:25 Moore Notes 8 18 10 (diff; hist) . .  (+1,063) . . Katie Pollard (Talk | contribs) (New page: PI Call * Follow up with Kelly - JE will email * Cal Academy ** California microbial diversity ** JE talking to them about curator of microbial diversity position * Planning for Future ...)
  N    18:25 Moore Notes 8 11 10 (diff; hist) . .  (+2,447) . . Katie Pollard (Talk | contribs) (New page: Group Call * No-cost extension ** Until the end of June 2011 ** Outcomes due then ** Most labs will be spent down prior to that ** JG will sub-award some money to James at SFI * Future ...)
  N    18:25 Moore Notes 8 4 10 (diff; hist) . .  (+892) . . Katie Pollard (Talk | contribs) (New page: PI Call: JG & KP * Global Viral Forecasting Initiative ** JG had meeting in SF with Nathan Wolfe (met at TED) ** KP knows Joseph Fair (director of global field operations) * No-cost ext...)
  N    18:24 Moore Notes 7 28 10 (diff; hist) . .  (+2,655) . . Katie Pollard (Talk | contribs) (New page: Group Call * Kelly visiting UCD today * Steve's PLoS Bio paper ** JG made major edits *** streamlining to remove repeated ideas ** SK working on it this afternoon, close to submitting **...)
  N    18:24 Moore Notes 7 21 10 (diff; hist) . .  (+4,666) . . Katie Pollard (Talk | contribs) (New page: == General business == * Jess attendied Moore Foundation senior invetigator meeting - theme was metatranscriptomics. Lots of interest in whether iSEEM has made progress on building phyloge...)
  N    18:23 Moore Notes 7 14 10 (diff; hist) . .  (+702) . . Katie Pollard (Talk | contribs) (New page: PHYLOTU group call: Pollard lab, James, Steve * Name: PhylOTU? PhyloTU? PHYLOTU? * Tom will send submit version before sending in * Richness underestimation issue ** PID vs. PD distance...)
  N    18:23 Moore Notes 7 7 10 (diff; hist) . .  (+1,151) . . Katie Pollard (Talk | contribs) (New page: Group Call * Audio files from Eugene, OR * Progress Report ** Eisen lab wrapping up their parts * Funding ** Josh summary of discussion at Eugene Meeting ** Foreign people (not OK for ...)
  N    18:23 Moore Notes 7 2 10 (diff; hist) . .  (+545) . . Katie Pollard (Talk | contribs) (New page: PI Call * Progress report http://iseem.private.openwetware.org/wiki/ISEEM_Progress_June_2010 ** Finish project updates, other sections ** JE will submit next week * JG talk with Kelly **...)
  N    18:22 Moore Notes 6 17 10 (diff; hist) . .  (+815) . . Katie Pollard (Talk | contribs) (New page: Group Call * Planning for Eugene meeting http://iseem.private.openwetware.org/wiki/Jun10_Annual_Schedule ** Every one will sign up for sessions today * Proposal for future work http://i...)
  N    18:22 Moore Notes 6 9 10 (diff; hist) . .  (+585) . . Katie Pollard (Talk | contribs) (New page: PI Call * No-cost extension ** Davis will forward estimated remaining balances to Moore ** Range of extension periods *** MW has 7 months *** JG has 5 months *** KP has <1 month *** JE h...)
  N    17:00 Moore Notes 6 2 10 (diff; hist) . .  (+1,947) . . Katie Pollard (Talk | contribs) (New page: Group Call * June meeting plans ** getting room with projector etc ** audio recording - laptop ** chalk or dry erase board (take photos) ** head count: 4 UCSF, 2 UVA, 4? UCD ** copy forma...)
  N    16:59 Moore Notes 5 19 10 (diff; hist) . .  (+1,598) . . Katie Pollard (Talk | contribs) (New page: Group Call * June meeting: ** fly in Weds evening June 23 ** start Weds morning June 24 ** finish by 4pm June 25 * Katie: Report on Cold Spring Harbor Biology of Genomes meeting ** Meta...)
  N    16:58 Moore Notes 5 5 10 (diff; hist) . .  (+2,036) . . Katie Pollard (Talk | contribs) (New page: Group Call * No-cost extension ** KP: email Gail/Lauren to get estimates ** JE: UCD Chancellor is working on admin efficacy * CAMERA ** JE: Elke (Kepler project lead at UCSD) wants to t...)
  N    16:58 Moore Notes 4 27 10 (diff; hist) . .  (+2,207) . . Katie Pollard (Talk | contribs) (New page: OTU Project Group Call * Update from Tom: Slides ** OTU pipeline ** Simulation process (two types, one with reads that run off the end of the gene) **...)
  N    16:57 Moore Notes 4 21 10 (diff; hist) . .  (+3,484) . . Katie Pollard (Talk | contribs) (New page: Group Call * Update from Sam **Sam has been selected to give a talk at the Cold Spring Harbor Biology of Genomes Meeting. If people have time to provide feedback in the next two weeks, sh...)
  N    16:57 Moore Notes 4 14 10 (diff; hist) . .  (+2,262) . . Katie Pollard (Talk | contribs) (New page: PI Call * No-cost extension ** UCD burn-rate: still working on it ** UCD financial department wants to put in the official extension request ** They sent Kelly updated financials (through...)
  N    16:56 Moore Notes 4 7 10 (diff; hist) . .  (+3,648) . . Katie Pollard (Talk | contribs) (New page: Group Call * Steve will check with PLoS about our paper * Update from Steve ** GOS analysis *** Guillaume and Dongying produced new marker gene families for GOS **** Now have good archae...)
  N    16:56 Moore Notes 3 31 10 (diff; hist) . .  (+1,578) . . Katie Pollard (Talk | contribs) (New page: PI Call * Problems with skype * New weekly mtg time: proposed new time is Weds 11-12 * Quarterly report ** submitted ** UCD working on financials * No-cost extension/budget ** How much...)
  N    16:55 Moore Notes 3 23 10 (diff; hist) . .  (+2,094) . . Katie Pollard (Talk | contribs) (New page: Group Call * Quarterly report (due end of March) ** a few bullet-points each, not more than 1 paragraph ** what have you done in March? (since annual report) ** post to wiki by Friday * ...)
  N    16:54 Moore Notes 3 16 10 (diff; hist) . .  (+1,231) . . Katie Pollard (Talk | contribs) (New page: PI Call * Davis cluster problems ** issues *** sys admin problems *** people can overload *** complicated prioritization ** Jonathan will talk to Mike Lewis * Kelly will visit UCSF on Ap...)
  N    16:54 Moore Notes 3 9 10 (diff; hist) . .  (+1,159) . . Katie Pollard (Talk | contribs) (New page: Group Call * Steve: Did we track down the GOS PCR 16S data (Shaw et al)? * Steve: Is ZORRO available for masking Guillaume's alignments? * Every one should check that they are correctl...)
  N    16:54 Moore Notes 3 2 10 (diff; hist) . .  (+1,524) . . Katie Pollard (Talk | contribs) (New page: PI Call * Annual report ** JE doing final edits ** additional info section needs polishing ** JE will ask Kelly if we can submit on 3/3 * Kelly visiting UO on Thursday * Budget issues *...)
  N    16:53 Moore Notes 2 16 10 (diff; hist) . .  (+2,779) . . Katie Pollard (Talk | contribs) (New page: Group Call * OTU pipeline * Annual Report * Update wiki, e.g. papers in progress '''DESTINATION MANUSCRIPT on OTU pipeline: TOM'S DISCUSSION''' Workflow has been completely packaged....)
  N    16:50 Moore Notes 2 2 10 (diff; hist) . .  (+6,104) . . Katie Pollard (Talk | contribs) (New page: Group Call * Reports ** Quarterly OK? *** Not sure yet ** Annual due in 1 month *** Template added to wiki by Katie http://iseem.private.openwetware.org/wiki/Main_Page#Progress_Reports *...)
  N    16:49 Moore Notes 1 26 10 (diff; hist) . .  (+831) . . Katie Pollard (Talk | contribs) (New page: PI call (KP, JG) * Steve's paper ** feedback on cover letter ** submit this week * Josh's paper ** Figures need work ** JG will work on intro/discussion etc. ** Giving talk at Gladstone...)
  N    16:49 Moore Notes 1 19 10 (diff; hist) . .  (+2,946) . . Katie Pollard (Talk | contribs) (New page: Group Call: Steve, Tom, Morgan, Guillaume, Katie, Sam, Josh * Reports ** Quarterly report - does Jonathan need anything from group? ** Annual report due end of Feb * How to use conferenc...)
  N    16:49 Moore Notes 1 15 10 (diff; hist) . .  (+1,640) . . Katie Pollard (Talk | contribs) (New page: OTU group call: JG, SK, KP, TS, SR, JL * Mitch Sogin manuscript ** JG: looks at three attributes that affect OTU estimation *** PCR/seq error, *** multiple seq alignment (overestimates)...)
  N    16:48 Moore Notes 1 12 10 (diff; hist) . .  (+2,388) . . Katie Pollard (Talk | contribs) (New page: PI Call: MW, JG, JE, and KP * JG: Bill Cresko review - any metagenomics for conservation ecology? * Revising grant activities ** 1.2d: Rephrase along lines of Tom's comments ** 1.3: Refe...)
  N    16:48 Moore Notes 2010 (diff; hist) . .  (+1,838) . . Katie Pollard (Talk | contribs) (New page: = 2010 Conference Call Notes = * Notes 1_12_10 * Notes 1_15_10 * Notes 1_19_10 * [[Moore_Notes_1_26_10 | Not...)

15 August 2017

       23:18 Qin (diff; hist) . .  (-31) . . Zhenpeng Qin (Talk | contribs)

14 August 2017

       07:36 Forster Lab (diff; hist) . .  (+220) . . Anthony C. Forster (Talk | contribs) (The Boss!?: )
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