Day 2. Beginning.
Since I was leaving that PM I could not borrow a hotel bike and bike over again. So I walked from the hotel, along the river 2 or so miles, after getting coffee. I got to the meeting a bit late and thus missed much of the opening Keynote, which was a bummer since it seemed very good. But I find if I do not get some exercise every day at a meeting I go crazy so it was worth it. Here are some notes on Day 2.
Day 2. Part 1. Keynote
Alas, I missed much of the keynote. But what I caught was good. Here are some notes, mostly from twitter. And also see Rob G's slides below
Rob Guralnick: Biodiversity Discovery and Documentation in the Information and Attention Age
- rdmpage Convention Center resembles a ghost town as #evol2010 has left town, but day 2 of #ievobio is about to kick off...
- rdmpage #ievobio kicks off with keynote by @robgural
- rdmpage "Biodiversity Discovery and Documentation in the Information and Attention Age" @robgural #ievobio
- rdmpage Linnean shortfall (too few taxonomists and antiquated and laborious process) #ievobio
- rdmpage Wallacean shortfall (very coarse reosluton, scattered data, no integration) #ievobio
- rdmpage Darwinian shortfall (trees scattered in literature, no "mother of all trees") #ievobio
- rdmpage Darwinian shortfallª @robgural #ievobio
- rdmpage Discovery and documentation of new species are closely coupled #ievobio
- rdmpage Linnaean taxonomy easier than phylogeny to deal with as an ontology #ievobio
- rdmpage Key step is decoupling discovery and documentation @robgural #ievobio
- cydparr @robgur Use web as collaborative platform to publish knowledge as soon as it is generated. He knows he's preaching to the converted #ievobio
- phylogenomics Always good to show up for talk and discover speaker wearing #PLoS shirt #ievobio
- rdmpage GenSent "...near real-time monitoring of evolutionary trends in biological systems" http://code.google.com/p/gensent/ @robgural #ievobio
- rdmpage GeoPhylo Engine http://geophylo.appspot.com/ @robgural#ievobio
- rdmpage Ultimate goal should be ever-growing "mother of all trees" to wich we attach new twigs as we discover them @robgural#ievobio
- rdmpage "Map of Life:An infrastructure for integrating global species distribution knowledge" @robgural #ievobio
- rdmpage Data publishing and "sahring" is as important as academic "kudos" @robgural #ievobio
- rdmpage Let's change model of credit @robgural #ievobio#datacitation
- robgural My first SlideShare upload : RPG #ievobio 2010 Keynote http://slidesha.re/8X6u3L
- Todd Vision: The Dryad Digital Repository: Published evolutionary data as part of the greater data ecosystem.
- NOTE - In my opinion, efforts like Dryad are one of the most important things in open science ...
- toranaga Todd makes a great point about how data has been left behind in the history of publishing in part because of print publishing #ievobio
- phylogenomics Todd Vision discussing uneven release/reporting of data behind evolution studies (w/ exception of sequences which do get released) #ievobio
- phylogenomicsVision - marginal costs of data archiving related to papers are small compared to cost of papers themselves #ievobio
- rdmpage Todd Vision talking about @datadryad #ievobio
- rdmpage Wicherts 2006 is http://dx.doi.org/10.1037/0003-066X.61.7.726 PDF here http://wicherts.socsci.uva.nl/datasharing.pdf #ievobio
- rdmpage GenBank data submission model works, not clear any other model works - voluntary submission #fail #ievobio
- rdmpage Todd Vision shoutout to @systbiol for good data sharing record #ievobio
- rdmpage American Naturalist requires data archiving http://dx.doi.org/10.1086/650340 #ievobio
- rdmpage Archiving solutions: author-managed, specialised database, supplementary material, or shared public archive @datadryad#ievobio
- Long term funding of databases is big problem, e.g. http://dx.doi.org/10.1038/462258b #ievobio
- See http://datadryad.org/ #ievobio
- rdmpage Long term funding of databases is big problem, e.g. http://is.gd/dacce #ievobio
- Rutger Vos: TreeBASE2: Rise of the Machines
- TreeBASE2: Rise of the Machines
View more presentations from Rutger Vos. - rdmpage Next up, @rvosa talking about http://www.treebase.org #ievobio
- rdmpage TreeBASE supports embargoed data while paper uder review @rvosa #ievobio
- toranaga Rutger Vos discussing TreeBase: http://bit.ly/9PxIinat #ievobio
- phylogenomics Next up Rutger Vos @rvosa on the hip new model for TreeBase http://treebase.org #ievobio
- rdmpage TreeBASE has permanent URLs, data can be serialised in various formats @rvosa #ievobio
- rdmpage TreeBASE supports CQL queries #ievobio
- rdmpage TreeBASE supports PhyloWS resource URIs #ievobio
- toranaga PhyloWS is everywhere at #ievobio Here's more info on it: http://bit.ly/cOjb6Q
- rdmpage TreeBASE has permanent URLs, data can be serialised in various formats @rvosa #ievobio
- toranaga Ok, twitter, you get one chance to guess who is wearing the "what would jesus sequence?" t-shirt at #ievobio.
- toranaga PhyloWS is everywhere at #ievobio Here's more info on it: http://bit.ly/cOjb6Q
- cydparr Vos: Machine interface to TreeBASE sounds like it is shaping up nicely<-- I'm hoping for better human interfaces too #ievobio
- phylogenomics Treebase going to integrate more with external services like connoteae citeulike uniprot etc#ievobio @rvosa
- rdmpage TreeBASE to Uniprot via http://pipes.yahoo.com/pipes/ @rvosa #ievobio
- rdmpage Scary that my gla:mapping LSID vocabulary is still in use at uBio :O @rvosa #ievobio
- rdmpage TreeBASE to Uniprot via http://pipes.yahoo.com/pipes/ @rvosa #ievobio
- phylogenomics Treebase going to integrate more with external services like connoteae citeulike uniprot etc#ievobio @rvosa
- rdmpage TreeBASE supports embargoed data while paper uder review @rvosa #ievobio
- rvosa #ievobio TreeBASE2 talk slides:http://www.slideshare.net/rvosa/treebase2-rise-of-the-machines
- Nico Franz: Biological taxonomy and ontology development: scope and limitations
- rdmpage The ontology of biological taxa http://dx.doi.org/10.1093/bioinformatics/btn158 #ievobio
- rdmpage Nico Franz on taxonomy and ontology #ievobio
- rdmpage Ontologies struggle with dynamic classifications #ievobio
- rdmpage Phenotypic terms are taxonomically underdetermined #ievobio
- rdmpage Abstract of Nico Franz's talk at http://hdl.handle.net/10101/npre.2010.4593.1 #ievobio
- phylogenomics One major challenge in a taxonomical ontology is aligning taxonomies to compare them #ievobio
- pmidford Nico Franz got the question I was expecting from Felsenstein #ievobio
- Rod Page: Phyloinformatics in the age of Wikipedia
- Phyloinformatics in the age of Wikipedia
View more presentations from Roderic Page. - rvosa Typo fix: RT @phylogenomics: Next up @rdmpagetalking about phyloinformatics in the age of wikipedia#ievobio
- cydparr Page: Biodiversity informatics does a lousy job with citations. It is like the web doesn't exist #ievobio
- phylogenomics Next up @rdmpage talking about phyloinformatics in the age of wikipedia #ievobio
- phylogenomics Page: giving props to wikigene database as a good way to use wikipedia to distribute biological information#ievobio
- robgural #ievobio Rod Page argues wikipedia could be our encyclopedia of life.
- phylogenomics Page @rdmpage says that searches of web for species names almost always pull up wikipedia entries as best hits #ievobio
- phylogenomics Page @rdmpage refs to IBM history flow system to track edits of wikipedia pages #ievobio
- cydparr Reversion wars over Physeter catadon and P. macrocephalus -- language not suitable for broadcast @rdmpage #ievobio
- phylogenomics Love how iPad editor edits @rdmpage to @rampage - consistent w/ Rod Page's entertaining rampaging efforts do Taxonomy on web #ievobio
- toranaga Best moment of #ievobio so far: @rdmpage posts a wikipedia user annotation log between two members (profanely) arguing about taxonomy
- phylogenomics See http://iphylo.org for @rdmpage efforts on mapping taxonomy to wikipedia and related actions#ievobio
- phylogenomics "I love wikipedia but wikipedia doesn't love me" says @rdmpage re: difficulty in getting wikipedia to link back to NCBI etc #ievobio
- cydparr @rdmpage Using semantic mediawiki to map NCBI id's to Wikipedia pages. Can't do it the other way because of wikinazis #ievobio
- pzmyers That stuff matters! RT @phylogenomics: Best moment of #ievobio: @rdmpage posts wiki usr log btween 2 membrs (profanely) arguing abt taxonomy
- toranaga @rdmpage cool talk. Do you think SEO methods should be adopted by various taxonomy sites to improve search engine relevance? #ievobio
- justsayinnn Rod Page's talk at #ievobio was fucking fantastic!
- ncellinese Best Xrated talk ever from @rdmpagehttp://ff.im/n5u0N #ievobio
- Dan Rosauer: Mapping phylogeography easily with Biodiverse
- Biodiverse - Rosauer talk @ iEvoBio conference June 2010
View more presentations from DanRosauer. - toranaga Next up at #ievobio is Dan Rosauer discussing Biodiverse
- robgural #ievobio Dan Rosauer presents on biodiverse; cool tool!
- rdmpage Next up (safe for family viewing) Biodiverse http://code.google.com/p/biodiverse/ #ievobio
- toranaga Biodiverse maps distribution of species (phylogeography), richness, turnover, phylogenetic diversity, etc. #ievobio
- robgural #ievobio Dan Rosaeur's Biodiverse: great visualization tools for linking space and phylogeny!
- rdmpage Nice distribution brushing effects in Biodiverse - mouse over tree see distribution #ievobio
- cydparr Rosauer: Biodiverse has nice interaction between map grid square, richness of those species in other cells, phylogenetic placement #ievobio
- phylogenomics Biodiverse can be used to look at phylogenetic diversity and endemism too #ievobio #nice
- phylogenomics Glad to see Wayne & David Maddison at#ievobio -they were TAs for Gould class I took that that got me into phylogeny; they demoed MacClade
- rdmpage Shoutout for Densitree http://www.cs.auckland.ac.nz/~remco/DensiTree/DensiTree.html #ievobio
- robgural: #ievobio Densitree (http://www.ncbi.nlm.nih.gov/pubmed/20228129) --- very cool.
- Jim_Croft @robgural: #ievobio Dan Rosauer presents on biodiverse; cool tool!Ó<< go Dan!
- Mark Holder
- toranaga Next up is Mark Holder discussing a biopython package to conduct phylogenetic operations (DendroPy)#ievobio
- rdmpage Arm waving (and possibly NSTW stuff) to come#ievobio
- phylogenomics Next up Mark Holder on DendroPy http://packages.python.org/DendroPy/ - a python library for phylogenetic operations #ievobio
- rdmpage beagle-lib http://code.google.com/p/beagle-lib/#ievobio
- tjvision DendroPy plans to support RDFa #ievobio
- robgural Holder shoutout to ETE: a python Environment for Tree Exploration - http://www.biomedcentral.com/1471-2105/11/24 #ievobio
- robgural #ievobio Holder shout out to NESCent! Agree!
- Tandy Warnow: SATe-II: co-estimation of trees and alignments
- phylogenomics Next up Tandy Warnow on SATe-II for coestimation of trees and alignments #ievobio
- rdmpage Tandy Warnow on SATe-II #ievobio
- phylogenomics Warnow : See http://phylo.bio.ku.edu/software/sate/sate.html for software#ievobio
- rdmpage "4 Gb machines, nothing special" Tandy Warnow (did most of my PhD with 64K RAM) #ievobio
- Ryan Gutenkunst: Diffusion Approximations for Demographic Inference: DaDi
- rdmpage Last 15 min talk for the day by http://cnls.lanl.gov/~ryang/ #ievobio (lightning talks follow lunch)
- phylogenomics Next up Ryan Gutenkunst on diffusion methods for demographic infernence DaDi http://code.google.com/p/dadi/ #ievobio
- rdmpage See http://dx.doi.org/10.1371/journal.pgen.1000695 for some background #ievobio
Went to lunch with a small group to the People's Sandwich of Portland. Took the light rail over the river. Portland has some really nice features - like free light rail in the city.
Day 2. Part 4. Lightning Talks
- General
- phylogenomics #ievobio back on after lunch (where I had fascinating discussion about open data ...)
- kcranstn Rod Page using physical distance as a proxy for time left in 5 min lightening talks. Very Ominous. #ievobio
- G. Lu: Mining phylogenetic markers through genome comparison and sequence database exploration
- phylogenomics First up at #ievobio G. lu oh phylomarker identification http://bioinfo-srv1.awh.unomaha.edu/phylomarker/
- Jim Wilgenbusch: The Shape and Dimensionality of Phylogenetic Tree-Space Based on Mitochondrial Genomes
- phylogenomics Next up Jim Wilgenbusch on the shape and dimensionality of phylogenetic tree space #ievobio - evaluating NLDR methods to do this
- phylogenomics Wilgenbusch at #ievobio has software for visualizing tree comparisons but I missed the web site, sorry
- Karen Cranston: Visualizing Phylogenies and Metadata at the Scale of One Million Tips
- phylogenomics Next up Karen Cranston @kcranstn on visualizing trees with 1,000,000 tips #ievobio also linking to other Dara through APIs
- cydparr @kcranstn showing iPToL (iPlant) attempts to handle viz for 500K to 1 million tips http://bit.ly/bbir6r #ievobio
- cydparr @kranstn https://pods.iplantcollaborative.org/wiki/display/iptol/Large+Tree+Viewer #ievobio
- tjvision K Cranston showing off the iPlant large tree visualization tool - 1 million tips with semantic zooming!#ievobio
- Dan Gaston: Evaluating the performance of Functional Divergence prediction methods in protein evolution
- cydparr Daniel Gaston: "When you are a Linux person strange things happen" #ievobio
- phylogenomics Next up @dgaston83 on MaxL method re sites in proteins associated w/ functional divergence#ievobio http://cortana.biochem.dal.ca/software
- cydparr Gaston: FunDi for functional divergence datasetshttp://cortana.biochem.dal.ca/software #ievobio
- phylogenomics: when giving presentation would help lto have short URLs for anything you want people to post about or remember #ievobio
- dgaston83 Shortened URL to FunDi http://bit.ly/b5pHW4#ievobio
- dgaston83 Lightning talk done at #ievobio after only minor technical difficulties. Open Office still has a way to go.
- Nico Cellinese: TOLKIN-WS: Running Bioinformatics Workflows in Web Services
- phylogenomics Next up N. Cellinese on TOLKIN-WS for running bioinformatics workflows in web services #ievobio ; discussing Kepler, Taverna, etc
- cydparr Nico Cellinese: workflow software in bioinformatics still requires technical expertise #ievobio
- phylogenomics TOLKIN is available at http://www.tolkin.org/#ievobio
- Anycas Check it out @ludovia @rhodnius :) RT @phylogenomics: TOLKIN is available athttp://www.tolkin.org/ #ievobio
- C. Chen: The Gramene Genetic Diversity Module: a resource for genotype-phenotype association analysis in grass species
- phylogenomics Next up C. Chen on http://gramene.org for genotype phenotype association analysis #ievobio
- Alex Lancaster: PyPop - a software pipeline for large-scale multilocus population genomics
- phylogenomics Now at #ievobio A. Lancaster on PyPop - a software pipeline for population genomics http://www.pypop.org/
- Cecile Ane: Gene tree reconciliation: new developments in Bayesian Concordance Analysis with BUCKy
- phylogenomics Now at #ievobio Cecile Ane on gene tree species tree reconciliation w/ Bayesian concordance analysis using BUCKy (which we are using)
- robgural Cecile is presenting on bayesian concordance analysis at #ievobio
- Steven Kembel: Picante: R tools for integrating phylogenies and ecology
- note - Kembel is a collaborator of mine on my iSEEM project.
- dgaston83 Picante at #ievobio. I love programs that tie into R.
- run4ever79 RT @cydparr: Steven Kembel: Now more overlap in literature keywords for "ecology" and "phylogeny" than "evolution" and "phylogeny" #ievobio
- phylogenomics Next up #ievobio @stevenkembel on Picante: R tools for integrating phylogenies and ecologyhttp://picante.r-forge.r-project.org/
- S.J. Matthews: Effective Phylogenetic Compression with TreeZip
- phylogenomics Next at #ievobio Suzanne Matthews on TreeZip for phylogenetic compression http://code.google.com/p/treezip/
- Nick Matzke: Biopython (bio) Geography Module
- phylogenomics Nick Matzke on biopython module for geography allows access to Global biodiversity information facility (GBIF) data #ievobio
- Rutger Vos: Bio::Phylo - Phyloinformatic Analysis Using Perl
- phylogenomics Next @rvosa Rutger Vos on Bio::Phylo a bioperl compatible toolkit for phyloinformatics implements evoIO concepts #ievobio
- phylogenomics First time I have heard @rvosa says "if you want to learn more you can just tweet me" #ievobio
- tjvision From Python to Perl to evangelism at #ievobio
- N.D. Pentcheff: Copyrights and digitizing the systematic literature: the horror the horror
- phylogenomics Dean Pentcheff discussing copyrights and digitizing the systematic literature "the horror, the horror"#ievobio
- phylogenomics Pentcheff says one needs access to entire history of biodiversity literature to do systematics work and that access is bad #ievobio
- phylogenomics Pentcheff: systematics lit fits under fair use b/c natural history not creative; purpose is educational; market effect minimal; #ievobio
- phylogenomics Pentcheff: stop pussyfooting around, acting elitist - we need to make data and literature available for all for free for the world #ievobio
- pentcheff #ievobioBof Followup on "Digitizing systematic literature... 'Fair Use' to open the 20th Century": Lightning abstract: http://bit.ly/b7fTdy
- Carl Boettiger: My experiment with open science: Why the benefits of sharing go beyond source code
- cboettig My #ievobio lightning talk slides in my lab notebook: http://is.gd/das5G
- phylogenomics Next at #ievobio from #ucdavis @cboettig on open science -should share everything; discussions, reading, research, data, code
- dukeleto This is a nice trend in open science: wikified lab notebooks with OpenWetWare http://openwetware.org/wiki/Lab_Notebook #ievobio
- Wayne and David Maddison
- phylogenomics Wayne & David Maddison now demoing software live for going chromatogram -> tree #ievobio
- dgaston83 Live demo of unreleased version of Mesquite at#ievobio. Some interesting new alignment and tree building integrations (as well as R)
- robgural Maddison lightening talk- great stuff in Mesquite, including Mesquite-R integration. #ievobio
Then there were breakout sessions which were called "Birds of a feather" I went to one discussing open access and fair use issues.
Day 2. Part 6. Wrap up and other general information
And then I had to go home. The meeting wrapped up as I was leaving. Here are some ending tweets:
- cydparr Birds of a feather done, now doing wrap-up discussion #ievobio
- cydparr #ievobio officially adjourned!
- phylogenomics at PDX airport - heading home -#ievobio was great - really great - and I almost never say that about meetings
- rvosa Thank you all for a wonderful #ievobio!
- rdmpage ...as well as all who presented, entered the challenge, organised bird sof a feather, or just came along to see what buzz was about #ievobio
- Jim_Croft thnx for the #ievobio tweets @cydparr @robgural@phylogenomics @rdmpage - surprised there were not more active tweeters - but lots to read..
- justsayinnn #ievobio was great but man, how can so many computer scientist be so bad at getting talks set-up and projected!
- trinaeroberts Enjoyed #iEvoBio even though somewhat in the minority as a biologist. Many new project ideas!
- dgaston83 Up at a ridiculous hour. Heading to PDX and back to the east coast. #ievobio and #evol2010 were great. Happy Canada Day!
- Apotomoderes The iEvoBio conference - http://ievobio.org/- is over, now preparing for tomorrow's collecting trip north of Portland.
- tmkeesey http://3lbmonkeybrain.blogspot.com/2010/07/wrapping-up-in-portland.html #ievobio
- cydparr @pigsonthewing @rdmpage Abstracts for talks are collecting at Nature Precedings http://bit.ly/9NZSlj
- cydparr if you are a speaker for #ievobio don't forget to upload your extended abstract at Nature Precedingshttp://bit.ly/9NZSlj
- phylogenomics Number one lesson from #ievobio so far?#opensource #openaccess #openscience taking over phyloinformatics
- jcbradley Open science and data sharing at Evolution 2010 and iEvoBio http://ff.im/mYkM9
- run4ever79 Just landed had a great time @ievobio@NesCENT. Great meeting with a lot of very interesting presentations #ievobio #phyloWS
- iEvoBio Thanks to everyone who helped make iEvoBio 2010 such an awesome event!
- iEvoBio If you took pictures at the event, we'd love for you to post those online. Please use the tag ievobio10 and tweet us where you put them.
- rdmpage I've put a few photos of @iEvoBio on Flickr tagged "ievobio10" http://www.flickr.com/photos/tags/ievobio10/#ievobio
- robgural with sleep and lack of stress, I can turn a critical eye to #ievobio and say without a doubt that it was completely fantastic and fun.
- iEvoBio: Check out http://bit.ly/aws1h7for presentations (and Flickr photos) from #ievobi
Post meeting posts and blogs
No comments:
Post a Comment