Final GC Workshop & Collaborative Project Announcement 11-12-08
The iPlant Collaborative Grand Challenge Workshop Proposals & Grand Challenge Collaborative Project Proposals
Table of Contents
Overview
of
the
iPlant
Collaborative
Overview
of
the
Grand
Challenge
Identification
&
Recommendation
Process
How
to
propose
a
Grand
Challenge
Workshop
or
a
Collaborative
Project
A.
Proposing
a
Grand
Challenge
Workshop
A.1
Grand
Challenge
Workshop
Proposal
Content
A.2
Grand
Challenge
Workshop
Proposal
Review
A.3
Grand
Challenge
Workshop
Output
B.
Proposing
a
Grand
Challenge
Collaborative
Project
B.1
Grand
Challenge
Collaborative
Project
Proposal
Content
B.2
Grand
Challenge
Collaborative
Project
Proposal
Review
1
2
3
4
4
6
7
7
8
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Overview of the iPlant Collaborative
The iPlant Collaborative (iPC1) is funded by the National Science Foundation (NSF) to foster the development of a multi-disciplinary community to address Grand Challenges2 in plant biology through the cooperative development of computational infrastructure, (computational approaches & cyberinfrastructure3, referred to as “CI” in this document). Compelling Grand Challenge (GC) problems in the plant sciences must drive CI development. GC Collaborative Projects are proposed by multi-disciplinary community teams and evaluated by a Board of Directors representing the broad scientific research community. As directed by the NSF’s Plant Science Cyberinfrastructure Collaborative (PSCIC) solicitation (www.nsf.gov/pubs/2006/nsf06594/nsf06594.htm), GC Collaborative Projects suitable for the iPC must be beyond the scope of normal NSF funding programs and require development of community-wide CI by the iPC4. Furthermore, GC Collaborative Projects and the resulting CI must support training a new generation of scientists in innovative, multi-disciplinary research and provide educational opportunities for K-12 students, teachers and the public.
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“iPC” and “iPlant” are used interchangeably in this document and refer to the iPlant Collaborative.
“Grand Challenges” are major plant science research problems that are difficult or impossible to address without cross-disciplinary efforts and/or novel analytical approaches. 3 Cyberinfrastructure is abbreviated “CI” in this document. From Wikipedia: “The term ’cyberinfrastructure’ describes the new research environments that support advanced data acquisition, data storage, data management, data integration, data mining, data visualization and other computing and information processing services over the Internet. In scientific usage, cyberinfrastructure is a technological solution to the problem of efficiently connecting data, computers, and people with the goal of enabling derivation of novel scientific theories and knowledge.” 4 iPlant Collaborative funding from NSF is not to be used to generate new data, but restricted to the creation and testing of CI on existing data or data that is being generated in other ongoing or future projects.
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Final GC Workshop & Collaborative Project Announcement 11-12-08
GC Teams are an organizing principle of the overall process. These are crossdisciplinary, community-driven groups (research, teaching, humanitarian, business/commercial/private sector, etc) that will work cooperatively with the iPC’s CI development team to design and develop the custom software platforms and computational approaches to address specific GC Problems. The CI to address GC Problems in the plant sciences will be the principal direct outcome produced by the iPC for the research community. Custom software platforms making up the CI will be modular, open source resources that can be modified, expanded and ultimately sustained by the community after the iPC project ends. The CI and related computational approaches will also be used to engage the broader scientific community by forming the core of the iPC's Education, Outreach and Training (EOT) efforts. The cyberinfrastructure created by the iPC will create two main capabilities for the community. It will provide access to world-class physical infrastructure - for example, persistent storage and compute power via local and national resources. It will also make available services that promote interactions, communications and collaborations that advance the understanding and use of computational thinking in plant biology. Through these capabilities, the iPC will catalyze progress in targeted areas of plant biology, and more broadly advance the whole of plant science through new, creative, synthesis activities, and training the next generation of scientists in computational and collaborative thinking.
Overview: GC Identification & Recommendation Process
The Grand Challenge identification and recommendation process is initiated by the Plant Science Research Community and generally will follow the process shown in Figure 1.
Figure 1. The Grand Challenge Identification and Recommendation Process. Two
distinct paths are shown for GC Identification. The main route will be via a GC Workshop as
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Final GC Workshop & Collaborative Project Announcement 11-12-08
depicted on the left. If specific GC problems can be identified and clearly formulated into a Collaboration proposal, the workshop step may not be necessary. Finally, GC Team members proposing a Collaboration can come from any part of the research community with or without participating in a GC Workshop. GC Workshop Organizers are not necessarily the leaders or GC Teams proposing a Collaboration.
In the typical first step, a GC Workshop is proposed by a group of research community members to identify and discuss the various plant science GCs in a specific area of plant science. Note that a GC Collaborative Project can be proposed without first proposing or holding a GC workshop in cases where a GC Problem has been identified and it is clear that a collaboration could address the problem with CI development. GC Workshop Proposals will be accepted with deadlines once or twice each year5. The proposals will be reviewed by the iPlant Board of Directors6 who will recommend specific GC Workshops to be supported. iPlant staff will help community GC Workshop Organizers arrange recommended GC Workshops to take place at either CSHL in New York or Biosphere 2 in Arizona7. At each GC Workshop, cross-disciplinary teams will identify and discuss GC Problems that cannot be addressed efficiently by individual research groups. Once GC Problems are identified that require CI and cross-disciplinary solutions, community members will be encouraged to form teams to prepare GC Collaborative Project proposals. These teams are not necessarily led by GC Workshop organizers but can be formed by any collaborative group interested in a specific GC Problem. The GC Problems should be biological rather than technical. GC Collaborative Project proposals will describe the plant biology GC and will outline the projected CI requirements in sufficient detail to allow evaluation by the Board of Directors8. Following review and evaluation by the iPlant Board of Directors, recommendations on specific GC Collaborative Projects will be made and iPlant staff will initiate work with the GC teams. iPlant will facilitate assembly of a team of computing researchers, analysts, programmers and plant scientists to work closely with GC teams to develop a detailed Collaborative Project Specification plan. This process, which is described in more detail in the Grand Challenge Collaborative Project Specification Document9, will require close interaction between the GC team and the iPlant team. The process of developing specifications for a collaborative project may take several iterations and require a significant time commitment. This Project Specification will be necessary for appropriate CI development, testing, and deployment to the community.
How to propose a GC Workshop or Collaborative Project
Both GC Workshops and Collaborative Projects emerge from the community. Teams of organizers from the research community normally will propose GC Workshops to identify
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The deadlines for GC Workshop proposals will be posted at the iPlant Collaborative website www.iplantcollaborative.org.
The iPlant Collaborative Board of Directors is an independently chosen and impartial group of research community representatives. iPlant Board of Directors serve on a rotating basis. Current membership can be found at the iPC website. 7 Other locations can also be considered depending on various logistical factors. 8 Note that the detailed CI requirements of any proposed collaboration will only be possible after a complete project plan has been created using an iterative process and a cross-disciplinary team of biologists and computer scientists. Sufficient detail needs to be in the proposal to allow the Board of Directors to evaluate the collaborative proposal. iPlant staff can assist with this step if necessary. 9 The GC Collaborative Project Specification Document is posted at the iPlant website.
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Final GC Workshop & Collaborative Project Announcement 11-12-08
appropriate biological GC Problems in the plant sciences. Following the workshop, community teams will coalesce around a GC concept to create a GC Collaborative Project Proposal. Note that the organizers of GC Workshops are not the sole source of GC Collaborative Project Proposals. Collaborative Project Proposals can originate from any self-identified community team, and multiple teams can form following a workshop. Under exceptional circumstances it is also possible to propose a GC Collaborative Project without proposing a workshop (see Figure 1). Grand Challenge Workshops are intended to provide an opportunity for plant and computing scientists to develop an understanding of their common research interests as well as work together on the identification of relevant and tractable GC Problems in the plant sciences. The focus of a Grand Challenge Workshop can range from well-defined problems with large, existing datasets to broader, less well-defined problems with developing datasets. After an appropriately diverse, multi-disciplinary Grand Challenge Team10 coalesces around a Grand Challenge Problem in plant science, one or more teams can submit a Grand Challenge Collaborative Project proposal to the iPlant Board of Directors. When to submit a proposal: Target dates for GC Workshop and GC Collaborative Project Proposals will be posted and updated at the iPC website (www.iplantcollaborative.org). Note again that any GC Workshop participant can lead the formation of a team to propose a GC Collaborative Project Proposal, and more than one proposal can originate from a single workshop. Any group considering submitting a GC Collaborative Project Proposal in the absence of a GC Workshop is encouraged to contact Steve Goff, iPlant Collaborative Director of Community Interactions, at sgoff@iplantcollaborative.org, early in the planning process.
A. Proposing a Grand Challenge Workshop
Grand Challenge Workshops should facilitate: • • • • Identification of compelling GC problems/questions that can be addressed with existing data (or data being generated soon) and iPC resources. Assessment of the current state of resources and computational thinking in the field. Identification of relevant datasets that currently exist, or are expected to be available within the next 6-24 months. Participation of both plant and computational researchers, including interested individuals who have not previously worked in the specific area of plant biology or collaborated with the workshop organizers. Identification of barriers that currently prevent effective utilization of available data. Identification of barriers that could be overcome with additional datasets. Identification of Education, Outreach and Training opportunities the GC problems/questions could create.
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A.1 Grand Challenge Workshop Proposal Content
Please provide the following, in the order indicated, in a single PDF file: Front page:
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Any group of community members with a common interest in addressing a specific GC Problem.
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Final GC Workshop & Collaborative Project Announcement 11-12-08
Up to five GC Workshop Organizers to include at least one from the plant science and one from the computational science communities. Designate the main contact person for the GC Workshop. Provide contact information for each workshop organizer (Institution, Department, phone, email), and a short description of each organizer’s research, education and outreach interests. Propose up to ~40 key workshop participants (see below)11. Second page: Summary of the proposed GC Workshop that would be understandable to a knowledgeable lay person. Following pages: The description of the proposed GC Workshop should be 3-5 pages long. Please use a format that conforms to NSF proposal requirements (e.g., no smaller than 11 point Times New Roman font and minimum of 1" margins; full NSF specifications are at http://www.nsf.gov/pubs/policydocs/pappguide/nsf08_1/gpg_2.jsp#IIA). Please include the following information in the GC Workshop Proposal: 1. Statement of the GC Problem/Question being addressed, including past and current research toward the GC by the group submitting the proposal. 2. An explanation of why the GC Problem/Question requires custom cutting-edge computer science, cyberinfrastructure, bioinformatics, computational biology, statistical or modeling tools, rather than off-the-shelf solutions. 3. A general description of relevant data sets currently available or that will be available to the community during the next 6-24 months. Please note the NSF mandate that iPlant Collaborative Project funds may not be used for data generation. 4. A general description of the Education, Outreach and Training opportunities related to the GC question and how the cyberinfrastructure can support the effort. 5. Projected goals for the proposed GC Workshop - what are the expected outputs and outcomes? 6. What other biology or interdisciplinary groups are working in this or related areas? Which individuals from the other groups are anticipated to be involved in the proposed GC Workshop? 7. The general format of the proposed GC Workshop including a preliminary agenda for the meeting. Note that GC Workshops supported by the iPC are not typical scientific research meetings but are expected to focus presentations and discussion on the GC Problems and potential routes toward solutions using CI. Approximately 75% of the GC Workshop should be dedicated to discussions rather than formal presentations. iPC Advice on organizing a workshop agenda can be found at the following URL: http://www.iplantcollaborative.org/grandchallenge-proc/submit-gc-proposal. Members of the iPlant Collaborative staff are available to help in a variety of ways, including identifying scientists in the community with expertise and interest in different technical and outreach domains including EOT. Please feel free to provide a description of areas where you anticipate that iPlant Collaborative staff can help in the organization
Please do not invite participants before the GC Workshop is reviewed/approved by the Board of Directors and the iPlant staff confirms appropriate diversity & representation (Gender, institution, field of interest, location, etc).
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Final GC Workshop & Collaborative Project Announcement 11-12-08
of the GC Workshop. This will not be used in review of the proposal, but will be of value to the Collaborative members in planning for successful GC workshops. GC Workshop Proposals should include NSF format Biographical Sketches for each GC Workshop organizer. Please include an up-to-date list of trainees and current collaborators. Use this link for information on format of Biographical Sketches: http://www.nsf.gov/pubs/policydocs/pappguide/nsf08_1/gpg_2.jsp#IIC2f.
A.2 Grand Challenge Workshop Proposal Review
The iPlant Collaborative Board of Directors (BoD; http://iplantcollaborative.org/aboutipc/board-of-directors), with representatives from a broad range of relevant disciplines, has the responsibility to make recommendations on major resource allocations by the iPlant Collaborative, including sponsoring GC Workshops. Because the iPlant Collaborative is intended by NSF to be “by, for, and of the community”, all GC Workshop proposals will be posted at www.iplantcollaborative.org upon submission, and will be open for community comments during the review process. The iPC BoD summary of the review and the recommendation will be sent to the listed contact person for each GC Workshop proposal. Recommendation categories will be (1) high priority, (2) strong potential but needs improvement, and (3) not recommended at this time. Proposal Review Criteria The BoD will consider a variety of criteria in making recommendations to the iPlant Collaborative. These include, but are not limited to: • The context and significance of the GC Field/Problem/Question for advancing our understanding of plant biology and the likely existence of true Grand Challenge Projects suitable for iPC but not suitable for solution through normal funding channels. The types of data that are currently available, or will become available in the next 624 months, their scope, scale, quality and accessibility to a GC Project. How and why scientific advancement in the area is being limited by existing computational tools and cyberinfrastructure. Clear information on how advanced the proposing group is in its planning and how the proposed GC Workshop would bring the group and larger community closer to a Grand Challenge Collaboration Request. Note that GC Workshop Proposals will be considered for groups at all stages of development, but it is important to describe explicitly the current status of the group. Diversity of expertise in the proposed workshop participants. Participation of plant scientists is expected to be broadly multi-disciplinary, for instance spanning the molecular to the ecological, to ensure fully-informed discussion of Grand Challenges. Participation of a broad range of computational and computing researchers is also very important to help assess the tractability of GC questions. Plan for ensuring broad participation in Education and Outreach discussions at the workshop. Plan for involvement of individuals from different domains. How the proposed GC Workshop will increase discussion between or collaborative efforts of researchers in computer science, information systems, computational biology/bioinformatics, mathematics and modeling.
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Final GC Workshop & Collaborative Project Announcement 11-12-08
A.3 Grand Challenge Workshop Output
• Self-forming or self-identified team(s) of researchers with common interests in cross-disciplinary research targeted at one or more Plant Science Grand Challenge problems. Identification and further definition of specific GC Problems that suggest a route toward a GC Collaborative Project Proposal. A high-level description of the activities required to progress toward the solution of a specific Grand Challenge Problem (the broad and general scientific activities that a team of collaborating researchers would take). A description of the barriers that scientists face today in executing the scientific activities described above (if any). A description of the types of data and tools required to perform the activities described above (available today and in the near future). A description of cyberinfrastructure-enabled EOT opportunities related to the GC problem.
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The final GC Workshop outputs may require multiple iterations between participants. A “strawman” proposal from one or more individuals could be useful to allow the broader team to outline a general approach toward a specific Grand Challenge Problem. Output from a Grand Challenge Workshop could generate one or more proposals for Grand Challenge Collaborative Projects.
B. Proposing a Grand Challenge Collaborative Project
While each GC Collaborative Project Proposal will have distinct attributes and requirements, it is anticipated that each proposal will address the following points: • • • Description of the Grand Challenge Problem/Question. Description of the impact a successful infrastructure development would have on the broader field, beyond the research of the proposing team. Description of the high-level process for addressing the Grand Challenge Problem/Question (the broad scientific activities that a collaborating team would take to explore and make progress toward solution of the GC). Description of the current barriers in performing these scientific activities. Description of the types and quality of data and computational activities needed to perform these activities (data and approaches available today or anticipated in the near future). Estimated collaboration needs with researchers in the Computer and Information Science & Engineering (CISE) domains, and available expertise on the proposed GC project team. Projected Cyberinfrastructure needs, including high-level software and hardware requirements. What falls within the scope of the GC Collaborative Project and what is considered out-of-scope. Clearly defined education, outreach, and training objectives, how EOT is integrated into the project, and how it will be enabled by the CI.
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Final GC Workshop & Collaborative Project Announcement 11-12-08
Grand Challenge Team: • Proposed composition of the GC Team, including proposed team members available to interact with iPlant personnel on a regular basis. • Expertise in plant biology needed and expertise available. • Projected personnel resource needs for each project stage or deliverable. • Projected expertise needed to assess and ensure usability of the developed CI and expertise available. Management: • Expected GC Team and iPC responsibilities for each project deliverable. • Projected outline of expected project stages with timelines. • Milestones for critical project decisions. • Project team meeting schedule. • Project progress review plan, including monitoring committee needs and plans. • Potential Intellectual Property constraints (if any are known). • Projected bottlenecks or difficult steps. • Estimated completion date.
B.1 Grand Challenge Collaborative Project Proposal Content
For GC Collaborative Project Proposals please provide the following, in the order indicated, in a single PDF file: Front page: Names of 2-5 principal leaders of the proposed GC Collaborative Project, with at least one leader each from the plant science and computational science communities. The main contact person should be designated. Please provide contact information for each (Institution, Department, phone, email), and a 1-2 sentence description of their research, education and outreach interests. List other proposed key participants in the Participants section (see below). Second page: Summary of the proposed GC project that would be understandable to a knowledgeable lay person. Following pages: GC Collaboration Project Proposal descriptions should address the topics outlined in Proposing a Grand Challenge Project (bullet points in Section B above), in a total of 515 pages. Please use a format corresponding to NSF proposals (e.g., no smaller than 11 point Times New Roman and minimum of 1" margins full specifications can be found at http://www.nsf.gov/pubs/policydocs/pappguide/nsf08_1/gpg_2.jsp#IIA). Sufficiently described CI requirements should be included to allow the proposal to be evaluated broadly for feasibility of addressing the Grand Challenge goals. The specific CI requirements to address the proposed Grand Challenge Collaborative Project will be decided in an iterative, and ongoing process undertaken jointly by the iPC and the Grand Challenge Team.
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Final GC Workshop & Collaborative Project Announcement 11-12-08
GC Collaborative Project Proposals should include Biographical Sketches in NSF format for each GC project leader (see http://www.nsf.gov/pubs/policydocs/pappguide/nsf08_1/gpg_2.jsp#IIC2f. for formatting details). Please include an up-to-date list of trainees and current collaborators. On the final page of the GC Collaborative Project proposal, please provide a list of suggested reviewers in the domain areas related to the proposal (names, contact information and areas of expertise); please avoid suggesting reviewers with whom the principal leaders of the proposal are currently collaborating, their PhD and postdoctoral advisors and individuals from their home institutions. Individuals to be excluded as potential external reviewers with conflicts should be named with a short explanation. Conflict of Interest Document. A single integrated document (in table or spreadsheet form) should be emailed to Vicki Bryan (vbryan@iplantcollaborative.org). The document should consist of a list in the form of a single alphabetized table, with the full names of all people having a conflict of interest with any principle leader of the proposed GC Collaborative Project. Conflicts to be identified are (1) Ph.D. thesis advisors or advisees, (2) collaborators or co-authors for the past 48 months, including postdoctoral advisors and advisees and (3) any other individuals or institutions with which the investigator has financial ties. Consultation with the iPC during proposal preparation. Subject to resource availability, the iPC staff is available to advise Grand Challenge Teams on their description of cyberinfrastructure needs for specific proposals. However, iPC staff cannot comment on the viability of the Grand Challenge itself before proposals are reviewed by the Board of Directors. Please contact Rick Blevins for information on CI needs for a specific proposal (rblevins@iplantcollaborative.org).
B.2 Grand Challenge Project Proposal Review
The iPlant Collaborative BoD (http://iplantcollaborative.org/about-ipc/board-of-directors), which has representatives from a broad range of relevant disciplines, has the responsibility to make recommendations on the allocation of resources within the iPC project, including the review of GC Collaboration Project Proposals and execution of GC Collaborative Projects. During review of GC Collaborative Project Proposals, the BoD will obtain input from members of the community to supplement its expertise, if necessary, and then make recommendations to the Collaborative. Because the iPlant Collaborative is intended by NSF to be “by, for, and of the community”, all GC Collaborative Project Proposals will be published at www.iplantcollaborative.org upon submission and will be open for community comment during the review process. However, the names of external reviewers chosen by the BoD and the text of their reviews will be kept confidential. The BoD will use this input in making its recommendations to the Collaborative Director. GC Collaborative Project Proposal reviews and Board of Directors review summaries will be sent to the main contact person for each proposal.
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Final GC Workshop & Collaborative Project Announcement 11-12-08
Proposal Review Criteria The BoD will consider a variety of criteria in making recommendations to the Collaborative. These include, but are not limited to: • • The context and significance of the GC problem for advancing our understanding of plant biology. Whether a compelling case exists for how and why advancement of this area is being limited by lack of availability of computational tools and cyberinfrastructure, and the feasibility of overcoming existing obstacles. The capability of the proposed cyberinfrastructure projects to be transformative with respect to the GC questions. The scope, scale, quality and accessibility of the necessary data to the iPC project team and GC team during the project execution period, and the likelihood of additional relevant data becoming available in the near future. The feasibility of developing the proposed cyberinfrastructure. Appropriate expertise of the identified or proposed GC Team participants. Anticipated bottlenecks within the proposed GC Collaborative Project. Expectations for a division of responsibilities between the iPC project team and the proposed GC Team. The scope, scale and quality of EOT, its creative use of the cyberinfrastructure and its benefits/potential outcomes within the plant biology and computing communities. Plan for involvement of individuals from different domains. How will the group use the GC Collaborative Project to increase involvement of researchers in computer science, information systems, computational biology/bioinformatics, mathematics and modeling? Impact of the proposed project on community-building and computational thinking within the plant biology community and the larger community.
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If you have any questions as you plan a GC workshop or GC project proposal, please contact Steve Goff, iPC Director of Community Interactions at sgoff@iplantcollaborative.org.
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