FAQs

Frequently Asked Questions (FAQs)

Q: What is the iPlant Collaborative and what does it do?
Q: How do I propose a Grand Challenge Workshop or Project?
Q: How does a Grand Challenge Workshop differ from a Grand Challenge Project?
Q: How can I participate in a Grand Challenge Workshop?
Q: How does iPlant select Grand Challenge Workshops and/or Projects?
Q: Is iPlant a funding agency?
Q: What are the current Grand Challenge Projects?
Q: What is a Discovery Environment?

Q: What is the iPlant Collaborative and what does it do?

A: The iPlant Collaborative (iPlant) is a project funded in 2008 by the National Science Foundation (NSF) under its Plant Science Cyberinfrastructure Collaborative (PSCIC) program to foster the growth of a multi-disciplinary community that seeks to address Grand Challenges in plant biology through the development of cyberinfrastructure.  An organizing principle of iPlant is Grand Challenge teams--cross-disciplinary, community driven research groups--that work collaboratively with iPlant staff to design and develop ‘Discovery Environments’--software platforms custom-designed to help the team address a Grand Challenge question.

The scientific community is encouraged to participate in, and take ownership of, the iPlant Collaborative via a wide range of activities, including smaller Discovery Environment design groups that are not necessarily associated with Grand Challenge Teams; a web-based virtual community center; outreach teams that train users, including those at undergraduate and minority-serving institutions, to use the iPlant infrastructure to its best effect; and by partnering and developing synergistic, integrated ties with other centers, such as the ecology synthesis center (NCEAS), the evolution synthesis center (NESCent), the mathematical and biological synthesis center (NIMBioS), and others.

A key part of iPlant’s mission involves EOT—education, outreach, and training—to prepare the next generation of scientists to integrate computational thinking and the cyber tools that iPlant is developing into their research and teaching. Ultimately, researchers cross-trained to apply computational thinking to biology are the real infrastructure that iPlant is working to create.  iPlant’s EOT staff works with community groups to develop innovative curricula and training programs at the K-12 and university levels, and with Grand Challenge teams to find suitable opportunities to apply the Discovery Environments into existing educational and citizen science programs.

The original iPlant team institutions included the University of Arizona, Cold Spring Harbor Laboratory, Arizona State University, University of North Carolina-Wilmington, and Purdue University; to this team, the Texas Advanced Computing Center at University of Texas-Austin has been added.  Here is iPlant’s directory.

While iPlant is not a funding agency, we do have the capability to provide some level of financial support and in-kind resources to researchers, postdocs, students, teachers, and community members involved in the process of identifying Grand Challenge questions and developing the requirements and specifications of the cyberinfrastructure needed to solve them. 

Q: How do I propose a Grand Challenge Workshop or Project?

A: Please see the GC Identification and Recommendation Process, which outlines the specific process and timeframe for proposing a GCW and/or a GCP to the iPlant Collaborative.  For questions, contact iPlant’s Project Director, Steve Goff.

Q: How does a Grand Challenge Workshop differ from a Grand Challenge Project?

A: Generally speaking, Grand Challenge Workshops are short (3-4 days), intensive physical meetings in which an idea for Grand Challenge Project can evolve, develop, and mature to become the basis for a Grand Challenge Collaboration Project white paper.  While it is possible to propose a GC Project without holding a GC Workshop, a Workshop is a valuable opportunity for members of the broader community to physically meet, share ideas, and intensively discuss both the Grand Challenge question the group seeks to solve, as well as the cyberinfrastructural tools needed to address the problem. 

A GC Project, on the other hand, reflects a longer-term engagement between iPlant staff and the GC team.  During an approximately 2-year timeframe we estimate for each Grand Challenge Project, iPlant staff, GC team community leads, and interested community members work collaboratively to identify the user requirements the CI must meet, evaluate existing tools that can be integrated, work to develop data and workflow standards the community will support, design and test the CI, and conduct EOT activities to train the next generation of scientists in how to use the tools.

Another difference between a GC Workshop and a GC Project is iPlant’s role.  In keeping with our “by, for, and of the community” mission, iPlant management and faculty take a light-handed, back-seat approach to the Workshops, primarily providing guidance rather than direction to the organizers to ensure broad community diversity of participants and a biological focus to the GC question.  In contrast, in collaborating with the GC teams to develop the desired CI, iPlant staff takes an active role in providing and seeking the technical expertise and resources necessary to accomplish all the needed steps to successfully build, launch, and use the CI.

Q: How can I participate in a Grand Challenge Workshop?

A: Please see “How to Engage”.  In general, potential workshop participants are identified by the workshop’s community organizers, with input from iPlant to ensure broad and diverse membership from the plant biology, computational science, and education communities.  While physical participation is limited to about 40 individuals, including organizers, remote participation via the WebEx teleconferencing platform by any number of participants is possible and encouraged. 

If you are interested in participating physically or remotely in a GCW or other iPlant event, please contact Steve Goff, iPlant’s Project Director.

Q: How does iPlant select Grand Challenge Workshops and/or Projects?

A: In the first round of GC Workshop proposals and GC Project white papers, iPlant’s community-representative Board of Directors reviewed all submissions and then made recommendations to iPlant's Executive Team on the efforts that should be prioritized for support.

Going forward from our two existing Grand Challenge projects, all future workshop or project proposals will undergo the same review and recommendation process by the Board.

Q: Is iPlant a funding agency?

A: No, iPlant is not a funding agency.  However, there are several efforts and activities that iPlant anticipates community members could undertake on behalf of  developing Grand Challenge project proposals that iPlant will consider supporting on a case-by-case basis.  Requests for funding of GC project planning meetings prior to submission of a white paper can be considered.  Additionally, after the Board recommends a GC Project, iPlant can compensate GC Team members (faculty, post-docs, etc.) for their time working with iPlant to develop design specifications for CI development and for usability testing. In general, iPlant can only fund the effort necessary to develop, modify, and maintain the CI; it cannot support the research by the community using the CI developed for a GC Project.  Participation by international researchers and community members, including travel to the U.S. for participation in GC Team meetings, is strongly encouraged.  The iPlant Collaborative seeks to coordinate and cooperate with CI efforts in the plant sciences worldwide.

Q: What are the current Grand Challenge Projects?

A: As of September 2009, iPlant is undertaking two Grand Challenge projects, referred to as “iPToL” and “iPG2P”, as recommended by the Board of Directors. 

The iPlant Tree of Life (iPToL) Grand Challenge Project is lead by community leaders Michael Sanderson (UA), Pam and Doug Soltis (UFL), Michael Donoghue (Yale), Todd Vision (UNC, NESCent), Alexis Stamatakis (TUM), and Val Tannen (UPenn).  iPTOL seeks iPlant cyberinfrastructure to answer the Grand Challenge question “What does the tree of life look like for over 500,000 green plant species?” (for which there are genomic data).  This GC Team has six working groups-- “Data Integration,” “Data Assembly,” “Big Trees,” “Tree Reconciliation,” “Visualization,” and “Trait Evolution"--each tackling aspects of solving the larger question.  For more information about this GC Project, visit http://iptol.iplantcollaborative.org.

The iPlant Genotype-to-Phenotype (iPG2P) Grand Challenge is a joint effort led by Steve Welch (KSU), Ruth Grene (VT), and Tom Brutnell (Cornell), the community leads of three collaboration proposals seeking to understand the effects of biological, physical, chemical, and other factors affecting plants’ expression of genotype in its phenotype.   This team has five working groups, including  “NextGen Sequencing,” “Visual Analytics,” “Data Integration,” “ Inferential Tools,” and “Integrated Modeling Framework”.   For more information about this GC Project, visit http://ipg2p.iplantcollaborative.org.

Q: What is a Discovery Environment?

A: ‘Discovery Environment’ is a term iPlant uses to describe custom-designed software platforms that will allow the GC teams to address their selected Grand Challenges -- by accessing the relevant dat sets, integrating across them to identify connections and relationships, visualizing them in ways that allow "the big picture" to appear, manipulating the data with analytic tools, and sharing results by facilitating computational steering. Discovery Environments (DEs) typically take the form of “mashup” or "Web 2.0" applications, which facilitate the construction and integration of diverse types of data and tools.  Beneath their surface simplicity, Discovery Environments support sophisticated systems for semantic integration, description, and manipulation of biological data types. Discovery Environments are integrated into the growing iPlant cyberinfrastructure, becoming in time an open-source resource that will be expanded and maintained by the community as a whole.

During the formative phases, DEs will provide a way to exchange ideas and prototypes, and collaboratively create and refine an approach.  During the DE production phase, they will provide a collaborative environment in which to share ideas, integrate data sets, share protocols, and explore algorithmic approaches. Ultimately, iPlant's DEs will be a way to publish Grand Challenge teams' research findings to the world and to invite participation by the wider community.