rbold: An R Interface for Bold Systems barcode repository

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.

Below is a screenshot of an example query using function getsampleids to get barcode identifiers for specimens. You can then use getseqs function to grab barcode data for specific specimens or many specimens.

iEvoBio 2011 Synopsis

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):

1. Vistrails: workflow tool, awesome project by Claudio Silva
2. Commplish: purpose is to use via API's, not with the web UI
3. Phylopic: a database of life-form silouhettes, including an API for remote access, sweet!
4. Gloome
5. MappingLife: awesome geographic/etc data visualization interace on the web
6. SuiteSMA: visualizating multiple alignments
7. treeBASE: R interface to treebase, by Carl Boettiger
8. VertNet: database for vertebrate natural history collections
9. RevBayes: revamp of MrBayes, with GUI, etc. 
10. Phenoscape Knowledge Base
• Peter Midford lightning talk: talked about matching taxonomic and genetic data
11. BiSciCol: biological science collections tracker
12. Ontogrator 
13. TNRS: taxonomic name resolution service
14. Barcode of Life data systems, and remote access
15. Moorea Biocode Project
16. Microbial LTER's data
17. BirdVis: interactive bird data visualization (Claudio Silva in collaboration with Cornell Lab of Ornithology)
18. Crowdlabs: I think the site is down right now, another project by Claudio Silva
19. Phycas: Bayesian phylogenetics, can you just call this from R?
20. RIP MrBayes!!!! replaced by RevBayes (see 9 above)
21. Slides of presentations will be at Slideshare (not all presentations up yet)          
22. 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)! 
23. Synopses of Birds of a Feather discussion groups: http://piratepad.net/iEvoBio11-BoF-reportouts

PLoS journals API from R: "rplos"

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.

Get your own API key here.