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Re: [Treebase-devel] ABI proposal for phyloinformatics
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From: Arlin S. <ar...@um...> - 2011-07-13 14:00:39
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I think we should consider some ways to publicize elements of the approaches we all have been advocating in various ways, which depends on open standards and web services and so on, e.g., the idea that any tool should be able to submit an annotated record to an archive using a standard protocol. There might be other people around the world who would cooperate with us if they knew what we were thinking. Of course we are discussing these things on public lists, but still I would guess that many people who would be interested in this have no idea what we are considering. Arlin On Jun 14, 2011, at 9:28 AM, Rutger Vos wrote: > I just shared some sketches (thinking out loud about TreeBASE3) with > various people on these lists (Arlin, Hilmar, Karen, Bill, Harry). > MIAPA might play a role in the automated submission process, so if > anyone else is interested in seeing these documents please let me or > any of the other people with access now and we can share it with you. > > On Mon, Jun 13, 2011 at 1:22 PM, Arlin Stoltzfus <ar...@um...> > wrote: >> After our telecon, which suggested that splitting out the MIAPA >> part was a better strategy, I started a separate doc for this here: >> >> https://docs.google.com/document/d/16bno1sB3gBHHnew5TnoCLawScuoydG-i5LCPcB30OZY/edit?hl=en_US >> >> The focus of this, as currently conceived, is to combine problem- >> solving with development of a draft standard. The problem-solving >> attempts to address relevant user needs (e.g., helping users to >> create a properly formatted and annotated archive submission). >> This way, we will be developing technology support at the same time >> as the draft standard (which, ideally, will encourage the broader >> community to try it out and work with us). >> >> If you are interested, please take a look at the proposal, help us >> to identify problems to address and possible strategies to address >> them by leveraging available technologies and resources. Those who >> are interested will need to solidify partnerships as soon as >> possible, as there is only a month left to formulate the plan and >> write the proposal. >> >> Arlin >> ________________________________________ >> From: mia...@go... [miapa- >> di...@go...] On Behalf Of Karen Cranston [kar...@ne... >> ] >> Sent: Thursday, June 09, 2011 12:58 PM >> To: ph...@go...; MIAPA; TreeBASE devel >> Subject: Re: ABI proposal for phyloinformatics >> >> Hilmar and I talked to Anne Maglia from NSF this morning. The notes >> are on the "Pitches for TreeBASE_ABI" document (which is now editable >> by anyone with the link, BTW). She did not see any major issues and >> had plenty of advise on how to avoid common pitfalls when writing for >> the ABI panel. >> >> Summary: >> 1. Making the MIAPA component into a separate Innovation proposal is >> probably a good idea. >> 2. The TreeBASE / ToLWeb piece is well-suited for a Development >> proposal, and we can discuss MIAPA in this proposal as long as we >> have >> a concrete contingency plan for the possibility that this gets funded >> and the MIAPA proposal does not. >> 3. There is no general rule about incremental improvement vs major >> re-engineering, but the goals of the proposal must be novel in some >> way and have intellectual merit. A re-engineering proposal could be >> computationally novel, while a proposal with only incremental >> improvements must instead have novel interface components or strong >> biological motivations. >> 4. There seems to be an empty niche for proposals that include novel >> front-end as well as back-end development, but we need to make sure >> we >> have the appropriate expertise for the former. >> 5. She suggests sharing the draft with someone from BIO (perhaps >> Maureen Kearney) to get the user community perspective >> >> Please fill out the doodle poll so that we can plan the next course >> of action! >> >> Cheers, >> Karen >> >> On Wed, Jun 8, 2011 at 4:24 PM, Hilmar Lapp <hl...@ne...> >> wrote: >>> It looks like a response from NSF is still pending. There is not a >>> lot of >>> time left until the submission deadline, and I'll be out of >>> commission for >>> at least 7 days during that time starting Wed next week. So I >>> suggest we >>> start planning and get together independently of the NSF response >>> to hash >>> out over a conference call possible contributions and commitments. >>> Here's a >>> Doodle poll for scheduling. >>> >>> http://www.doodle.com/8zvwbidtxm9gzxcp >>> >>> To make sure that we can have a relatively targeted discussion, my >>> suggestion would be that everyone who is willing to play a role in >>> this >>> proposal enter their availability, and come prepared for the >>> following >>> questions: >>> >>> 1. What aims would a proposal need to have to for you to commit to >>> be part >>> of it, and conversely, what aims should it not have. (Ideally, the >>> aims >>> would be from either pitch A or pitch B that Karen sent to NSF for >>> feedback.) >>> >>> 2. What aims, expertise, and partners are we missing from the >>> group. Do you >>> have suggestions for how to pull those in. >>> >>> 3. What role are you interested in playing, for which aim(s). What >>> kind and >>> how many resources do you anticipate requiring support for to >>> accomplish >>> those aims. >>> >>> At the end of this, ideally we have a concrete sense for whether >>> there are >>> 0, 1, or 2 proposals that are viably going to come together, what >>> size of >>> proposal(s) we are talking about, who would take responsibility >>> for what, >>> and who else we need to reach out to. >>> >>> Comments / suggestions / additional items for the enumeration >>> above welcome. >>> >>> -hilmar >>> -- >>> =========================================================== >>> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >>> =========================================================== >>> >>> >>> >>> >> >> >> >> -- >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> Karen Cranston, PhD >> Training Coordinator and Informatics Project Manager >> nescent.org >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> >> -- >> You received this message because you are subscribed to the Google >> Groups "MIAPA" group. >> For more options, visit this group at >> http://groups.google.com/group/miapa-discuss?hl=en >> >> -- >> You received this message because you are subscribed to the Google >> Groups "MIAPA" group. >> For more options, visit this group at >> http://groups.google.com/group/miapa-discuss?hl=en >> > > > > -- > Dr. Rutger A. Vos > School of Biological Sciences > Philip Lyle Building, Level 4 > University of Reading > Reading, RG6 6BX, United Kingdom > Tel: +44 (0) 118 378 7535 > http://rutgervos.blogspot.com ------- Arlin Stoltzfus (ar...@um...) Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST IBBR, 9600 Gudelsky Drive, Rockville, MD tel: 240 314 6208; web: www.molevol.org |
