Difference between revisions of "NSF Interop Proposal"

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= Overview and talking points =
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As a followup activity to the successful [[Database Interop Hackathon]], a group of individuals submitted a proposal to NSF for a multi-year $750000 project to fund an [[EvoIO Network]].
  
Through the work of NESCent's informatics staff, the Evolutionary Informatics working group, and the participants in the recent data interop hackathon, we are in a position to apply for an NSF [http://www.nsf.gov/pubs/2007/nsf07565/nsf07565.htm Interop proposal].
+
= Background =
  
This funding program provides 250 K per year to support interoperability projects that are multidisciplinary and that have a community aspect and a technology aspect.  The next deadline (possibly the last deadline for this program) is July 23.
+
Due to the foundation laid (over several years) by many people, including NESCent's informatics staff, the Evolutionary Informatics working group, and the participants in the recent data interop hackathon, we are in a position to apply to the NSF [http://www.nsf.gov/pubs/2007/nsf07565/nsf07565.htm INTEROP] program.  This program provides up to 250 K per year to support a ''data interoperability network''.  The network should be multidisciplinary; the network proposal should have a community aspect and a technology aspect.  The deadline (possibly the last deadline for this program) is July 23.
  
 
What makes us competitive:
 
What makes us competitive:
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* our connections with a network of researchers, programmers, and data providers
 
* our connections with a network of researchers, programmers, and data providers
  
= Planning documents =
+
Over the course of 4 weeks in June and July, a group of individuals developed a proposal for a data interoperability network focused on trees and associated data and metadata.  Two key features of the proposal are the use of hackathons, and the use of the "EvoIO Stack" (nexml, CDAO, phyloWS) as a technological nucleus for growing an interop network.
  
== Key aspects of the INTEROP program ==
+
= The Proposal =
  
The first priorities are to work out the scope of the project, and major aims that are consistent with
+
== Project Summary ==
# who we are, what we've done and what we want to do, and
 
# what is required for a successful NSF interop grant, and what kind of support the program provides
 
  
I think we are familiar with the first item, so lets get to the second one: what makes a successful INTEROP proposal?  Here are some key distinctions to keep in mind for INTEROP:
+
'''INTEROP: A network for enabling community-driven standards to link evolution into the global web of data (EvoIO)'''
# '''community involvement AND enabling technologies'''.  A successful proposal needs to have '''both'''.  We need to show that we are ready to respond to a community's needs, and that we have the technical expertise to support standards or conventions that arise in response to community needs.  If the community needs a web services standard, we need to be able to develop one.  In order to do this, we need to create a community, using workshops and web sites and mailing lists and so on.  We have been doing a lot of that, but it needs to be opened up even more.  I think we are on solid ground here. 
 
# '''cross-cutting'''.  A successful proposal needs to address more than one disciplinary area.  This may be a challenge for us.  We are diverse in terms of ranging from molecular evolution to species diversity, but this is all within the discipline of life sciences.  We have a computer scientist, but we might need more.  What other disciplines could be involved, e.g., earth sciences, physics, behavior?  The program also looks for diversity in the '''types of data''' involved.  So, if we address phylogenies, taxonomic classes, and comparative data, this is much broader than if we just focus on trees. 
 
# '''community engagement'''.  We need to do more than just involve a community, we need to be responsive.  "Proposals for activites not based on significant community engagement and consensus-building activities are not responsive to this solicitation and will be returned without review".  We have developed nexml, CDAO and phyloWS with the aim of serving community interop needs.  However, so far these tools are limited in their use.  Lets imagine some future point where these are full-fledged community resources, widely supported in the phylogenetics community (like BioPerl is now), with
 
#* many people involved in development (i.e., many "eyes on code")
 
#* documentation and training resources readily available for anyone who wants to learn
 
#* many people trained to use the tools
 
#* many research projects willing to contribute to maintaining and improving these tools
 
#* symposia and satellite conferences at major meetings
 
  
The NSF  Interop program will provide support for meetings and workshops, along with a modest amount of support for technical staff. The staff support could be used to pay programmers to develop the tools that support nexml, CDAO and phyloWS. We could focus this technical support on
+
PI: '''Arlin Stoltzfus''', Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute (CDAO, Bio::NEXUS, Nexplorer). Co-PIs: '''Karen Cranston''', EOL and Field Museum of Natural History; '''Enrico Pontelli''', New Mexico State University, Computer Science (CDAO); '''Sheldon McKay''', Cold Spring Harbor Laboratory (GMOD, modENCODE, iPlant), '''Hilmar Lapp''', NESCent (PhyloWS, BioSQL); '''Nico Cellinese''', University of Florida, Florida Museum of Natural History (TOLKIN, RegNum).
* one or a few integrative projects that we would implement in order to showcase the technologies
 
* generalized support for many projects carried out individually by members of the collaborative
 
  
There are a few advantages to the latter approach. First, we will be more focused on the standards and less on the final product. This will help to distinguish us from projects like the iPlant Tree of Life. Second, working with many projects will ensure that our solutions are generalized, rather than being biased by the choice of a few data types/ providers for a showcase project.
+
'''Intellectual Merit'''. Evolutionary trees (“phylogenies”) organize knowledge of biodiversity and
 +
provide a framework for rigorous methods of comparative analysis used throughout the bio-
 +
sciences. In the past, the scope of a tree-based analysis was limited to the researcher’s “own”
 +
small data set. The great mass of currently available data makes possible far-reaching and
 +
systematic analyses, but only if trees (and associated data and metadata) can be accessed,
 +
searched, retrieved, and repurposed— that is, only if the data are interoperable. An integrated
 +
solution to this problem requires attention to the syntax and semantics of data, metadata, and
 +
services. Over the past 3 years, an “Evolutionary Informatics” working group funded by NESCent (an NSF Center) developed an interoperability “stack” consisting of NeXML (a file format
 +
for comparative data), the Comparative Data Analysis Ontology (CDAO) and PhyloWS (a web
 +
services standard). Recently, the group staged a “hackathon” that engaged a fresh group of
 +
researcher-programmers (chosen to represent community data resources) to learn, apply, and
 +
extend the EvoIO Stack, with results that show the remarkable promise of this approach to
 +
train early-career scientists, disseminate standards, and improve interoperability. The investigators will build on this approach and on their unique technology and experience to engage a
 +
larger community in improving interoperability of trees with associated data and metadata
 +
(e.g., taxonomic affiliations, sources, character data, etc). The EvoIO Network will organize
 +
hackathons, hold training workshops, host working groups, and implement infrastructure for
 +
community-building around emerging standards. Network staff will provide technical expertise
 +
in knowledge representation and bioinformatics, working to support standards and to build
 +
reference implementations. The resulting EvoIO community will extend broadly into
 +
systematics-biodiversity, comparative genomics, and phylogenetics, and will penetrate into
 +
key areas of community ecology, phylogenetic epidemiology and paleobiology.
  
In addition to workshops and meetings aimed at development of standards and tools, we should also aim for some training workshops:
+
'''Broader impacts'''. The research areas affected by this proposal— all those areas in which
* for data providers (how do I share my data?)
+
phylogenetic trees are used routinely— are diverse and currently are not unified by professional organizations, software platforms, or standards. By bringing together scientists from
* for data users (what data is available and how do I find / obtain it?). This could be an independent workshop, or integrated into an existing program (Woods Hole Molecular Evolution, Bodega Bay Phylogenetics, Computational Phyloinformatics at NESCent, etc).
+
various disciplines, we will develop awareness of the need for standards, cohesion around
 
+
preferred approaches to interoperability, and ultimately a broad consensus on specific standards. This will be accomplished by building on the momentum of work done under prior NSF
== People and institutions ==
+
funding via NESCent. The key to developing a cohesive community in the absence of pre-
 
+
existing cohesion is the hackathon mechanism, which generates success stories and arms
=== PI, Co-PIs, and senior project personnel ===
+
young researcher-programmers with the know-how to create further successes. Through this
 
+
mechanism, user requirements will be translated into standards and specifications, and implemented in community software tools. Reference Implementations (developed concurrently
This proposal needs a '''single PI''' from the coordinating instiution. However, there is no limit to the number of Co-PIs.
+
with standards and specifications) will be used to aid in standards development and training.
 
+
Hackathons will take place in eastern, western, and central locations to maximize diversity in
Here are the people interested so far:
+
impact, and will include strategically selected participants as well as a large fraction of participants chosen in response to a broad solicitation in the biodiversity, systematics, genomics,
# Karen Cranston, EOL and Field Museum of Natural History (I would be coming at this from the perspective of both a provider (PhyLoTA) and user (EOL, Treeviz working group) of phylogenetic data. I am officially working with the EOL, and also have a connection to the iPlant Tree of Life group, both of which are going to need these tools.)
+
and phylogenetics communities.  Standards and specifications developed by the Network will
# Enrico Pontelli, New Mexico State University, Computer Science
+
be disseminated via the relevant international standards group (the TDWG Phylogenetics
# Rutger Vos, University of British Columbia, Zoology
+
Standard Interest Group).  Efforts will be made to integrate ideas from this project into existing
# Arlin Stoltzfus, University of Maryland Biotechnology Institute
+
educational and outreach programs, with particular focus on involving students from NMSU (a
 
+
minority-serving institution).
= Initial draft of NSF Proposal =
 
 
 
== Title ==
 
 
 
suggested titles (must begin with "INTEROP: "):
 
* INTEROP: Integration and re-use of phylogenetic and comparative data by an expanding research community
 
* INTEROP: As phyloGood as it phyloGets
 
 
 
== Project Summary ==
 
 
 
''the project summary has 3 parts:''
 
* ''Title, PI, Co-PIs, and senior project personnel''
 
* ''"a succinct summary of intellectual merit" including scope of activities (communities, data types, technologies), networking activities and mechanisms for participation, and ways of providing technical expertise''
 
* ''"a description of broader impacts" including interop, participation, education & training''
 
  
 
== Project Description ==
 
== Project Description ==
  
=== Aims ===
+
The [[Media:ProjectDescription_opt.pdf|Project Description]] is available as a PDF.
 
 
 
 
=== Background ===
 
 
 
=== Results from past research ===
 
 
 
=== Research Design ===
 
 
 
=== Budget justification ===
 
 
 
* meeting costs
 
* staffing  costs
 
** software design and implementation
 
** use case testing
 

Latest revision as of 11:41, 8 October 2009

As a followup activity to the successful Database Interop Hackathon, a group of individuals submitted a proposal to NSF for a multi-year $750000 project to fund an EvoIO Network.

Background

Due to the foundation laid (over several years) by many people, including NESCent's informatics staff, the Evolutionary Informatics working group, and the participants in the recent data interop hackathon, we are in a position to apply to the NSF INTEROP program. This program provides up to 250 K per year to support a data interoperability network. The network should be multidisciplinary; the network proposal should have a community aspect and a technology aspect. The deadline (possibly the last deadline for this program) is July 23.

What makes us competitive:

  • our past success in developing interop technologies nexml, CDAO and PhyloWS
  • the 3-part interop formula of data syntax (nexml), semantics (CDAO) and services (phyloWS)
  • our past success in actual demonstration projects that show off interop technology
  • our demonstrated commitment to including diverse projects
  • our connections with a network of researchers, programmers, and data providers

Over the course of 4 weeks in June and July, a group of individuals developed a proposal for a data interoperability network focused on trees and associated data and metadata. Two key features of the proposal are the use of hackathons, and the use of the "EvoIO Stack" (nexml, CDAO, phyloWS) as a technological nucleus for growing an interop network.

The Proposal

Project Summary

INTEROP: A network for enabling community-driven standards to link evolution into the global web of data (EvoIO)

PI: Arlin Stoltzfus, Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute (CDAO, Bio::NEXUS, Nexplorer). Co-PIs: Karen Cranston, EOL and Field Museum of Natural History; Enrico Pontelli, New Mexico State University, Computer Science (CDAO); Sheldon McKay, Cold Spring Harbor Laboratory (GMOD, modENCODE, iPlant), Hilmar Lapp, NESCent (PhyloWS, BioSQL); Nico Cellinese, University of Florida, Florida Museum of Natural History (TOLKIN, RegNum).

Intellectual Merit. Evolutionary trees (“phylogenies”) organize knowledge of biodiversity and provide a framework for rigorous methods of comparative analysis used throughout the bio- sciences. In the past, the scope of a tree-based analysis was limited to the researcher’s “own” small data set. The great mass of currently available data makes possible far-reaching and systematic analyses, but only if trees (and associated data and metadata) can be accessed, searched, retrieved, and repurposed— that is, only if the data are interoperable. An integrated solution to this problem requires attention to the syntax and semantics of data, metadata, and services. Over the past 3 years, an “Evolutionary Informatics” working group funded by NESCent (an NSF Center) developed an interoperability “stack” consisting of NeXML (a file format for comparative data), the Comparative Data Analysis Ontology (CDAO) and PhyloWS (a web services standard). Recently, the group staged a “hackathon” that engaged a fresh group of researcher-programmers (chosen to represent community data resources) to learn, apply, and extend the EvoIO Stack, with results that show the remarkable promise of this approach to train early-career scientists, disseminate standards, and improve interoperability. The investigators will build on this approach and on their unique technology and experience to engage a larger community in improving interoperability of trees with associated data and metadata (e.g., taxonomic affiliations, sources, character data, etc). The EvoIO Network will organize hackathons, hold training workshops, host working groups, and implement infrastructure for community-building around emerging standards. Network staff will provide technical expertise in knowledge representation and bioinformatics, working to support standards and to build reference implementations. The resulting EvoIO community will extend broadly into systematics-biodiversity, comparative genomics, and phylogenetics, and will penetrate into key areas of community ecology, phylogenetic epidemiology and paleobiology.

Broader impacts. The research areas affected by this proposal— all those areas in which phylogenetic trees are used routinely— are diverse and currently are not unified by professional organizations, software platforms, or standards. By bringing together scientists from various disciplines, we will develop awareness of the need for standards, cohesion around preferred approaches to interoperability, and ultimately a broad consensus on specific standards. This will be accomplished by building on the momentum of work done under prior NSF funding via NESCent. The key to developing a cohesive community in the absence of pre- existing cohesion is the hackathon mechanism, which generates success stories and arms young researcher-programmers with the know-how to create further successes. Through this mechanism, user requirements will be translated into standards and specifications, and implemented in community software tools. Reference Implementations (developed concurrently with standards and specifications) will be used to aid in standards development and training. Hackathons will take place in eastern, western, and central locations to maximize diversity in impact, and will include strategically selected participants as well as a large fraction of participants chosen in response to a broad solicitation in the biodiversity, systematics, genomics, and phylogenetics communities. Standards and specifications developed by the Network will be disseminated via the relevant international standards group (the TDWG Phylogenetics Standard Interest Group). Efforts will be made to integrate ideas from this project into existing educational and outreach programs, with particular focus on involving students from NMSU (a minority-serving institution).

Project Description

The Project Description is available as a PDF.