User contributions for Katie Pollard
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22 August 2017
- 14:5614:56, 22 August 2017 diff hist +3,416 N Moore Authorship Model proposal New page: '''UPDATES''' 1. We agreed it would be a good idea to circulate draft outlines to the group to invite people that want to contribute to the level of an author as discussed below. 2. Dr... current
- 14:5614:56, 22 August 2017 diff hist +1,970 N Moore JobAd3 Job Ad New page: A bioinformatics engineer position is available on a microbial metagenomics project called iSEEM (http://openwetware.org/wiki/ISEEM) under the direction of Jonathan A. Eisen (UC Davis) ... current
- 14:5614:56, 22 August 2017 diff hist +2,945 N Moore JobAd2 Job Ad New page: {{ISEEM}} Postdoctoral Positions in Metagenomic Informatics Microbes play fundamental roles in all biology-associated processes on the planet. A powerful new tool in such studies is meta... current
- 14:5514:55, 22 August 2017 diff hist +2,615 N Moore JobAd Job Ad New page: {{ISEEM}} '''Postdoctoral Positions in Metagenomic Informatics''' Microbes play fundamental roles in all biology associated processes on the planet. A powerful new tool in such studies ... current
- 14:5514:55, 22 August 2017 diff hist +1,266 N Notes 11-14-08 New page: {{ISEEM}} Josh, Sam, Dennis, Katie: entropy-based alpha diversity statistics * Set-up ** start with one site ** data=abundances of all observed species ** tree=subtree with these species... current
- 14:5514:55, 22 August 2017 diff hist +105 N Moore PollardLabNotes New page: {{ISEEM}} This is a place for notes on iSEEM projects in the Pollard lab. 11-14-08 current
- 14:5414:54, 22 August 2017 diff hist +993 N Moore GreenLabNotesMay-11-09 New page: ===Kunin et al. 2008 continued=== ==Binning== 1. Marker gene analyses is AMPHORA 2. Evolutionary distance methods - like neighbor joining. Most phylogenetic tree building methods req... current
- 14:5414:54, 22 August 2017 diff hist +2,849 N Moore GreenLabNotes1-28-09 New page: ===Schloss&Handelsman 2008=== ==Green== 1. Page 2 - "it is not possible to close a metagenome" - meaning what don't have the technical capacity to do this now? 2. Page 2 - what is th... current
- 14:5414:54, 22 August 2017 diff hist +559 N Moore GreenLabNotes1-21-09 New page: Group meeting (Jess, Steve + James): 1. Went through PhyloPipeline 2. Discussion: AMPHORA assumes that phylogenies will be the same if built for gene 1, gene 2, etc. This is because the... current
- 14:5314:53, 22 August 2017 diff hist +574 N Moore GreenLabNotes1-20-09 New page: Steve K.: 1. GOS data set analysis. Srijak is running that on GOS, should be done in 2 weeks. 2. Super concatination. In AMPHORA paper, in tree show, that was based on this technique. Us... current
- 14:5314:53, 22 August 2017 diff hist +556 N Moore GreenLabNotes1-14-09 New page: = Organization of research online = Steve will likely keep lab notebook on iseem page, Jess B. and James will focus on project pages for now. = Simulations update = Sam's simulations desi... current
- 14:5314:53, 22 August 2017 diff hist +1,503 N Moore GreenLabNotesJan-27-09 New page: == January 27 2009 meeting == Jess Green, Jess Bryant, James O'Dwyer, Steven Kembel == Short term goals == Steve's short term goals * develop/modify existing methods/code to measure phy... current
- 14:5314:53, 22 August 2017 diff hist +587 N Moore GreenLabNotesDec-9-08 New page: == Discussion of Huse et al. and Dethlefsen et al. 2008 tag pyrosequencing papers == 0. We are going to put together a roadmap for metagenomic research (to connect what people are doing)... current
- 14:5214:52, 22 August 2017 diff hist +919 N Moore GreenLabNotesNov-26-08 New page: == Chivian et al. Science 2008 == Jess questions: 1. What does it mean to assemble a genome using both shotgun Sanger and 454 pyrosequencing? *did each genomic library use a differ... current
- 14:5214:52, 22 August 2017 diff hist +1,473 N Moore GreenLabNotesNov-21-08 New page: {{ISEEM}} mtg notes 1. James will order new Mac Pro through Greg Soderstadt 2. Postpone reading Chivian et al paper 3. Steve will email OWW about deleting `members only' pages of the n... current
- 14:5214:52, 22 August 2017 diff hist +661 N Moore GreenLabNotesNov-14-08 New page: {{ISEEM}} == November 14 2008 == 1. Steve ordered MacPro and has started working with Amphora 2. Next week we will start talking about Kepler flow diagram, what types of data we need.... current
- 14:5114:51, 22 August 2017 diff hist +1,144 N Moore GreenLabNotesNov-7-08 New page: {{ISEEM}} == November 7 2008 == *James, Jess, Steve will meet weekly on Fridays from now on **Meetings will be a mixture of progress reports, brainstorming/analysis, and working together... current
- 14:5114:51, 22 August 2017 diff hist +3,819 N Moore GreenLabNotesSept-3-08 New page: 9.3.08 Conversation with Katie, Jonathan, James and Liz about Arrowhead project 1. Primary concern about using the GDD curve to infer eco-evo processes is that, even if we have a theor... current
- 14:5114:51, 22 August 2017 diff hist 0 N File:Vamosi 2008 chart.png No edit summary current
- 14:5114:51, 22 August 2017 diff hist 0 N File:JbReview.png No edit summary current
- 14:5014:50, 22 August 2017 diff hist +470 N Phylogenetic diversity metric review New page: This is an overview of alpha and beta phylogenetic diversity metrics. I only included metrics that quantify diversity using genetic distances or branch lengths. This excludes things like M... current
- 14:5014:50, 22 August 2017 diff hist +788 N Moore GreenLabNotes New page: {{ISEEM}} = Notes from Green lab iSEEM discussions = Phylogenetic diversity metric review [[Moore_GreenLabNotesSept-3-08|September 3 2008 note... current
- 14:5014:50, 22 August 2017 diff hist +190 N Moore EisenNotes Eisen Notes New page: Some papers to look at [http://www.ncbi.nlm.nih.gov/pubmed/15212376?ordinalpos=8&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum AP Martin on Cladogenesis in Microbe... current
- 14:4914:49, 22 August 2017 diff hist +75 N Moore PollardLabNotes iseem2 New page: {{ISEEM}} This is a place for notes on iSEEM2 projects in the Pollard lab. current
- 14:4914:49, 22 August 2017 diff hist +2,922 N Moore EisenNotes Eisen Notes iseem2 New page: {{ISEEM}} =Eisen lab Notes= == Metagenomic sample gathering == Places to look for metagenomic samples *Short Read Archive **134 marine samples. Appears to include GOS data. Has meta data... current
- 14:4914:49, 22 August 2017 diff hist 0 N File:ISEEM-report2.pdf No edit summary current
- 14:4914:49, 22 August 2017 diff hist 0 File:ISEEM-report1.pdf uploaded a new version of "Image:ISEEM-report1.pdf" current
- 14:4914:49, 22 August 2017 diff hist 0 N File:3300-NarrativeReport-Jun14.pdf No edit summary current
- 14:4814:48, 22 August 2017 diff hist +620 N Software2015 New page: Software made available publicly: * Shotmap: https://github.com/sharpton/shotmap * MRC: https://github.com/sharpton/MRC * SFam Updater: https://github.com/gjospin/Sfam_updater * Simulatio... current
- 14:4714:47, 22 August 2017 diff hist 0 N File:Unifrac cluster.png No edit summary current
- 14:4714:47, 22 August 2017 diff hist 0 N File:Skin Proteobacteria.png No edit summary current
- 14:4714:47, 22 August 2017 diff hist 0 N File:Skin Firmicutes.png No edit summary current
- 14:4714:47, 22 August 2017 diff hist 0 N File:Skin Actinobacteria.png No edit summary current
- 14:4714:47, 22 August 2017 diff hist 0 N File:Rankabundance TAR.png No edit summary current
- 14:4714:47, 22 August 2017 diff hist 0 File:Poweredby mediawiki 88x31.png uploaded a new version of "Image:Poweredby mediawiki 88x31.png" current
- 14:4714:47, 22 August 2017 diff hist 0 File:Picture 6.png uploaded a new version of "Image:Picture 6.png" current
- 14:4714:47, 22 August 2017 diff hist 0 File:PhotoRC Zonation.png uploaded a new version of "Image:PhotoRC Zonation.png" current
- 14:4614:46, 22 August 2017 diff hist 0 N File:Otu01 tree copynumber.png No edit summary current
- 14:4614:46, 22 August 2017 diff hist 0 File:OTU Workflow.png uploaded a new version of "Image:OTU Workflow.png" current
- 14:4614:46, 22 August 2017 diff hist 0 N File:Mucilage-Soil family abundance.png No edit summary current
- 14:4614:46, 22 August 2017 diff hist 0 File:Hotaloha-taxophylo.png uploaded a new version of "Image:Hotaloha-taxophylo.png" current
- 14:4614:46, 22 August 2017 diff hist 0 N File:Gut coherence data.png No edit summary current
- 14:4614:46, 22 August 2017 diff hist 0 N File:Four Coherence Patterns.png No edit summary current
- 14:4614:46, 22 August 2017 diff hist 0 N File:FigTopoError crop.png No edit summary current
- 14:4614:46, 22 August 2017 diff hist 0 N File:FigMetaPASSAGE.png No edit summary current
- 14:4614:46, 22 August 2017 diff hist 0 N File:FigDistortion crop.png No edit summary current
- 14:4614:46, 22 August 2017 diff hist 0 File:ClassificationWorkflow.png uploaded a new version of "Image:ClassificationWorkflow.png" current
- 14:4514:45, 22 August 2017 diff hist 0 N File:1000px-PhylOTU GOS.jpg No edit summary current
- 14:4514:45, 22 August 2017 diff hist 0 N File:1000px-Invasionrandomfissionv3.jpg No edit summary current
- 14:4514:45, 22 August 2017 diff hist 0 N File:1000px-Abundance adjusted.png No edit summary current