Difference between revisions of "NSF Interop Proposal"

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Please specific the type of conflict for each listing in the table.
Please specific the type of conflict for each listing in the table.
{| class="wikitable"
This table is available via google docs.  Please contact Arlin for the URL.
! Person !! type of conflict (PhD advisor-advisee; collaborator-coauthor; financial ties)
| Brandon Chisham || co-author of Arlin Stoltzfus
| Danny De Kee || co-author of Arlin Stoltzfus
| Vivek Gopalan || co-author of Arlin Stoltzfus
| Gopal Gupta || collaborator of Arlin Stoltzfus
| Francisco Prosdocimi || co-author of Arlin Stoltzfus
| Julie Thompson || co-author of Arlin Stoltzfus
| Lev Yampolsky || co-author of Arlin Stoltzfus

Revision as of 16:18, 6 July 2009


Overview and talking points

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 Interop proposal.

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.

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

Planning documents

Key aspects of the INTEROP program

The first priorities are to work out the scope of the project, and major aims that are consistent with

  1. who we are, what we've done and what we want to do, and
  2. 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:

  1. 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.
  2. 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.
  3. 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.

Possible components of a proposal

technology approach

The approach we have discussed is sometimes called the "evoinfo stack", consisting of

  • CDAO (semantics)
  • nexml (syntax)
  • phyloWS (services)

Together, these three represent an integrated approach to tackling interop problems.

a really good name

key collaborators

We have a core team composed of the PI and co-PIs, we also need collaborators.

The collaborators should be chosen strategically.

The collaborators should provide letters of commitment indicating their willingness to commit (as appropriate) to

  • send reps to attend meetings and workshops
  • contribute programmer hours from their own staff
  • offer services
  • participate in a working group or standards group

scientific challenges

The key challenge that we discussed was to ensure interoperability of trees with data and metadata. This has a nice focus but it can be expanded to cover anything.


Some money can be spent on salaries. Programmer post-docs in bioinformatics cost 40K or more plus benefits plus overhead, i.e., 70 or 80 K.


We bring together selected participants to work in an open-ended way, or to work on specific interoperability objectives, e.g., a reference implementation.


  • about $1K (??) per person for 4 days at NESCent
  • about $1200 per person for 4 days at FMNH in Chicago (incl. food, lodging and ground transportation)

training events

Training events could focus on developers or on end-users, e.g., on how to use nexml and nexml APIs. We could provide training

  • at a stand-alone workshop
  • as part of another workshop or course (Woods Hole Molecular Evolution, Bodega Bay Phylogenetics, Computational Phyloinformatics at NESCent, etc).
  • during a conference (which ones? SSE? SMBE?)
  • online (web course)

electronic resources

  • "help desk" concept
  • coordinate mailing lists
  • coordinate web sites
  • some sort of interaction portal

technical support

  • developing libraries
  • developing reference implementations
  • help desk


  • getting started with the EvoInfo stack
  • best practices for using the EvoInfo stack
  • making the most of EvoInfo stack implementations at (TOLKIN, iPlant, EOL, etc.)

demos, showcases, reference implementations

  • pick one project (e.g., TOLKIN) for thorough implementation of interop technologies
  • numerous small demos (e.g., as from the hackathon)
  • work with key projects (iPlant, EoL) for demo proejcts

working groups

might need to form some working groups to address specific issues:

  • metadata
  • taxonomic identifiers
  • scoping and conflicts between ontologies

a schedule with milestones

What are we going to accomplish in year 1?

What about year 2?

Year 3?

People and institutions

Some things to keep in mind:

  • NESCent can collaborate by providing meeting space (we pay travel and logistics overhead)
  • this is a US domestic program, but good to have international collaboration

PI, Co-PIs, and senior project personnel

This proposal needs a single PI from the coordinating instiution. However, there is no limit to the number of Co-PIs.

Here are the people interested so far:

  1. 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.)
  2. Enrico Pontelli, New Mexico State University, Computer Science
  3. Rutger Vos, University of British Columbia, Zoology
  4. Arlin Stoltzfus, University of Maryland Biotechnology Institute
  5. Sheldon McKay, Cold Spring Harbor Laboratory (GMOD, modENCODE, iPlant)
  6. Hilmar Lapp, NESCent

Potential participating projects

Large synthesis projects:

Other data providers and collaborators:

Initial draft of NSF Proposal


suggested titles (must begin with "INTEROP: "):

  • INTEROP: Integration and re-use of phylogenetic and comparative data by an expanding research community
  • INTEROP: Engaging an expanding community in developing and using the EvoInfo Stack
  • 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

INTEROP: As PhyloGood as it PhyloGets

PI: to be determined. Co-PIs: Karen Cranston, EOL and Field Museum of Natural History; Enrico Pontelli, New Mexico State University, Computer Science; Rutger Vos, University of British Columbia, Zoology; Arlin Stoltzfus, University of Maryland Biotechnology Institute; Sheldon McKay, Cold Spring Harbor Laboratory (GMOD, modENCODE, iPlant), Hilmar Lapp, NESCent

Intellectual Merit. The application of comparative methods based on phylogenies plays an expanding role in contemporary biological data analysis. Further advances in the use and the useability of phylogenetic comparative methods depends on improvements in interoperability. A key problem is the ability to compute interoperably with phylogenetic trees of arbitrary complexity and with various "metadata" or annotations such as taxonomic identifiers, literature references, and procedural notes. An integrated technological solution to this problem requires attention to the syntax, semantics, and services. The proposed Network will build on the work of the Evolutionary Informatics Working Group, which has developed . . .

in progress (needs: scope of network in terms of communities and data types; major networking activities; mechanisms for promoting participation; descrioption of technical expertise available to the Network)

Broader impacts (this should include impace of enhanced interop on science; plans to provide for diverse participation; educational training; outreach goals)

Project Description

1. Introduction and Network Objectives


  • example of kinds of data to be integrated

Network Objectives

2. Background and Rationale

Results from Prior NSF Support

Evolutionary Informatics Working Group (NESCent)
  • cohesion
  • practical gains during hackathon
  • the evoinfo stack
another NSF-supported project
another NSF-supported project
another NSF-supported project
another NSF-supported project

3. The Network Plan

Vision and Rationale for the Network

Network Organization

(groups and deliverables for each group)

Network Activities

Responsibilities of the Network

how will network meet dual responsibilities of engaging the community and providing expertise?

4. Broader Impacts

Education, Outreach and Training

5. Network Management Plan

Notes on additional parts of application

References Cited

indicate with an asterisk any cited publications from prior research frunded by NSF for the PI or co-PIs.

Biographical Sketchs

for PI, Co-PIs, senior personnel

Current and pending support

for PI, Co-PIs, senior personnel



  • most awards will be 3 years (special justification for 4 or 5 years)
  • restrictions on indirect costs on "partcipant support" costs (see solicitation)

Special Information and Supplementary Documentation

key personnel list

(max 3 pp): PI, Co-PI, senior personnel, with a brief descrioption of what each person brings to the network

current activities

current activities and results under prior NSF support for PI, co-PIs and senior personnel. Apparently this is the place for your other projects. Projects that are relevant precursors to teh Network proposal will be in another section.

letters of collaboration

letters from individuals or entities with a direct, integral and essential role in the nNetwork may be included. letters should document willingness to participate in or contribute to network activities. general letters of enorsement may not be included.

conflicts of interest list

"provide a list, in a single alphabetized table, with the full names of all people with conflicts of interest for 5he PI, co-PIs and senior personnel", including

  1. PhD advisors or advisees
  2. collaborators or co-authors for the past 48 months
  3. any other individuals or orgs with which the investigator has financial ties.

Please specific the type of conflict for each listing in the table.

This table is available via google docs. Please contact Arlin for the URL.