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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==Introduction==
 
==Introduction==
  
We are developing the first informatics system to integrate evolutionary, anatomical, developmental, and genetics data.  Such a system will serve the community of developmental and evolutionary biologists by providing web-based access to integrated information.
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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 appliedThus, 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 engages scientists from the fields of morphology, developmental and evolutionary biology, genetics, and ichthyology to collaboratively develop, refine, and prioritize how the research community will be able to use this system.  The goal of the workshop is to develop use-cases, or [[Driving Research Questions|driving biological research questions]] that push the limits of knowledge in the developmental and evolutionary biology fields. These will in turn drive the development of the database and web-based interfaces.
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==Final Report==
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For a summary of the outcomes of this report, see [[Needs_Analysis_Workshop/Summary|here]].
The workshop will also provide an interesting opportunity to brainstorm about the informatics tools and data required to push beyond these limits, thus fostering new discoveries at the interface between evolution and developmental genetics.
 
  
 
==Agenda==
 
==Agenda==
  
'''Monday, August 17'''
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'''Monday, September 17'''
  
''To be added soon.''
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* 8.30am NESCent introduction (K. Smith, J. Sturkey)
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* 8.45am Introduction to Workshop
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** Participant introductions (10mins)
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** [[Media:Needs_intro_final_Mabee.pdf|Linking Evolution to Genomics: Motivation, Approach, Project Goals]] (P. Mabee, 15mins)
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** [[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, 15mins)
 +
* 9.40am Opportunities and research challenges
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** [[Needs Analysis Workshop/Chalk talks|Chalk talks]] (5mins each)
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** [[Media:Workshop Goals.pdf|Goals of the workshop]] (H. Lapp)
 +
* 10.25am '''''Coffee break'''''
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* 10.45am Break-out groups
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** [[Needs Analysis Workshop/Breakout group 1|Break-out group 1]]: Developmental genetics of morphology
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** [[Needs Analysis Workshop/Breakout group 2|Break-out group 2]]: Evolution of morphology
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* 12.00pm '''''Lunch break'''''
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* 1.15pm Continuation of break-out groups, with some participants rotating to different groups
 +
* 2.45pm '''''Coffee break'''''
 +
* 3.15pm [[Needs Analysis Workshop/Report-out Day1|Report-out from break-out groups]], and large group discussion (40mins per group)
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* 4.40pm Discussion of topics for second day
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* 5:00pm shuttle to Millennium Hotel
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* 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, August 18'''
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'''Tuesday, September 18'''
  
''To be added soon.''
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* 9.00am Break-out groups (new composition, topics arisen from previous day)
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*# [[Needs Analysis Workshop/Semantics Breakout|Semantics]]
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*# [[Needs Analysis Workshop/Correlation Breakout|Correlation of traits]]
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*# [[Needs Analysis Workshop/Phylogeny Breakout|Phylogeny]]
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* 10.15am '''''Coffee break'''''
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* 10.30am [[Needs Analysis Workshop/Report-out Day2|Report-out from break-out groups]], and [[Needs Analysis Workshop/Prioritization|prioritization]]
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* 11.40am Future research avenues possibly enabled by this project: large-group brainstorming
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* 12.30pm '''''Adjourn'''''
  
 
==Logistics==
 
==Logistics==
  
* For long-distance participants, the hotel is the [http://www.millenniumhotels.com/MCIL.nsf/LU_HOTELDOC/113$$HotelDescription?OpenDocument Millenium Hotel] (2800 Campus Walk Ave, Durham, NC  27705; tel. (919) 383-8575)
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* For long-distance participants, the hotel is the [http://www.millenniumhotels.com/MCIL.nsf/LU_HOTELDOC/113$$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>)
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==Reading==
 
==Reading==
  
* We have started to use the tag "<span class="plainlinks">[http://www.connotea.org/tag/phenomap phenomap]</span>" on Connotea. Everyone is welcome to suggest references by using this 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.
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|-
 
|-
 
! Name !! Institution
 
! Name !! Institution
{{EventParticipant|Abzhanov|Arhat|abzhanov@fas.harvard.edu|Department of Organismic and Evolutionary Biology, Harvard University|}}
+
{{EventParticipant|Abzhanov|Arhat|abzhanov%40fas%2eharvard%2eedu|Department of Organismic and Evolutionary Biology, Harvard University|}}
{{EventParticipant|Balhoff|Jim|balhoff@nescent.org|NESCent|'''}}
+
{{EventParticipant|Balhoff|Jim|balhoff%40nescent%2eorg|NESCent|'''}}
{{EventParticipant|Dahdul|Wasila|dahdul@acnatsci.org|Department of Ichthyology, Academy of Natural Sciences|'''}}
+
{{EventParticipant|Dahdul|Wasila|dahdul%40acnatsci%2eorg|Department of Ichthyology, Academy of Natural Sciences|'''}}
{{EventParticipant|Hanken|Jim|hanken@oeb.harvard.edu|Museum of Comparative Zoology, Harvard University|}}
+
{{EventParticipant|Hoekstra|Hopi|hoekstra%40oeb%2eharvard%2eedu|Department of Organismic and Evolutionary Biology, Harvard University|}}
{{EventParticipant|Hoekstra|Hopi|hoekstra@oeb.harvard.edu|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@mail.utexas.edu|Dept. Integrative Biology, University of Texas at Austin|}}
+
{{EventParticipant|Jockusch|Elizabeth|elizabeth%2ejockusch%40uconn%2eedu|Department of Ecology & Evolutionary Biology, University of Connecticut|}}
{{EventParticipant|Jockusch|Elizabeth|elizabeth.jockusch@uconn.edu|Department of Ecology & Evolutionary Biology, University of Connecticut|}}
+
{{EventParticipant|Kellogg|Elizabeth|kellogge%40msx%2eumsl%2eedu|Dept. of Biology, University of Missouri - St. Louis|}}
{{EventParticipant|Kellogg|Elizabeth|kellogge@msx.umsl.edu|Dept. of Biology, University of Missouri - St. Louis|}}
+
{{EventParticipant|Kimmel|Chuck|kimmel%40uoneuro%2euoregon%2eedu|Institute of Neuroscience, University of Oregon|}}
{{EventParticipant|Kimmel|Chuck|kimmel@uoneuro.uoregon.edu|Institute of Neuroscience, University of Oregon|}}
+
{{EventParticipant|Lapp|Hilmar|hlapp%40nescent%2eorg|NESCent|'''}}
{{EventParticipant|Lapp|Hilmar|hlapp@nescent.org|NESCent|'''}}
+
{{EventParticipant|Lundberg|John|lundberg%40acnatsci%2eorg |Department of Ichthyology, Academy of Natural Sciences|'''}}
{{EventParticipant|Lundberg|John|lundberg@acnatsci.org |Department of Ichthyology, Academy of Natural Sciences|'''}}
+
{{EventParticipant|Mabee|Paula|pmabee%40usd%2eedu|University of South Dakota|'''}}
{{EventParticipant|Mabee|Paula|pmabee@usd.edu|University of South Dakota|'''}}
+
{{EventParticipant|Mast|Austin|amast%40bio%2efsu%2eedu|Department of Biological Science, Florida State University|}}
{{EventParticipant|Midford|Peter|petermidford@yahoo.com|Dept. of Ecology and Evolutionary Biology, Univ. of Kansas|'''}}
+
{{EventParticipant|Midford|Peter|petermidford%40yahoo%2ecom|Dept. of Ecology and Evolutionary Biology, University of Kansas|'''}}
{{EventParticipant|Stern|David|dstern@princeton.edu|Department of Ecology and Evolutionary Biology, Princeton University|}}
+
{{EventParticipant|Stern|David|dstern%40princeton%2eedu|Department of Ecology and Evolutionary Biology, Princeton University|}}
{{EventParticipant|Vision|Todd|tjv@bio.unc.edu|NESCent, and Department of Biology, University of North Carolina at Chapel Hill|'''}}
+
{{EventParticipant|Vision|Todd|tjv%40bio%2eunc%2eedu|NESCent, and Department of Biology, University of North Carolina at Chapel Hill|'''}}
{{EventParticipant|Wagner|Gunter|gunter.wagner@yale.edu|Yale University|}}
+
{{EventParticipant|Wagner|Gunter|gunter%2ewagner%40yale%2eedu|Yale University|}}
{{EventParticipant|Westerfield|Monte|monte@uoneuro.uoregon.edu|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

Linking Evolution to Genomics Using Phenotype Ontologies:
Needs Analysis Workshop


A workshop hosted by the National Evolutionary Synthesis Center (NESCent).

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

Tuesday, September 18

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:
  1. 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
  2. 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
  3. 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