Showing posts with label openaccess. Show all posts
Showing posts with label openaccess. Show all posts

Wednesday, November 30, 2011

rOpenSci won 3rd place in the PLoS-Mendeley Binary Battle!

Recology has moved go to http://recology.info/2011/11/ropensci-won-3rd-place-in-plos-mendeley

I am part of the rOpenSci development team (along with Carl Boettiger, Karthik Ram, and Nick Fabina).   Our website: http://ropensci.org/.  Code at Github: https://github.com/ropensci

We entered two of our R packages for integrating with PLoS Journals (rplos) and Mendeley (RMendeley) in the Mendeley-PLoS Binary Battle.  Get them at GitHub (rplos; RMendeley).

These two packages allow users (from R! of course) to search and retrieve data from PLoS journals (including their altmetrics data), and from Mendeley.  You could surely mash up data from both PLoS and Mendeley.  That's what's cool about rOpenSci - we provide the tools, and leave it up to users vast creativity to do awesome things.

3rd place gives us a $1,000 prize, plus a Parrot AR Drone helicopter.

Thursday, September 22, 2011

@drewconway interview on @DataNoBorders at the Strata conference

Recology has moved, go to http://recology.info/2011/09/drewconway-interview-on-datanoborders

The O'Reilly Media Strata Summit has many interviews on YouTube (just search YouTube for it)

Drew Conway is the author of a R packages, including infochimps, an R wrapper to the Infochimps API service.

The YouTube video:


Open science talk by Carl Boettiger

Recology has moved, go to http://recology.info/2011/09/open-science-talk-by-carl-boettiger

Carl Boettiger gave a talk on the topic of open science to incoming UC Davis graduate students.

Here is the audio: http://www.archive.org/details/ThingsIWishIKnewThreeYearsAgo-ByTheDavisOpenScienceGroup&reCache=1

Here are the slides: http://hazelnusse.github.com/DOS_WOW2011/#title-slide

Friday, September 9, 2011

My take on an R introduction talk

Recology has moved, go to http://recology.info/2011/09/my-take-on-r-introduction-talk

UPDATE: I put in an R tutorial as a Github gist below.


Here is a short intro R talk I gave today...for what it's worth...



Thursday, September 8, 2011

FigShare Talk

Recology has moved, go to http://recology.info/2011/09/figshare-talk

FigShare - I very much like this idea of a place to put your data online that is NOT published. Dryad is a nice place for datastes linked with published papers, but there isn't really a place for datasets that perhaps did not make the cut for a published paper, and if known to the scientific community, could potentially help resolve the "file-drawer" effect in meta-analyses. (wow, run on sentence)

 
"Figshare - Why don't you publish all your research?" Mark Hahnel Imperial College London from London Biogeeks on Vimeo.

Thursday, August 11, 2011

Wednesday at #ESA11

Recology has moved, go to http://recology.info/2011/08/wednesday-at-esa11

Interesting talks/posters:

  • Ethan White's poster describing EcologicalData.org was of course awesome given my interest in getting data into the hands of ecologists over at rOpenSci.org. Ethan also has software you can download on your machine to get the datasets you want easily - EcoData Retriever. [rOpenSci will try to take advantage of their work and allow you to call the retriever from R]
  • Carl Boettiger's talk was awesome. He explained how we need better tools to be able to predict collapses using early warning signals. He developed a way to estimate the statistical distribution of probabilities of system collapse. 
  • Jennifer Dunne: Explained how she put together an ancient network from Germany. Bravo. 
  • Carlos Melian explained his model of network buildup that starts from individuals, allows speciation, and other evolutionary processes. 
  • Rachel Winfree told us that in two sets of mutualistic plant-pollinator networks in New Jersey and California, that the least connected pollinator species were the most likely to be lost from the network with increasing agricultural intensity. 
  • Dan Cariveau suggests that pollination crop services can be stabilized even with increasing agriculture intensity if in fact pollinator species respond in different ways. That is, some pollinators may decrease in abundance with increasing ag intensity, while other species may increase - retaining overall pollination services to crops.

    Monday, August 8, 2011

    Monday at #ESA11

    Recology has moved, go to http://recology.info/2011/08/monday-at-esa11

    Monday was a good day at ESA in Austin. There were a few topics I promised to report on in my blogging/tweeting.


    ...focused on open source data. Carly Strasser's presentation on guidelines for data management was awesome (including other talks in the symposium on Creating Effective Data Management Plans for Ecological Research). Although this was a good session, I can't help but wish that they had hammered home the need for open science more. Oh well. Also, they talked a lot about how, and not a lot of why we should properly curate data. Still, a good session. One issue Carly and I talked about was tracking code in versioning systems such as Github. There doesn't seem to be a culture of versioning code for analyses/simulations in ecology. But when we get there...it will be easier to share/track/collaborate on  code.

    ...used R software. David Jennings talked about a meta-analysis asking if phylogenetic distance influences competition strength in pairwise experiments. David used the metafor package in R to do his meta-analysis. Good form sir.

    ...did cool science. Matt Helmus presented a great talk on phylogenetic species area curves (likely using R, or Matlab maybe?).


    p.s. We launched rOpenSci today.


    Oddities:
    • The Tilman effect - Tilman's talk was so packed it looked like there was a line waiting to get into a trendy bar. Here's a picture (credit: Jaime Ashander). Bigger room next time anyone? 
    • Wiley came out with an open source journal called Ecology and Evolution. This brings them to 3 open source journals (the other two are in other fields). We (rOpenSci) will attempt to hand-shake with these journals. 
    • The vegetarian lunch option was surprisingly good. Nice. 

    (#ESA11) rOpenSci: a collaborative effort to develop R-based tools for facilitating Open Science

    Recology has moved, go to http://recology.info/2011/08/esa11-ropensci-collaborative-effort-to_08

    Our development team would like to announce the launch of rOpenSci. As the title states, this project aims to create R packages to make open science more available to researchers.

    http://ropensci.org/

    What this means is that we seek to connect researchers using R with as much open data as possible, mainly through APIs. There are a number of R packages that already do this (e.g., infochimps, twitteR), but we are making more packages, e.g., for Mendeley, PLoS Journals, and taxonomic sources (ITIS, EOL, TNRS, Phylomatic, UBio).

    Importantly, we are creating a package called rOpenSci, which aims to integrate functions from packages for individual open data sources.

    If you are somewhat interested, follow our progress on our website, on Twitter, or contact us. If you are really^2 interested you could go to Github and contribute. If  you are really^3 interested, join our development team.

    Sunday, July 31, 2011

    Blogging/tweeting from #ESA11

    Recology has moved, go to http://recology.info/2011/07/bloggingtweeting-from-esa11

    I will be blogging about the upcoming Ecological Society of America meeting in Austin, TX. I will focus on discussing talks/posters that:

    1. Have taken a cool approach to using data, or
    2. Have focused on open science/data, or
    3. Done something cool with R software, or
    4. Are just exciting in general

    I will also tweet throughout the meeting from @recology_ (yes the underscore is part of the name, recology was already taken). 

    The hashtag for the meeting this year is #ESA11

    Friday, July 15, 2011

    Archiving ecology/evolution data sets online


    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.

    Does it make sense to post data sets linked to published works on Infochimps? I think probably not know that I think about it. But perhaps it makes sense for other data sets, or subsets of data sets that are not linked with published works to be posted there as I know at least Dryad only accepts data sets linked with published papers.

    One use case is there was a tweet from someone recently that his students were excited about getting their data sets on their resume/CV, but didn't think there was a way to put them any place where there wasn't a precondition that the data set was linked with a published work. Seems like this could be a good opportunity to place these datasets on Infcohimps, and at least they are available then where a lot of people are searching for data sets, etc.

    What I think would be ideal is if Dryad, KNB, etc. could link their datasets to Infochimps, where they could be found, then users can either get them from Infochimps, or perhaps you would have to go to the Dryad site, e.g. But at least you could search over all ecological data sets then.

    Tuesday, June 28, 2011

    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.
    Screen shot 2011-06-28 at 9.24.00 AM.png

    Wednesday, June 22, 2011

    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

    Tuesday, June 21, 2011

    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.