Group 02
From IPCMeeting042008
[edit] Evolution and development of form and function, from molecular, cellular and developmental biology to biodiversity, comparative biology, systematics and phylogenetics
[edit] Location
Grace Auditorium
[edit] Web Resources
- Live Stream/WebEx Virtual Conference
- Email List
- To subscribe to the mailing list associated with this discussion group, please send an email to breakout2-subscribe@iplantcollaborative.org
- Other administrative options, as well as at http://services.iplantcollaborative.org/mailman/listinfo/breakout2
[edit] Agenda
- Moderator: Mohan Tanniru, Oakland College
- Facilitator: Kobus Barnard, CS, Arizona
- Note Taker: TBD
- Discussion Leaders (tentative): Andrew Bangham, Edgar Spalding, Jody Banks, Todd Vision, Eric Kramer, Peggy Ozias-Akins, Bruce Kirchoff
Questions and goals for discussion in break-out groups
- What is the nature of a grand challenge that is both compelling and tractable?
- What are the essential infrastructural data sets that iPC should ensure are available to the community for these grand challenges? (Where are these datasets available? Would you like these to be linked to each other, and if so how? For these datasets, should iPC act as the primary repository, as a mirror, or as an interface? Which of these sets require curation? How frequently should these sets be refreshed? What sort of documentation and metadata do you need to have for these datasets? How would you want the quality of the data to be documented?)
- What algorithms and analytic methods should iPC ensure are available to the community for these grand challenges? (Are these currently available and if so where? If these methods/algorithms are computationally intensive, how should compute resources be allocated equitably?)
- What new types of algorithms, analytical models, and visualizations do you think are necessary to create in the iPC? Can you summarize these and show how they may be useful to the plant biology community at large.
- How will education, outreach, and training be addressed in these grand challenges? What knowledge and skills do the next generation need to work on such multidisciplinary questions?
- What sort of social networking tools do we need to enable effective collaboration?
- How do we engage the computing research community to make them aware of cutting edge research opportunities in their disciplines? How do we motivate computing researchers to participate in this collaborative?
- What do you think would help a diverse grand challenge team (diverse in terms of background and geography) collaborate effectively?
- What computer-based tools do you think would help the grand challenge teams in developing their questions and pursuing their research?
One major challenge is to understand how plants work at the molecular level. What are the regulatory elements that control their development, environmental responses to stress, the generation of bioenergy, resistance to pests, microbial interactions, growth, death and more processes?. One emerging field is the RNA regulation. Plants have a unique, large and almost unknown set of RNA machinery that control fundamental processes among all plant life. Even if microRNAs have been broadly studied in Arabidopsis, Oriza, Populus and Physcomitrella there are a lot of other RNA elements to be analyzed for example natsiRNAs, tasiRNA, long interference RNAs, there are new regulatory RNA processes that until now are specific to plants and also we have emerging genomes to explore. The expectative is that there is a core set of RNA elements shared between all land plants and unique sets for specific plant groups or species, the challenge is to identified this set, to identified these regulatory elements, to identify their targets, precursors, orientate phylogenetic studies of these regulatory elements to infer their function and identified evolutionary groups. The challenge is to understand the biodiversity of plant RNA regulatory elements and unique mechanisms of plants. Have you ever hear of systems biology, phylogeny or ontology of plant RNA species? Today there are databases that act as repositories, but there is not an integrative database to compile these information, there are not even bioinformatics tools to address this questions and some of the available algorithms are time consuming and require large amounts of computational power and memory, I guess probably with a collaborative approach it would be more easily. There are already collaborative teams for example the Arabidopsis Small RNA Project, but again it is focused in only one plant model.
Luis Servín lservin@lcg.unam.mx
