Neurobiology data


#1

I met a neurobiology data analyst person the other week and he informed of many potential places to get open neurobiology data. I started a repo at https://github.com/ropensci/neurobio to collect potential data sources we could interact with from R, and have any discussions about the subject area.

We’d love any thoughts on this study area - what data sources do people use a lot that they’d like to get programmatically? What can we do to help facilitate reproducible science workflows in R?


#2

Sounds good, Scott. We should try and get someone from the field involved. I’ll ping my coworker Fatma, a neueoscientist, for possible contacts who can participate.


#3

@karthik cool, haven’t dug into the data sources at all yet, would be great to have some people in the field to chat with


#4

Hi,

I just wanted to let you both, and anybody else, know that I am the ‘neurobiology data analyst’ that sckott is referring to. Wondering if anybody has any thoughts on the links/sources that I provided. I’m open to any questions or items for clarification.

One thought I had recently is that R would likely be most useful in aiding the recent development in discovery/data driven analyses and not necessarily on processing ‘raw’ MRI data. I can come up with a few method types if there is interest.


#5

@carpensa Thanks for dropping in!

That would be great if you could name some items. We are particularly interested in developing projects in R that will connect users with data or make visualizations - with less interest in doing statistics/etc. since that isn’t our strength.

Curious why you say R is less useful in processing raw data?


#6

Hi Scott,

just found this discussion by chance, having been directed to this web site by Ben Marwick re: other matters (thanks Ben!). I just added a couple of links to neuro projects that I know about. I don’t know that many neuro people working with R, but am happy to help out in any way I can.


#7

@sje30 Welcome! And thanks for stopping by.

I’ll head over to your comments in the repo


#8

Scott, I have some contacts at NITRC and NIF if that would be helpful.


#9

@mfenner Yeah, that would be great to talk to them, thanks


#10

Hi,

In response to early statement. The processing of ‘raw’ MRI data has already been established and many of the tools are already publicly available (e.g. fsl).

This is not to say that R cannot perform such tasks, but that it is not necessary to reinvent the wheel. In my limited opinion, R would be best suited to the 2nd level analyses such as; statistical comparisons, generating models and possibly classification/clustering analysis.

Sorry for the delay in response, happy to discuss this further…