Difference between revisions of "Needs Analysis Workshop"
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'''Venue:''' National Evolutionary Synthesis Center (NESCent) (<span class="plainlinks">[http://www.nescent.org/about/directions.php directions]</span>, also see <span class="plainlinks">[http://www.nescent.org/about/information.php information for visitors]</span>) | '''Venue:''' National Evolutionary Synthesis Center (NESCent) (<span class="plainlinks">[http://www.nescent.org/about/directions.php directions]</span>, also see <span class="plainlinks">[http://www.nescent.org/about/information.php information for visitors]</span>) | ||
| − | '''Date:''' September 17-18, 2007 | + | '''Date:''' September 17-18, 2007 |
'''Organizers:''' Paula Mabee, Monte Westerfield, Todd Vision, and Hilmar Lapp | '''Organizers:''' Paula Mabee, Monte Westerfield, Todd Vision, and Hilmar Lapp | ||
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This workshop brings together scientists from the fields of morphology, development, evolution, genetics, and ichthyology to define what informatic tools need to exist in order to enable synthetic research that takes full advantage of the accumulated data in each of these fields. The workshop organizers are funded by NSF to develop a system that provides web-based access to integrated evolutionary, anatomical, developmental, and genetics data in the Ostariophysii, and to make the software tools a community resource that can be more broadly applied. Thus, a major goal of the workshop is to identify [[Driving Research Questions|driving biological research questions]] that take advantage of these data to push the limits of what is currently possible, and to identify what informatic tools are needed in order to answer those questions. These will, in turn, be distilled to Use Cases that drive the software development activities at NESCent. | This workshop brings together scientists from the fields of morphology, development, evolution, genetics, and ichthyology to define what informatic tools need to exist in order to enable synthetic research that takes full advantage of the accumulated data in each of these fields. The workshop organizers are funded by NSF to develop a system that provides web-based access to integrated evolutionary, anatomical, developmental, and genetics data in the Ostariophysii, and to make the software tools a community resource that can be more broadly applied. Thus, a major goal of the workshop is to identify [[Driving Research Questions|driving biological research questions]] that take advantage of these data to push the limits of what is currently possible, and to identify what informatic tools are needed in order to answer those questions. These will, in turn, be distilled to Use Cases that drive the software development activities at NESCent. | ||
| + | |||
| + | ==Final Report== | ||
| + | For a summary of the outcomes of this report, see [[Needs_Analysis_Workshop/Summary|here]]. | ||
==Agenda== | ==Agenda== | ||
| − | + | '''Monday, September 17''' | |
| − | |||
| − | '''Monday, | ||
* 8.30am NESCent introduction (K. Smith, J. Sturkey) | * 8.30am NESCent introduction (K. Smith, J. Sturkey) | ||
* 8.45am Introduction to Workshop | * 8.45am Introduction to Workshop | ||
** Participant introductions (10mins) | ** Participant introductions (10mins) | ||
| − | ** Linking Evolution to Genomics: Motivation, Approach, Project Goals (P. Mabee, 15mins) | + | ** [[Media:Needs_intro_final_Mabee.pdf|Linking Evolution to Genomics: Motivation, Approach, Project Goals]] (P. Mabee, 15mins) |
| − | ** Uncovering gene function through mutant phenotypes in zebrafish, a model organism (M. Westerfield, 15mins) | + | ** [[Media:Monte-intro.pdf|Uncovering gene function through mutant phenotypes in zebrafish, a model organism]] (M. Westerfield, 15mins) |
| − | ** Managing of and computing with phenotypes, evolutionary change, and genetics: Informatics challenges (T. Vision | + | ** Managing of and computing with phenotypes, evolutionary change, and genetics: Informatics challenges (T. Vision, 15mins) |
* 9.40am Opportunities and research challenges | * 9.40am Opportunities and research challenges | ||
| − | ** Chalk talks (5mins each) | + | ** [[Needs Analysis Workshop/Chalk talks|Chalk talks]] (5mins each) |
| − | ** Goals of the workshop ( | + | ** [[Media:Workshop Goals.pdf|Goals of the workshop]] (H. Lapp) |
* 10.25am '''''Coffee break''''' | * 10.25am '''''Coffee break''''' | ||
* 10.45am Break-out groups | * 10.45am Break-out groups | ||
| Line 35: | Line 36: | ||
* 1.15pm Continuation of break-out groups, with some participants rotating to different groups | * 1.15pm Continuation of break-out groups, with some participants rotating to different groups | ||
* 2.45pm '''''Coffee break''''' | * 2.45pm '''''Coffee break''''' | ||
| − | * 3.15pm Report-out from break-out groups, and large group discussion (40mins per group) | + | * 3.15pm [[Needs Analysis Workshop/Report-out Day1|Report-out from break-out groups]], and large group discussion (40mins per group) |
* 4.40pm Discussion of topics for second day | * 4.40pm Discussion of topics for second day | ||
| + | * 5:00pm shuttle to Millennium Hotel | ||
| + | * 6:00pm shuttle from Millennium to Kanki restaurant (Charlene's Safe Ride, '''not''' the Millennium shuttle), [http://maps.google.com/maps?f=q&hl=en&geocode=&q=3504+Mount+Moriah+Rd,+Durham,+NC+27707&sll=35.950357,-78.97007&sspn=0.091161,0.11158&ie=UTF8&z=16&iwloc=addr&om=1 3504 Mt. Moriah Road, Durham]. Reservations are for 6:30pm. | ||
| − | '''Tuesday, | + | '''Tuesday, September 18''' |
* 9.00am Break-out groups (new composition, topics arisen from previous day) | * 9.00am Break-out groups (new composition, topics arisen from previous day) | ||
| + | *# [[Needs Analysis Workshop/Semantics Breakout|Semantics]] | ||
| + | *# [[Needs Analysis Workshop/Correlation Breakout|Correlation of traits]] | ||
| + | *# [[Needs Analysis Workshop/Phylogeny Breakout|Phylogeny]] | ||
* 10.15am '''''Coffee break''''' | * 10.15am '''''Coffee break''''' | ||
| − | * 10.30am Report-out from break-out groups | + | * 10.30am [[Needs Analysis Workshop/Report-out Day2|Report-out from break-out groups]], and [[Needs Analysis Workshop/Prioritization|prioritization]] |
| − | * 11. | + | * 11.40am Future research avenues possibly enabled by this project: large-group brainstorming |
| − | * | + | * 12.30pm '''''Adjourn''''' |
==Logistics== | ==Logistics== | ||
| − | * For long-distance participants, the hotel is the [http://www.millenniumhotels.com/MCIL.nsf/LU_HOTELDOC/113$$HotelDescription?OpenDocument | + | * For long-distance participants, the hotel is the [http://www.millenniumhotels.com/MCIL.nsf/LU_HOTELDOC/113$$HotelDescription?OpenDocument Millennium Hotel] (2800 Campus Walk Ave, Durham, NC 27705; tel. (919) 383-8575) |
* For dining & entertainment, NESCent is right across from [http://www.ninthst.com/ Ninth Street] | * For dining & entertainment, NESCent is right across from [http://www.ninthst.com/ Ninth Street] | ||
* For the venue, NESCent is in the historic [http://www.owdna.org/mill.htm Erwin Mills] building (<span class="plainlinks">[http://www.nescent.org/about/directions.php directions]</span>) | * For the venue, NESCent is in the historic [http://www.owdna.org/mill.htm Erwin Mills] building (<span class="plainlinks">[http://www.nescent.org/about/directions.php directions]</span>) | ||
| Line 54: | Line 60: | ||
==Reading== | ==Reading== | ||
| − | * We have started to use the tag "<span class="plainlinks">[http://www.connotea.org/tag/ | + | * We have started to use the tag "<span class="plainlinks">[http://www.connotea.org/tag/phenoscape phenoscape]</span>" on Connotea. Everyone is welcome to suggest references by using this tag. |
| − | * Relevant manuscripts by members of the project team: | + | * Relevant manuscripts by members of the project team: |
| − | # Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, and Westerfield M. Phenotype ontologies: the bridge between genomics and evolution. Trends Ecol Evol 2007 Jul; 22(7) 345-50. [http://dx.doi.org/10.1016/j.tree.2007.03.013 doi:10.1016/j.tree.2007.03.013] | + | # Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, and Westerfield M. Phenotype ontologies: the bridge between genomics and evolution. Trends Ecol Evol 2007 Jul; 22(7) 345-50. [http://dx.doi.org/10.1016/j.tree.2007.03.013 doi:10.1016/j.tree.2007.03.013] |
# Mabee PM, Arratia G, Coburn M, Haendel M, Hilton EJ, Lundberg JG, Mayden RL, Rios N, and Westerfield M. Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish. J Exp Zoolog B Mol Dev Evol 2007 Jun 28. [http://dx.doi.org/10.1002/jez.b.21181 doi:10.1002/jez.b.21181] | # Mabee PM, Arratia G, Coburn M, Haendel M, Hilton EJ, Lundberg JG, Mayden RL, Rios N, and Westerfield M. Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish. J Exp Zoolog B Mol Dev Evol 2007 Jun 28. [http://dx.doi.org/10.1002/jez.b.21181 doi:10.1002/jez.b.21181] | ||
# Haendel, M.A., Neuhaus, F., Osumi-Sutherland, D.S., Mabee, P.M., Mejino J.L.V., Mungall, C.J., and Smith, B. (2008) [[Media:Caroreprint.pdf|CARO - The Common Anatomy Reference Ontology]]. ''In:'' Albert Burger, Duncan Davidson and Richard Baldock (Editors): ''Anatomy Ontologies for Bioinformatics: Principles and Practice''. ISBN 978-1-84628-884-5. | # Haendel, M.A., Neuhaus, F., Osumi-Sutherland, D.S., Mabee, P.M., Mejino J.L.V., Mungall, C.J., and Smith, B. (2008) [[Media:Caroreprint.pdf|CARO - The Common Anatomy Reference Ontology]]. ''In:'' Albert Burger, Duncan Davidson and Richard Baldock (Editors): ''Anatomy Ontologies for Bioinformatics: Principles and Practice''. ISBN 978-1-84628-884-5. | ||
| Line 70: | Line 76: | ||
{{EventParticipant|Balhoff|Jim|balhoff%40nescent%2eorg|NESCent|'''}} | {{EventParticipant|Balhoff|Jim|balhoff%40nescent%2eorg|NESCent|'''}} | ||
{{EventParticipant|Dahdul|Wasila|dahdul%40acnatsci%2eorg|Department of Ichthyology, Academy of Natural Sciences|'''}} | {{EventParticipant|Dahdul|Wasila|dahdul%40acnatsci%2eorg|Department of Ichthyology, Academy of Natural Sciences|'''}} | ||
| − | |||
{{EventParticipant|Hoekstra|Hopi|hoekstra%40oeb%2eharvard%2eedu|Department of Organismic and Evolutionary Biology, Harvard University|}} | {{EventParticipant|Hoekstra|Hopi|hoekstra%40oeb%2eharvard%2eedu|Department of Organismic and Evolutionary Biology, Harvard University|}} | ||
{{EventParticipant|Hofmann|Hans|hans%40mail%2eutexas%2eedu|Dept. Integrative Biology, University of Texas at Austin|}} | {{EventParticipant|Hofmann|Hans|hans%40mail%2eutexas%2eedu|Dept. Integrative Biology, University of Texas at Austin|}} | ||
| Line 86: | Line 91: | ||
{{EventParticipant|Westerfield|Monte|monte%40uoneuro%2euoregon%2eedu|Zebrafish Information Network (ZFIN) and Institute of Neuroscience, University of Oregon|'''}} | {{EventParticipant|Westerfield|Monte|monte%40uoneuro%2euoregon%2eedu|Zebrafish Information Network (ZFIN) and Institute of Neuroscience, University of Oregon|'''}} | ||
|} | |} | ||
| + | |||
| + | [[Category:Needs Analysis Workshop]] | ||
| + | [[Category:Events]] | ||
Latest revision as of 19:29, 11 January 2009
Needs Analysis Workshop
A workshop hosted by the National Evolutionary Synthesis Center (NESCent).
Contents
Location and Date
Venue: National Evolutionary Synthesis Center (NESCent) (directions, also see information for visitors)
Date: September 17-18, 2007
Organizers: Paula Mabee, Monte Westerfield, Todd Vision, and Hilmar Lapp
Introduction
This workshop brings together scientists from the fields of morphology, development, evolution, genetics, and ichthyology to define what informatic tools need to exist in order to enable synthetic research that takes full advantage of the accumulated data in each of these fields. The workshop organizers are funded by NSF to develop a system that provides web-based access to integrated evolutionary, anatomical, developmental, and genetics data in the Ostariophysii, and to make the software tools a community resource that can be more broadly applied. Thus, a major goal of the workshop is to identify driving biological research questions that take advantage of these data to push the limits of what is currently possible, and to identify what informatic tools are needed in order to answer those questions. These will, in turn, be distilled to Use Cases that drive the software development activities at NESCent.
Final Report
For a summary of the outcomes of this report, see here.
Agenda
Monday, September 17
- 8.30am NESCent introduction (K. Smith, J. Sturkey)
- 8.45am Introduction to Workshop
- Participant introductions (10mins)
- Linking Evolution to Genomics: Motivation, Approach, Project Goals (P. Mabee, 15mins)
- Uncovering gene function through mutant phenotypes in zebrafish, a model organism (M. Westerfield, 15mins)
- Managing of and computing with phenotypes, evolutionary change, and genetics: Informatics challenges (T. Vision, 15mins)
- 9.40am Opportunities and research challenges
- Chalk talks (5mins each)
- Goals of the workshop (H. Lapp)
- 10.25am Coffee break
- 10.45am Break-out groups
- Break-out group 1: Developmental genetics of morphology
- Break-out group 2: Evolution of morphology
- 12.00pm Lunch break
- 1.15pm Continuation of break-out groups, with some participants rotating to different groups
- 2.45pm Coffee break
- 3.15pm Report-out from break-out groups, and large group discussion (40mins per group)
- 4.40pm Discussion of topics for second day
- 5:00pm shuttle to Millennium Hotel
- 6:00pm shuttle from Millennium to Kanki restaurant (Charlene's Safe Ride, not the Millennium shuttle), 3504 Mt. Moriah Road, Durham. Reservations are for 6:30pm.
Tuesday, September 18
- 9.00am Break-out groups (new composition, topics arisen from previous day)
- 10.15am Coffee break
- 10.30am Report-out from break-out groups, and prioritization
- 11.40am Future research avenues possibly enabled by this project: large-group brainstorming
- 12.30pm Adjourn
Logistics
- For long-distance participants, the hotel is the Millennium Hotel (2800 Campus Walk Ave, Durham, NC 27705; tel. (919) 383-8575)
- For dining & entertainment, NESCent is right across from Ninth Street
- For the venue, NESCent is in the historic Erwin Mills building (directions)
Reading
- We have started to use the tag "phenoscape" on Connotea. Everyone is welcome to suggest references by using this tag.
- Relevant manuscripts by members of the project team:
- Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, and Westerfield M. Phenotype ontologies: the bridge between genomics and evolution. Trends Ecol Evol 2007 Jul; 22(7) 345-50. doi:10.1016/j.tree.2007.03.013
- Mabee PM, Arratia G, Coburn M, Haendel M, Hilton EJ, Lundberg JG, Mayden RL, Rios N, and Westerfield M. Connecting evolutionary morphology to genomics using ontologies: a case study from Cypriniformes including zebrafish. J Exp Zoolog B Mol Dev Evol 2007 Jun 28. doi:10.1002/jez.b.21181
- Haendel, M.A., Neuhaus, F., Osumi-Sutherland, D.S., Mabee, P.M., Mejino J.L.V., Mungall, C.J., and Smith, B. (2008) CARO - The Common Anatomy Reference Ontology. In: Albert Burger, Duncan Davidson and Richard Baldock (Editors): Anatomy Ontologies for Bioinformatics: Principles and Practice. ISBN 978-1-84628-884-5.
Participants
Members of the project team are in bold font.
| Name | Institution |
|---|---|
| Arhat Abzhanov | Department of Organismic and Evolutionary Biology, Harvard University |
| Jim Balhoff | NESCent |
| Wasila Dahdul | Department of Ichthyology, Academy of Natural Sciences |
| Hopi Hoekstra | Department of Organismic and Evolutionary Biology, Harvard University |
| Hans Hofmann | Dept. Integrative Biology, University of Texas at Austin |
| Elizabeth Jockusch | Department of Ecology & Evolutionary Biology, University of Connecticut |
| Elizabeth Kellogg | Dept. of Biology, University of Missouri - St. Louis |
| Chuck Kimmel | Institute of Neuroscience, University of Oregon |
| Hilmar Lapp | NESCent |
| John Lundberg | Department of Ichthyology, Academy of Natural Sciences |
| Paula Mabee | University of South Dakota |
| Austin Mast | Department of Biological Science, Florida State University |
| Peter Midford | Dept. of Ecology and Evolutionary Biology, University of Kansas |
| David Stern | Department of Ecology and Evolutionary Biology, Princeton University |
| Todd Vision | NESCent, and Department of Biology, University of North Carolina at Chapel Hill |
| Gunter Wagner | Yale University |
| Monte Westerfield | Zebrafish Information Network (ZFIN) and Institute of Neuroscience, University of Oregon |
