March 2005 - lsg-rg - lists.ogf.org

ACM SIGMOD Record, Special Section on Scientific Workflows
by Carole Goble 23 Mar '05

23 Mar '05

Subject: CFP: ACM SIGMOD Record, Special Section on Scientific Workflows ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ C A L L F O R P A P E R S SIGMOD RECORD, September 2005 Issue ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Special Section on Scientific Workflows ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Guest editors: Bertram Ludaescher & Carole Goble University of California at Davis, USA & University of Manchester, UK ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Today computational scientists across all disciplines (from biology, medicine, ecology, and other life sciences to chemistry, physics, geosciences, and astronomy) create ever increasing amounts of often highly complex data. Generated raw and derived data may come from wet lab experiments (possibly under control of a LIMS), large-scale data-intensive and compute-intensive simulations, or real-time observations e.g. from remote sensors. Technical challenges include not only the volume of data, but also the complexity of data of "metadata-intensive" applications. In order to support scientists in their data management and analysis tasks, scientific workflows have recently gained increased interest and momentum as a unifying mechanism for handling scientific data. While loosely related to the more traditional business workflows studied earlier by the database community, scientific workflows pose a quite different set of challenges due to the special nature of scientific data and the specific needs for large-scale data collection, querying, analysis, and visualization. Scientific workflows are often designed or depicted in a block diagram style, with connections indicating data-flow (and sometimes control-flow) between individual tasks. A comprehensive scientific workflow system should be able to schedule workflow tasks (typically in a distributed/Grid environment), monitor and control execution, allow on-the-fly visualization and computational steering, support user-interaction, facilitate "pause & rerun" of workflows, keep track of data provenance, and support various static and dynamic analysis and optimization techniques. Moreover, the underlying scientific workflow model and paradigm should facilitate component and subworkflow reuse. We invite contributions on all aspects of database technologies for scientific workflows (SWFs) including but not limited to: - conceptual modeling and design of SWFs - computation models for SWFs - scheduling, resource allocation, and planning for SWFs - static analysis, validation, verification of SWFs - distributed and Grid-based SWFs - web-service based SWFs (incl. overcoming limitations of web services) - data-intensive, compute-intensive, metadata-intensive SWF applications - data mining, data analysis, and statistics in SWFs - highly interactive SWFs - long running and non-interactive SWFs - transaction management and SWFs - fault tolerance in SWFs - scientific visualization and SWFs - problem-solving environments for SWFs (scientific workflow systems) - coupling SWF systems with other systems (databases, LIMS, statistics packages, visualization tools, etc) - data and workflow provenance in SWFs - knowledge representation and semantic extensions to SWFs ---------------- IMPORTANT DATES: ---------------- Paper submission deadline : May 21th, 2005 Notification of acceptance: June 26th, 2005 Camera ready copies due : July 10th, 2005 Submitted articles should not exceed 6 pages in the 2-column, 10-point SIGMOD Record format (see http://www.sigmod.org/record/author.html) Please email your contributions in PDF format, using Subject: SIGMOD-Record/SWF to LUDAESCH(a)UCDAVIS.EDU. -- Bertram Ludaescher Dept. of Computer Science & UC Davis Genome Center University of California at Davis One Shields Avenue, Davis, CA 95616 530-754-8576 (ph), 530-752-4767 (fax) ludaesch(a)ucdavis.edu

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gid security & health
by Richard Sinnott 16 Mar '05

16 Mar '05

Hi All, I made the mistake here at GGF13 of not looking down when Abbas asked for volunteers to putting some form of document together looking at Grid security and how far it goes to addressing the needs of healthcare. >From my perspective there are numerous ways this document might be structured: review of Grid security standards (AuthZ etc), review of Grid security implementations (GSI, PERMIS, VOMS, CAS, ...), review of Grid security practice, review of healthcare security infrastructures, practices, do's/don't, privacy, ethical concerns, etc etc It would be nice if this could be based on a realistic use case, e.g. accessing hospital data sets, ... If people are interested in joining this effort then feel free to drop me an email. I'm open to suggestions ... Rich -- Dr Richard Sinnott Technical Director National e-Science Centre University of Glasgow, Glasgow G12 8QQ, Scotland Email: ros(a)dcs.gla.ac.uk Mob: +44-(0)7952-376627 Tel: +44-(0)141-330--8606/Fax: --8625

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RE: [lsg-rg] Problem with conference line and AG node (Modified by Angela Broussard Hyderkhan)
by Angulo, David 14 Mar '05

14 Mar '05

John, I'm very sorry to say that you have already missed the workshop. Maybe you did the time conversion the wrong way around or missed the date line. Anyway, the conference was Saturday night Louisiana (and Chicago) time. The AG problems with video eventually got straightened out. The audio did come on line, but the quality was not good. Dave David S. Angulo Faculty College of Computer Science, Telecommunications and Information Science DePaul University dangulo(a)cti.depaul.edu > -----Original Message----- > From: John I Quebedeaux Jr [mailto:johnq@cct.lsu.edu] > Sent: Monday, March 14, 2005 10:52 AM > To: Angulo, David > Cc: lsg-rg(a)gridforum.org > Subject: Re: [lsg-rg] Problem with conference line and AG node (Modified > by Angela Broussard Hyderkhan) > > David, > > Check your times? I've left a message on Joe's phone. Unless I'm > showing up for something else? Someone forwarded this to me to warn me > of possible problems. > > LSU Baton Rouge is scheduled to come online tonight for the workshop > (tonight our time the 14th, morning their time the 15th). > > Although, no test was scheduled... hope it works. > > -John Q. > -- > John I. Quebedeaux, Jr. > Louisiana State University > Computer Manager / LBRN & CCT / 131 Life Sciences Bldg. & 339 Johnston > Hall > e-mail: johnq(a)lsu.edu or johnq(a)cct.lsu.edu / web: http://lbrn.lsu.edu & > http://cct.lsu.edu > phone: 225-578-0062 / fax: 225-578-2597 > > On Mar 12, 2005, at 6:16 PM, Angulo, David wrote: > > > John (from angela) just wanted to send you this to let you know about > > some potential problems with AG in korea. > > > > > > Dear all: > > > > If anyone is there in Seoul, please let us know what the problem is > > with the AG node and what the problem is with the coferece phone line. > > Neither are working ad the conference is already started. We're here > > live ith our AG node and we're in the correct virtual venue. > > > > Perhaps someone could even call us or send us a phoe number. We're at > > > > 773-834-0450 > > Cell: 773-396-2485 > > > > Send e-mail to jcs(a)uchicago.edu > > > > Thanks a bunch! > > > > Dave > >

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LS Grid 2004 post processing (from Konagaya Akihiko)
by Angulo, David 13 Mar '05

13 Mar '05

Dear All Here is an information about LSGRID2004 postprocessing. http://www.springerlink.com/app/home/issue.asp?wasp=e7a39b2add914b12a5db277… Regards, - Konagaya -- Konagaya Akihiko <konagaya(a)gsc.riken.jp>

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Problem with conference line and AG node
by Angulo, David 13 Mar '05

13 Mar '05

Dear all: If anyone is there in Seoul, please let us know what the problem is with the AG node and what the problem is with the coferece phone line. Neither are working ad the conference is already started. We're here live ith our AG node and we're in the correct virtual venue. Perhaps someone could even call us or send us a phoe number. We're at 773-834-0450 Cell: 773-396-2485 Send e-mail to jcs(a)uchicago.edu Thanks a bunch! Dave

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RE: GGF13 Workshop in Seoul - Schedule and AG information
by Angulo, David 12 Mar '05

12 Mar '05

Dear all: The materials are all posted. Dave David S. Angulo Faculty College of Computer Science, Telecommunications and Information Science DePaul University dangulo(a)cti.depaul.edu > -----Original Message----- > From: Angulo, David > Sent: Friday, March 11, 2005 7:30 AM > To: 'lsg-rg(a)ggf.org' > Cc: 'Dennis Gannon'; matsu(a)is.titech.ac.jp; 'Craig Lee' > Subject: GGF13 Workshop in Seoul - Schedule and AG information > > Dear all: > > We have a wonderful workshop planned for GGF 13 this Sunday (Saturday > night in the US). > > Attached is what should be the final version of the schedule. I am having > troubles uploading it and uploading the presentations. Perhaps this is > because of VERY poorly timed updates to gridforge? > > This document has the AG node information and the conference call > information on the document. Thanks to Dr. Jeong for setting up the AG > node and to Dr. Farazdel and IBM for the use of the conference call. > > When I can get the schedule uploaded, it will be available (an older > version is there now) at: > > https://forge.gridforum.org/projects/lsg-rg/document/GGF13-Agenda > > When I can get the documents uploaded, they will be available at > > > https://forge.gridforum.org/docman2/ViewCategory.php?group_id=39&categor y_ > id=831 > > Dave > > > > David S. Angulo > Faculty > College of Computer Science, Telecommunications and Information Science > DePaul University > dangulo(a)cti.depaul.edu

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Call-in information for - GGF13 LSG Healthgrid Workshop in Seoul
by Abbas Farazdel 12 Mar '05

12 Mar '05

Folks, Here is our call-in information for both the workshop (sunday 11Mar2005, 9am-6pm) and our regular group meeting (wednesday 16Mar2005, 9am-12:30pm). Dial-in numbers: Toll Free (USA): 1-888-430-3655 Toll (non-USA): 1-719-884-0807 Participant PC: 168548 Best Regards, Dr. Abbas Farazdel farazdel(a)us.ibm.com Senior Solutions Architect tel: +1.845.433.1652; fax: +1.845.491.3569 IBM Healthcare and Life Sciences cell: +1.845.216.4066 http://www.ibm.com/industries/healthcare/ Konagaya Akihiko <konagaya(a)gsc.riken.jp> 03/11/2005 08:06 PM To "Angulo, David" <dangulo(a)cti.depaul.edu> cc "Peter Arzberger" <parzberg(a)sdsc.edu>, "Tan Tin Wee (Biochemistry)" <bchtantw(a)nus.edu.sg>, "Karpjoo Jeong" <jeongk(a)konkuk.ac.kr>, Abbas Farazdel/Poughkeepsie/IBM@IBMUS, konagaya(a)gsc.riken.jp Subject Re: GGF13 Workshop in Seoul Dave Is there any telephone line for LSG-WG on Sunday? I will try to attend the WG from Japan. Regards, - Konagaya On Fri, 11 Mar 2005 15:36:59 -0600 "Angulo, David" <dangulo(a)cti.depaul.edu> wrote: > Tin Wee, > > We will have access grid, and we would very much welcome you presenting > via AG. > > Thank you for letting me know. I really appreciate it. > > Dave > > David S. Angulo > Faculty > College of Computer Science, Telecommunications and Information Science > DePaul University > dangulo(a)cti.depaul.edu > > > > -----Original Message----- > > From: Peter Arzberger [mailto:parzberg@sdsc.edu] > > Sent: Friday, March 11, 2005 12:31 PM > > To: Tan Tin Wee (Biochemistry) > > Cc: Angulo, David; Karpjoo Jeong; Abbas Farazdel; Konagaya Akihiko > > Subject: RE: GGF13 Workshop in Seoul > > > > > > Dear Tin Wee > > > > I am copying a few people on this. Since Konagaya-san won't be coming > - > > having you present via access grid would be good - but I'll admit that > I > > about about to get on an airplane and won't land until 12 hours before > > the workshop would begin ... > > > > So, I won't hold my breadth. > > > > However, if you have a short presentation about LSF2005 - (one or two > > slides) I could give them - and promote the meeting > > > > > > -----Original Message----- > > From: Tan Tin Wee (Biochemistry) [mailto:bchtantw@nus.edu.sg] > > Sent: Friday, March 11, 2005 9:19 AM > > To: Angulo, David; Angulo, David; jcs(a)uchicago.edu; > farazdel(a)us.ibm.com > > Cc: jcs(a)uchicago.edu; tinwee(a)bic.nus.edu.sg; breton(a)clermont.in2p3.fr; > > parzberg(a)sdsc.edu; parzberg(a)ucsd.edu; jeongk(a)konkuk.ac.kr; > > gskim(a)ncc.re.kr; Carolyn.Sheiman(a)uchospitals.edu; > c00hsh00(a)nchc.org.tw; > > yskwak(a)mail.knu.ac.kr; akazawas(a)who.int; akazawa(a)who.ch; dhlee; > > kimcm(a)pusan.ac.kr; Hiroshi MIZUSHIMA; hmizushi(a)ncc.go.jp; Jill > Kaufman; > > arun(a)bii.a-star.edu.sg; larryang(a)pacific.net.sg; Dennis Gannon; > > matsu(a)is.titech.ac.jp; Craig Lee > > Subject: RE: GGF13 Workshop in Seoul > > > > can someone please kindly forward Arun's and my replies to David as he > > doesn't seem to be receiving messages from us. Must be some silent > spam > > filters. > > > > Arun is not going. > > I don't have funding. > > Larry is unlikely to go. > > however, I can do AG into Seoul > > if I can get our National Grid Office to oblige me. As I cannot speak > on > > behalf of BII on a Life Sciences Grid in Singapore, I can speak on an > > A*STAR funded project on Biomanufacturing Grid for rapid response to > > emerging infectious diseases, details sent under separate email (which > I > > hope David has received). > > > > bestrgds > > tin wee > > > > > > -----Original Message----- > > From: Angulo, David [mailto:dangulo@cti.depaul.edu] > > Sent: Fri 3/11/2005 9:25 PM > > To: Angulo, David; jcs(a)uchicago.edu; farazdel(a)us.ibm.com > > Cc: jcs(a)uchicago.edu; tinwee(a)bic.nus.edu.sg; > > breton(a)clermont.in2p3.fr; parzberg(a)sdsc.edu; parzberg(a)ucsd.edu; > > jeongk(a)konkuk.ac.kr; gskim(a)ncc.re.kr; Carolyn.Sheiman(a)uchospitals.edu; > > c00hsh00(a)nchc.org.tw; yskwak(a)mail.knu.ac.kr; akazawas(a)who.int; > > akazawa(a)who.ch; dhlee; kimcm(a)pusan.ac.kr; Hiroshi MIZUSHIMA; > > hmizushi(a)ncc.go.jp; Jill Kaufman; arun(a)bii.a-star.edu.sg; > > larryang(a)pacific.net.sg; Dennis Gannon; matsu(a)is.titech.ac.jp; Craig > Lee > > Subject: GGF13 Workshop in Seoul > > Dear all: > > > > Thanks for a wonderful effort in getting this setup. I think we have > a > > wonderful workshop planned. > > > > Attached is what should be the final version of the schedule. I am > > having troubles uploading it and uploading the presentations. Perhaps > > this is because of VERY poorly timed updates to gridforge? > > > > We had one last minute cancellation, so I've moved Dr. Kwak's talk up > > half an hour. > > > > I also have the AG node information and the conference call > information > > on the document. Thanks to Dr. Jeong for setting up the AG node and > to > > Dr. Farazdel and IBM for the use of the conference call. > > > > Dave > > > > > > > > David S. Angulo > > Faculty > > College of Computer Science, Telecommunications and Information > Science > > DePaul University dangulo(a)cti.depaul.edu > > > > > > > -----Original Message----- > > > From: Angulo, David > > > Sent: Friday, March 11, 2005 12:49 AM > > > To: Angulo, David; Jonathan C Silverstein <jcs(a)uchicago.edu>; > > > 'farazdel(a)us.ibm.com' > > > Cc: 'jcs(a)uchicago.edu'; 'tinwee(a)bic.nus.edu.sg'; > > > 'breton(a)clermont.in2p3.fr'; 'parzberg(a)sdsc.edu'; > 'parzberg(a)ucsd.edu'; > > > 'Karpjoo Jeong <jeongk(a)konkuk.ac.kr>'; 'GSKim <gskim(a)ncc.re.kr>'; > > > 'Carolyn.Sheiman(a)uchospitals.edu'; 'Bonita Hung > > <c00hsh00(a)nchc.org.tw>'; > > > 'yskwak(a)mail.knu.ac.kr'; 'akazawas(a)who.int'; 'akazawa(a)who.ch'; > > 'dhlee'; > > > 'kimcm(a)pusan.ac.kr'; 'Hiroshi MIZUSHIMA'; 'hmizushi(a)ncc.go.jp'; > 'Jill > > > Kaufman'; 'arun(a)bii.a-star.edu.sg'; 'larryang(a)pacific.net.sg' > > > Subject: RE: IMPORTANT REPLY REQUESTED: GGF13 Workshop in Seoul > > > > > > Dear all, > > > > > > I received presentations from Kaufman/Silverstein, Kwak. I also > > received > > > a reply and a promise from Mizushima. Thanks to you all. > > > > > > I am still waiting for presentations from: > > > > > > 1. Bonita Hong > > > 2. Shunichi Akazawa > > > 3. Young Woo Kim > > > 4. Tin Tan Wee, Larry Ang, or Arun, or alternate > > > > > > > > > > > > These can not go on the AG unless I get the presentations quickly. > > > > > > Thanks again to all. > > > > > > Dave > > > > > > David S. Angulo > > > Faculty > > > College of Computer Science, Telecommunications and Information > > Science > > > DePaul University > > > dangulo(a)cti.depaul.edu > > > > > > > > > > -----Original Message----- > > > > From: Angulo, David > > > > Sent: Monday, March 07, 2005 4:11 PM > > > > To: Angulo, David; 'Jonathan.Silverstein(a)uchospitals.edu'; > > > > 'farazdel(a)us.ibm.com' > > > > Cc: 'jcs(a)uchicago.edu'; 'tinwee(a)bic.nus.edu.sg'; > > > > 'breton(a)clermont.in2p3.fr'; 'parzberg(a)sdsc.edu'; > > 'parzberg(a)ucsd.edu'; > > > > 'Karpjoo Jeong <jeongk(a)konkuk.ac.kr>'; 'GSKim <gskim(a)ncc.re.kr>'; > > > > 'Carolyn.Sheiman(a)uchospitals.edu'; 'Bonita Hung > > <c00hsh00(a)nchc.org.tw>'; > > > > 'yskwak(a)mail.knu.ac.kr'; 'akazawas(a)who.int'; 'akazawa(a)who.ch'; > > 'dhlee'; > > > > 'kimcm(a)pusan.ac.kr'; 'Hiroshi MIZUSHIMA'; 'hmizushi(a)ncc.go.jp'; > > 'Jill > > > > Kaufman'; 'arun(a)bii.a-star.edu.sg'; 'larryang(a)pacific.net.sg' > > > > Subject: IMPORTANT REPLY REQUESTED: GGF13 Workshop in Seoul > > > > > > > > Dear all speakers: > > > > > > > > Would you send me draft versions of your presentations (PPT, PDF, > > MS- > > > Word, > > > > or other formats) ASAP, please? We want to put them on our web > > site so > > > > that people on the AG or tele-conference will be able to follow > the > > > talks. > > > > Even rough drafts are appreciated, but please send something as > soon > > as > > > > you can. > > > > > > > > Thanks. > > > > > > > > Dave > > > > > > > > David S. Angulo > > > > Faculty > > > > College of Computer Science, Telecommunications and Information > > Science > > > > DePaul University > > > > dangulo(a)cti.depaul.edu > > > > > > > > > > > > > > -- Konagaya Akihiko <konagaya(a)gsc.riken.jp>

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GGF13 Workshop in Seoul - Schedule and AG information
by Angulo, David 11 Mar '05

11 Mar '05

Dear all: We have a wonderful workshop planned for GGF 13 this Sunday (Saturday night in the US). Attached is what should be the final version of the schedule. I am having troubles uploading it and uploading the presentations. Perhaps this is because of VERY poorly timed updates to gridforge? This document has the AG node information and the conference call information on the document. Thanks to Dr. Jeong for setting up the AG node and to Dr. Farazdel and IBM for the use of the conference call. When I can get the schedule uploaded, it will be available (an older version is there now) at: https://forge.gridforum.org/projects/lsg-rg/document/GGF13-Agenda When I can get the documents uploaded, they will be available at https://forge.gridforum.org/docman2/ViewCategory.php?group_id=39&categor y_id=831 Dave David S. Angulo Faculty College of Computer Science, Telecommunications and Information Science DePaul University dangulo(a)cti.depaul.edu

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GGF 13 Draft Schedule
by Angulo, David 02 Mar '05

02 Mar '05

Dear Life Sciences Grid member: GGF 13 in Seoul is quickly approaching. LSG-RG is having a workshop on "Healthcare Applications on Grids" on Sunday, March 13. The schedule for the LSG-RG workshop is available at https://forge.gridforum.org/projects/lsg-rg/document/GGF13-Agenda This will be updated as changes occur. It will also contain the phone numbers for dial-in access and information about the AG node Virtual Venue, since we will have AccesGrid access for this meeting. Dave David S. Angulo Faculty College of Computer Science, Telecommunications and Information Science DePaul University dangulo(a)cti.depaul.edu

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