We had several meetings while creating the proposal. The agendas and/or minutes for some of those meetings are here.
The minutes taken by User%253ARobertBuels, any inaccuracies or omissions are his.
Purpose of the hackathon
The hackathon was proposed to bring more support for evolutionary biology into the GMOD toolkit. We should thinks of what current needs are not being addresses or adequately addressed and take care to keep the focus on this topic. Some ideas I have are:
mckays 14:55, 12 February 2010 (UTC)
The purpose of the hackathon is to add more support for evolutionary biology in GMOD tools. I think hackathons are great, and GMOD will benefit from one.
The basic structure is that some number of people make a pitch for a thing to work on, and hope that people will nucleate around that and form working groups, and work for 5 days or however long.
It falls into Nescent’s whitepaper program, on the Nescent website, click on ‘informatics’ and the ‘whitepaper program’. It’s relatively informal, you put forward a proposed activity that convinces our directors to throw money at it. For hackathons, the amount of money is relatively significant, from $28-40K, depending on how many participants. The budget is significant, so you want to work out a relatively coherent argument as to why the activity itself is needed. How you expect to conduct it (which is not a big question in this case, we have done them before), and then what you expect to come out of it. What are the holes that you expect to be filling with that activity.
The proposal gets reviewed by the governing body of Nescent (currently called the operations committee, but that name could change soon).
When that is clear, the next step is to invite the key people and make sure you have those on board for the dates.
It’s good to keep in mind that the whole process takes 4-5 months, allow a couple of weeks for writing the submission, submitting it, etc. Couple weeks for the invitations to go out and get responses. Couple weeks for an ‘open call’ for participants and responses.
Ideally, all the participants and invitations are known 2 months in advance. It’s possible to violate that to some extent, but you don’t want to stretch it too much.
SM: For dates, I like the second week of June.
SC: I also am invited sometimes to arthropod genomics
HL: FYI, in July the ISMB conference ends on July 14. A significant fraction of the people would be going to ISMB, we need to be careful of that. Probably makes the week of July 19 not such a good candidate. The really oppressive heat here starts in July and ends mid-August, when it’s oppressively hot here.
SM: I really want to try to make June work for the reasons you laid out. I have some other stuff in early July, then ISMB and the plant biology meeting.
NW: early June would also work for me.
Group decided to shoot for week of June 7-11.
SM: We need to think about the kind of people we want to invite, we need people that can actually sit down and implement working products at this session.
HL: I would suggest with drafting the proposal whitepaper, the key people would probably naturally fall out of that. The first step would be to start fleshing out some ideas for what good focus areas would be. Unless you think we need those key people to put us in a position to flesh those out in the first place.
SM: Whitepapers from previous accepted hackathons, are those available for us to see?
HL: Yes, there are some linked from their respective home pages. HL TODO: provide links to the accepted whitepapers
HL: I wouldn’t go too overboard with the whitepaper, what is more critical than exhausting it there is to keep pushing forward within the time-frame and nailing down key points.
SM: Given our timeline, I’d say we should probably be communicating offline quite a bit and iterating very fast on the whitepaper. For the mechanics, I think it would be good to set up a google doc and a google group mailing list
SM: I think it would be good if we each stated the personal agendas we have in participating in this hackathon.
SM: My agenda is improving comparative genomics support for things that are in the GMOD toolkit. Bringing the synteny browser up to a standard similar to GBrowse is near and dear to my heart.
RB: My personal agenda is good software engineering. I want to make sure that things are put together well.
SC: Anything having to do with GMOD, I’m there.
HL: Chado natural diversity module, handling taxonomies well, handling phylogenies. Subgroup sizes of 4 to 5 in working groups are by far the best.
SM: set up google doc for the whitepaper
SM: set up organizer mailing list for organizing committee, and one for the participants
SM: send out a Doodle poll for the next conference call
HL/SM: find links to past accepted proposals
Please add/change items.
Sheldon McKay, Hilmar Lapp, Scott Cain, Nicole Washington
Action item - Sheldon to create new wiki page
Action item - Sheldon/Hilmar to write skeleton of proposal.
Action item - Sheldon/Hilmar to solicit input from Scott/Nicole/Robert
Please add/change items.
Discussed possible inclusion of atlas-based interfaces for phenotype, expression, and fate map data. This came out of a recent NESCent working group. This would be attractive to support evo-devo work.
Have Motivation section be overview. Details will be in the Specific Objectives sections. NESCent doesn’t actually care about structure. The document should just get its point across clearly, both to NESCent reviewers, and to the GMOD community.
Issues that affect everyone and are not specific to evolutionary biology should not be in the proposal. If such are issues are needed by all/most evolutionary biologists, then they will emerge at the hackathon. Dropped schema evolution objective.
Need to specify budget and some recommended requirements. Budget largely driven by number of participants, and that is largely driven by the number of specific objectives being proposed. We should get good faith intent to participate commitments from anyone who we think is vital to have at the event.
Should we investigate integration between phylogeny, organism, and natural diversity module? If so, we should identify any pain points and address them.
Visualizing phylogenetic data in GBrowse_syn came up. We decided that NGS data in GBrowse_syn was of vital interest to the evo community, based on recent working group at NESCent that Dave and Hilmar contributed to. Getting GBrowse_syn into the GBrowse 2.0 infrastructure is a key item. (But I wasn’t clear on if this should happen at the Hackathon, or before it.) We determined that we should not do any work that rests on top of the GBrowse 1.x platform.
Rob suggested “soliciting gripes” as a good way to identify work items and then what could be done about them.