Neil Gemmell's Report from PRAGMA 12
From BeSTGRID
Below please find a brief report on the PRAGMA 12 workshop held in Bangkok, Thailand, March 20-22, 2007, that I attended last week on behalf of BeSTGRID. I attended the main sessions, making a presentation on BeSTGRID, and also the Biosciences working group, where I outlined some of the portal developments ongoing at UC. Full details of the meeting can be found at: http://pragma12.thai-research.net/pragma12/index.php/Main_Page , but here is my summary of highlights.
1. I had a stimulating discussion with George McLauglin (TIN2, Pacific Northwest Gigapop etc.) about research networks and the challenges associated with uptake of these resources by researchers. He was also helpful in terms of discussions about future partnerships that REANNZ and BeSTGRID could make into Asia once the TIN2 pathways into Australia are finalised. I think it would be hugely beneficial if BeSTGRID make a case for inclusion of George McLauglin in the upcoming REANNZ meeting in July. I suggest I write to make this recommendation if this is viewed as useful.
2. Jacqueline Brown (University of Washington, Pacific Northwest Gigapop) and I met again at PRAGMA 12. We had originally met at PRAGMA 11 she was very enthusiastic about the progress we are making, which is useful as she will be down here for the REANNZ meeting in July and could be a strong advocate for what we are trying to achieve. One thing that came of this meeting was an invitation to attend the GidAsia meeting (Singapore 6-9 June), where I am told it would be useful to have me present because of my background in genomics. I have yet to confirm, but my intention at present is to attend if my other activities allow this.
3. I met with Jim deRoest (Research Channel). Jim is involved with some trials of Microsoft's Conference XP. This looks like a useful piece of software that might fit into the Evo space as and additional or competing tool. Conference XP will be free to academic users. I recommend that we explore conference XP further. Apparently Nathan Gardiner (HITLab) is actively exploring conference XP too, so this may be another collaboration solution we can adopt quickly.
4. There seem to be ongoing advances with Opal and Opal OP, which may be worth Vladimir, Andrey, and others exploring further. From the opal website "Opal Operation Provider (Opal OP) is an application wrapper which is implemented as an operation provider on Globus Toolkit 4 (GT4). The Opal OP provides a way to wrap up existing scientific applications rapidly as WSRF services on GT4. Originally, Opal is a software which has been developed by National Biomedical Computation Resource (NBCR) in San Diego Super Computer Center (SDSC). Basic features of the Opal OP are same as the Opal. Please refer the Opal's site. The Opal can provide a fixed wrapping web services implementation for applications. But, The Opal OP provides an extensible wrapping method to application developers as an operation provider." http://www.ais.cmc.osaka-u.ac.jp/~kohei/opalop/. Vladimir is going to explore the usefulness or not of this software over coming weeks.
5. I had a brief discussion with David Abramson (Monash University). David's team is developing a software solution called NIMROD for parametric analyses. http://www.csse.monash.edu.au/~davida/nimrod/. This might be very useful for research undertaken by groups such as Peter Hunter's and I recommend we investigate deployment of this software on our systems.
6. I attended the Biogrid working group break out session. The biogrid group mostly focused on modelling molecular interactions, so our phylogenetics focus was somewhat new to them. However, this was quite a profitable group to interact with as we were invited to participate in the Telemedicine and Advanced Technology Research Center (TATRC) funded influenza project. The full press release is attached, but an excerpt is below.
"We will use modern high-throughput biology to annotate the biological structures of different subtypes of the avian influenza virus, at the same time as we study their variations," said principal investigator Peter Arzberger, director of Life Science Initiatives at UC San Diego. "We will also construct a grid infrastructure to support avian flu research - an infrastructure that could one day handle research on other infectious diseases as well."
Added Arzberger: "Fighting a pandemic will also be easier if we put in place the infrastructure to replicate data, support medical informatics, and even assist in remote diagnosis."
7. I met Steve Downey of NCSA about his presentation on MaeViz (http://mae.ce.uiuc.edu/software_and_tools/maeviz.html). MAEviz takes advantage of the NEESgrid to redefine how earthquake engineering can support decision making. A product of the University of Illinois at Urbana-Champaign's Mid-America Earthquake Center and NCSA, it uses the grid and collaboratories to organize researchers across disciplines and synthesize their latest results. MAEviz combines spatial information, data, and visual information into a cyberenvironment for assessing and analyzing losses that might occur in an earthquake. In other words, it's a single community interface that integrates a variety of data sources and types and multiple types of analyses, so that earthquake engineers and policy makers can understand the physical, social, and economic ramifications of the next temblor. MaeViz maybe something NEES@Auckland or our folk at UC are aware of, but if not then perhaps it needs to be brought to their attention.
8. Peter Arzberger (chair of PRAGMA) and I discussed the way forward if BeSTGRID wishes to formally join PRAGMA. I think there is much to be gained from our ongoing involvement in this organisation and recommend we seek to join soon. Currently PRAGMA has about 30 member organisations and more are applying each meeting. I think it would be prudent to begin this process now. Details on how to join PRAGMA are attached.
