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

Here is one of the talks by Thomas Brouquet, and see the rest here.



Thomas Broquet by mez_en_video

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.

Cloudnumbers and CRdata are two new cloud computing services.


I tested the two services with a very simple script. The script simply creates a dataframe of 10000 numbers via rnorm, and assigns them to a factor of one of two levels (a or b). I then take the mean of the two factor levels with the aggregate function.


In CRdata you need to put in some extra code to format the output in a browser window. For example, the last line below needs to have '<crdata_object>' on both sides of the output object so it can be rendered in a browser. And etc. for other things that one would print to a console. Whereas you don't need this extra code for using Cloudnumbers.

 
dat <- data.frame(n = rnorm(10000), p = rep(c('a','b'), each=5000))
 
out <- aggregate(n ~ p, data = dat, mean)
 
#<crdata_object>out</crdata_object>

1. Speed of entire process (not just running code): CRdata
2. Ease of use: CRdata
3. Cost: CRdata (free only)
4. Least annoying: Cloudnumbers (you don't have to add in extra code to run your own code)
5. Opensource: CRdata (you can use publicly available code on the site)
6. Long-term use: Cloudnumbers (more powerful, flexible, 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.

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.