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Re: [Treebase-devel] ABI proposal for phyloinformatics
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From: Enrico P. <epo...@cs...> - 2011-07-13 14:25:25
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I agree. Some of the components are taking shape or are already well defined (MIAPA 0.1/1.0, Nexml). I hope that the standard record will have a semantic foundation (let it be MIAPA?). It would be good to start formulating the structure of such annotated record and perhaps move forward the creation of a PhyloWS service that at least, as a start, provides validation (and possibly completion) of the record. Enrico -- Dept. Computer Science, New Mexico State University MSC CS, Box 30001, Las Cruces, NM 88003 Voice: 575-646-6239 Fax: 575-646-1002 On 7/13/11 8:00 AM, "Arlin Stoltzfus" <ar...@um...> wrote: >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-i5LCP >>>cB30OZY/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 > >-- >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 |
