CollabIT BioCenters Meeting Report

Participants

SESYNC: Mike Smorul (organizer), Mary Shelley, Ian Munoz
BEACON: Tracy Teal (local host)
iDigBio: Deb Paul, Matt Collins
NESCent: Karen Cranston
iPlant: Martha Narro
NCEAS: Mark Schildhauer (remotely, only for Karen's presentation)

Summary of Key Topics

Data Carpentry and Software Carpentry

Data Carpentry grew out of Software Carpentry and last year's CollabIT meeting. Software Carpentry's target audience is developers. Data Carpentry's target audience is scientists who need some informatics proficiency to do their science, but who are not software developers (i.e., people with little to no prior knowledge of programming, shell scripting, or command line tools). Thus far, there have been Data Carpentry workshops at SESYNC, BEACON, NESCent and iDigBio. They have been very well received and NSF seems interested in them and the fact the BioCenters are working together on Data Carpentry; NSF also enthusiastic about the workshop at iDigBio which had participants from many domains (not just biology). Materials are on GitHub. They need Train the Trainers workshops to develop a pool of instructors. They design the training around a science topic and currently only have an ecology module. They want to develop a genomics module next and very much want iPlant to be involved.

Joint Funding Opportunities

Tracy Teal and Karen Cranston are taking the lead on drafting a white paper about the centers doing some joint training, in part focused on Data Carpentry, but also beyond that to capitalize on each center's expertise. iPlant's role (obviously) could to provide CI support for data and analyses whether the scale is small or large, but especially when the scale is large. The draft will be circulated for additional input.

Planning for a Center's End of Life

Karen Cranston gave a very insightful presentation. Her slides (and all other slides) are here.

Miscellaneous

Martha talked with Karen about the phylogenetic products (e.g., big tree viewer, Naim's workflow, perpetual tree workflow) from the iPTOL effort that (in Martha's opinion) never went through a strong "adoption" push. Karen thought it would be worth considering, more broadly, what pieces (phylogenetics tools) have been developed by various centers that could be pulled together, updated if necessary, and packaged for an adoption push.

Karen pointed out that iPlant could include publishing datasets to Dryad in the DE (same as for NCBI). She's developing a workflow for publishing to Dryad and will let Martha know when it's ready.

NESCent's TraitDB still needs a home. Martha suggested a call to see if iPlant could take it on.

NESCent found that their community members used wiki's much more after they switched to Wikispaces since users didn't have to figure out wiki markup to use it. It's free for educational use.

All centers expressed interest in booth sharing at conferences, or being located near one another's booths. ESA is the conference iPlant is likely to want to share a booth. Maybe TDWG.

Follow-up

Data Carpentry: Discussion with EOT group about 1) the prospects of working with Tracy Teal to develop a genomics module for Data Carpentry and 2) if/how iPlant could participate in Data Carpentry workshops or use Data Carpentry materials. IN PROGRESS (Jason)
Funding opportunity: The white paper on potential joint training among centers will be circulated. Martha will review and edit, pulling in others at iPlant (esp. EOT). Let her know if you are interested. (Waiting for the paper.)
Dryad: Martha to find out if iPlant is interested in making it possible to publish datasets, analysis results to Dryad via the DE. (DONE - discussed with Ramona. OK for later. Not now.)
Adoption of iPToL phylogenetics products: Martha and Karen will discuss this again. Any Science Analysts or EOT folks who are interested should contact Martha.
NESCENT TraitDB: Martha and Karen to follow up to see if iPlant could provide a home for it. Include Ramona on the call. (Ramona said there was interest from Karen and EOL when met at TDWG.)
MERRA: Martha to show Mary what iPlant and NASA MERRA are doing to make satellite datasets available. (DONE)
Getting Started with iPlant: Tracy wants a "Getting Started with iPlant" webinar for Michigan State folks (she'll organize them). Martha to talk to Jason about this. (DONE - told Jason)
Booth sharing: Martha to talk to Ramona about this for ESA 2015; not booth, but Ramona will connect with Karen and Deb at TDWG. (DONE)

CollabIT BioCenters Meeting Report