Openaccess

We now have many options for archiving data sets online: Dryad, KNB, Ecological Archives, Ecology Data Papers, Ecological Data, etc. However, these portals largely do not communicate with one another as far as I know, and there is no way to search over all data set sources, again, as far as I know. So, I wonder if it would ease finding of all these different data sets to get these different sites to get their data sets cloned on a site like Infochimps, or have links from Infochimps. Infochimps already has APIs (and there’s an R wrapper for the Infochimps API already set up here: http://cran.r-project.org/web/packages/infochimps/index.html by Drew Conway), and they have discussions set up there, etc. ...

Have you ever wanted to search and fetch barcode data from Bold Systems? I am developing functions to interface with Bold from R. I just started, but hopefully folks will find it useful. The code is at Github here. The two functions are still very buggy, so please bring up issues below, or in the Issues area on Github. For example, some searches work and other similar searches don’t. Apologies in advance for the bugs. ...

We just wrapped up the 2011 iEvoBio meeting. It was awesome! If you didn’t go this year or last year, definitely think about going next year. Here is a list of the cool projects that were discussed at the meeting (apologies if I left some out): Vistrails: workflow tool, awesome project by Claudio Silva Commplish: purpose is to use via API’s, not with the web UI Phylopic: a database of life-form silouhettes, including an API for remote access, sweet! Gloome MappingLife: awesome geographic/etc data visualization interace on the web SuiteSMA: visualizating multiple alignments treeBASE: R interface to treebase, by Carl Boettiger VertNet: database for vertebrate natural history collections RevBayes: revamp of MrBayes, with GUI, etc. Phenoscape Knowledge Base Peter Midford lightning talk: talked about matching taxonomic and genetic data BiSciCol: biological science collections tracker Ontogrator TNRS: taxonomic name resolution service Barcode of Life data systems, and remote access Moorea Biocode Project Microbial LTER’s data BirdVis: interactive bird data visualization (Claudio Silva in collaboration with Cornell Lab of Ornithology) Crowdlabs: I think the site is down right now, another project by Claudio Silva Phycas: Bayesian phylogenetics, can you just call this from R? RIP MrBayes!!!! replaced by RevBayes (see 9 above) Slides of presentations will be at Slideshare (not all presentations up yet) A birds of a feather group I was involved in proposed an idea (TOL-o-matic) like Phylomatic, but of broader scope, for easy access and submission of trees, and perhaps even social (think just pushing a ‘SHARE’ button within PAUP, RevBayes, or other phylogenetics software)! Synopses of Birds of a Feather discussion groups: http://piratepad.net/iEvoBio11-BoF-reportouts

The Public Libraries of Science (PLOS) has an API so that developers can create cool tools to access their data (including full text papers!!). Carl Boettiger at UC Davis and I are working on R functions that use the PLoS API. See our code on Github here. See the wiki at the Github page for examples of use. We hope to deploy rplos as a package someday soon. Please feel free to suggest changes/additions rplos in the comments below or on the Github/rplos site. ...