- lsg-rg - lists.ogf.org

[wg-all] Mailing List Changes
by Andre Merzky 03 Sep '06

03 Sep '06

Sorry for duplicates ------------------------------------------------------------ As of yesterday, all GGF/OGF mailing lists are migrated to the ogf domain. They are now managed by mailman, the web interface is available at http://www.ogf.org/mailman/listinfo With that migration, all list can be now reached via <list>@ogf.org The old @ggf.org addresses will be available for some time, but are bound to disappear eventually - please start using the ogf addresses! A number of lists have changed their names: ggf-it --> ogf-it ggf-office --> ogf-office ggf-proc-wg --> ogf-proc-wg ggf-sponsors --> ogf-sponsors ggf-tutorials --> ogf-tutorials ggf-compute --> ogf-compute ggflistowners --> ogflistowners ggfstudentmembers --> ogfstudentmembers Postings to the old list names get forwarded to the new ones. With the migration we have also been able to fix the archives - you may have noticed that list archiving stopped sometime in mid June. Well, now its working again, and all mails from June to now have been added to the archive. The list archives can be found at: http://www.ogf.org/archives/<list> If you are an list administrator, and would like to receive the list admin password, please contact postmaster(a)ogf.org. In general, however, we tried to map the old majordomo settings to the mailman settings, in terms of privacy etc, so no or little changes should be required from your side. The spam avoidance policy has been changed to some extent, and is somewhat stricter than before. Please let us know if you experience any trouble with that. On all questions in respect to mailing lists, or mails in general, please contact postmaster(a)ogf.org. Best regards, Andre. -- "So much time, so little to do..." -- Garfield -- wg-all mailing list wg-all(a)ogf.org http://www.ogf.org/mailman/listinfo/wg-all

1 0

FW: LSGRID2006: Call for Paper (Deadline Extended to August 15, 2006)
by Angulo, David 31 Jul '06

31 Jul '06

We apologize if you are receiving duplicates. The deadline for submission of abstracts for papers, posters and demonstrations is extended to August 15, 2006. The 3rd International Life Science Grid Workshop (LSGRID2006) is scheduled to be held on Oct 13-14, 2006, at RIKEN Yokohama Institute, Japan. This is right before the PRAGMA 11 (Oct 15-17, 2006) at Osaka University, Japan, and after the 7th International Conference on Systems Biology, Oct 9-13, 2006 in Yokohama, Japan. Important Dates (Updated) * 15th August 2006 Submission deadline of Abstracts for posters/demonstration (800 words or more) * 15th August 2006 Submission deadline of Abstracts for Papers (up to 10 pages A4 format) * 1st September 2006 Notification of Acceptance * 15th September 2006 Submission of Camera Ready Paper Research Topics for Submission The program committee welcomes the submission of original manuscripts addressing the problem of Grid Systems for Life Sciences. Authors should report relevant experiences, present novel approaches to existing problems and describe and raise issues that must be overcome to facilitate Grid-based Life Science e-Research. Topics of interest include, but are not limited to: * Grid architectures for life sciences * Security of clinical and life science data sets * Usability of Grid based life science systems * Interoperability of Grid systems to support life science research * Grid based data access and integration of life science data sets * Applications and case studies on using the Grid in the life science domain * Computational workflows to support life science research processes * Development and usage of ontologies for the life sciences * Grid based drug discovery and pharmacogenomics * Grid based clinical trials and epidemiological studies * Semantic Grid approaches for the life sciences * High performance Grid architectures and systems for life sciences Please visit the website for the detail: (http://big.gsc.riken.jp/index_html/lsgrid2006/)

1 0

GGF 17 Life Science Grid Agenda
by Angulo, David 08 May '06

08 May '06

Dear all: Our meeting in Tokyo this week will be at the following location and will feature the following presentations: Theme of the meeting: Future Directions of Life Sciences Grid Date: Wednesday, May 10, 2006 Time: 3:45 PM - 5:15 PM (Tokyo local time) Location: Tokyo International Forum, Tokyo, Japan 1. The State of the LSG Community 2. Life Sciences at AIST: Achievements and Outlook by Yutaka Akiyama, AIST Japan 3. Trust in On Demand Systems by David Martin, IBM 4. General discussion on Future Directions of Life Sciences Grid Our subsequent meeting will be in Washington, DC and will have the theme "Medical Imaging." Dave Angulo and Abbas Farazdel

1 0

US-IL-Chicago Bioinformatician Programmer Postdoc Position
by Angulo, David 21 Apr '06

21 Apr '06

I am looking to fill the following postdoc position: Proteomics Join an exciting research group as a postdoc in an NIH funded study to analyze complete proteomic data. The Illinois Bio-Grid is a leading research group creating proteomic software using grid technology for Mass Spectrometry applications. With over 50 publications in the area, the group runs a large public database of empirical Mass Spectra, a public web site to search this database in order to identify unknown proteins, advances MS analysis algorithms, MS data management, and other advanced software techniques. We have a large software development group with 3 PhD students, 20 graduate students, and 5 undergraduate students. We are funded by the NIH, the NSF, Pfiszer, the Ben May Cancer Institute, and other places. We are looking for a postdoc to join this exciting group to work on software to support MALDI cancer assays. For a summary of our research, see http://facweb.cti.depaul.edu/bioinformatics, or contact Dave Angulo at dangulo(a)cti.depaul.edu or at 312-362-5041. JOB SUMMARY: The research associate will provide the leadership and general management of all operations. This will cover areas of coordinating activities with consultants, writing grants and assisting the PI in developing budgets and timelines. FUNCTIONAL RESPONSIBILITES: 1. Direct and facilitate all operations. 2. Maintain close contact with consultants and key community figures regarding grant development. 3. Assist PI in writing of research papers and reports 4. Assist PI in strategic planning, developing budgets and setting timelines for grants. MAJOR JOB CHARACTERISTCS: * General management: 20% * Coordination/ Communications: 10% * Writing/ Editing / Programming 60% * Strategic planning/ Budgeting: 10% KNOWLEDGE, SKILLS, AND ABILITIES: 1. The ability to plan, organize and manage the development of grant proposals. 2. The ability to provide necessary leadership: helping to maintain a high morale among co-workers. 3. The ability to write code in Java, C++, Struts, CGI, SQL, XML, Windows, Linux, Grids, Torque/Maui/DCC or other cluster environments, Ant, Make, shell scripts, autoconf, and other advanced technologies. 4. The ability to write strong, meaningful documentation in JavaDocs and/or Doxygen. 5. The ability to design and perform strong unit and integration testing using standard means such as JUnit. 6. Strong interpersonal skills for communicating with community officials who will be involved or contacted over the course of the project. 7. Proficiency in both written and oral communication, research report writing, and the delivery of such papers at national conferences. 8. The ability to develop agendas, and establish and meet time lines. EDUCATION AND REQUIREMENTS * Ph.D. degree in Computer Science with special focus on biology, chemistry, or biochemical applications. * Experience in collaborating with various external communities. * Experience making research presentations at national conferences. Date of last update: April, 2006 The above statements are intended to describe the general nature and level of the work being performed by people assigned to this work. This is not an exhaustive list of all duties and responsibilities associated with it. DePaul management reserves the right to amend and change responsibilities to meet business and organizational needs. David Sigfredo Angulo Faculty College of Computer Science, Telecommunications and Information Science DePaul University dangulo(a)cti.depaul.edu

1 0

LSGRID2006: Call for Paper
by Angulo, David 21 Apr '06

21 Apr '06

[We apologize if you receive multiple copies of this message] ---------------------------------------------------- CALL FOR PAPERS SUBMISSION DEADLINE: August 1st, 2006 LSGRID2006 13-14 October, 2006 RIKEN Genomic Sciences Center (GSC), TOKYO Web site: http://www.lsgrid.org/2006/ ---------------------------------------------------- Area and Scope The life science community is experiencing a period of unprecedented change, challenge and opportunity. With the completion of the sequencing of the human genome (and ever increasing numbers of other genomes), the opportunities of in-silico scientific research offer a new horizon of possibilities: from rapid targeted drug discovery, identification of genetic factors to disease causes and epidemiological studies through to complete biological understanding of complete organisms and tailored genetic treatments supporting e-Health solutions. The possibilities abound! Fundamental to the realization of this vision is the infrastructure needed to use and analyze the vast array of data sets associated with such research. These data sets are growing exponentially, often have radically different characteristics, are often maintained by completely different groups and bodies, and importantly are perpetually evolving. In this context, the development of an infrastructure that allows to access, use, and analyze such changing and growing amounts of data is both technically challenging, offers huge benefits to the scientific community and is potentially extremely viable commercially. The Grid represents one way in which such an infrastructure can be developed and supported, providing seamless access to computational and data resources. This workshop will focus on all aspects related to the application of Grid technologies to the challenges facing the life science community. Topics The program committee welcomes the submission of original manuscripts addressing the problem of Grid Systems for Life Sciences. Authors should report relevant experiences, present novel approaches to existing problems and describe and raise issues that must be overcome to facilitate Grid-based Life Science e-Research. Topics of interest include, but are not limited to: -Grid architectures for life sciences -Security of clinical and life science data sets -Usability of Grid based life science systems -Interoperability of Grid systems to support life science research -Grid based data access and integration of life science data sets -Applications and case studies on using the Grid in the life science domain -Computational workflows to support life science research processes -Development and usage of ontologies for the life sciences -Grid based drug discovery and pharmacogenomics -Grid based clinical trials and epidemiological studies -Semantic Grid approaches for the life sciences -High performance Grid architectures and systems for life sciences Paper Submission Authors are invited to submit original and unpublished work. Papers should not exceed 10 single-spaced pages on A4 paper size, using at least 1 inch margins and 12-point font. Authors should submit a PDF or PostScript file that will print on a PostScript printer. Electronic submission through the symposium website is strongly encouraged. Submission implies the willingness of at least one of the authors to register and present the paper. Important Dates 1st August 2006 Submission deadline of Abstracts for posters/demonstration (800 words or more) 1st August 2006 Submission deadline of Abstracts for Papers 1st September 2006 Notification of Acceptance 15th September 2006 Submission of Full Paper Program Chairs Professor SINNOTT Richard National e-Science Centre, Glasgow, UK Email: ros(a)dcs.gla.ac.uk Professor ANGULO David DePaul Univ., USA Email: dangulo(a)cti.depaul.edu Further Information For local information please contact: Professor KONAGAYA Akihiko RIKEN Institute, Japan Email: konagaya(a)gsc.riken.jp Download Instructions for Call for Papers here : http://www.lsgrid.org/2006/ -- Konagaya Akihiko <konagaya(a)gsc.riken.jp>

1 0

RE: [lsg-rg] new impetus...?[MESSAGE NOT SCANNED]
by Richard Sinnott 18 Apr '06

18 Apr '06

I see the agenda for GGF17 in Tokyo has been established (http://www.ggf.org/gf/event_schedule/index.php?id=298) Is this confirmed and will all people listed be attending and presenting? I must admit that I have no idea what will be presented above since I have not seen any visible activity in this group/email list, and most of the agenda look similar to previous GGFs (has the Best Practices in Life Science Grids changed since last time or the time before that etc?). Unfortunately I will not be able to attend the next GGF, but I am keen to see the work of this group progress. I previously suggested future activities in two areas described below. Are people happy with this idea? Can we start identifying people/resources/projects that can be used to explore the bioinformatics and HealthGrid problem spaces, and how we want to align ourselves with the GGF Grid Interoperability Now activity for example? My NeSC colleague (Anthony Stell) will be available to give a presentation and demonstration on security focused Grid based clinical trials and epidemiological studies. Can this be put in the agenda? Are there other projects out there that are in this area that want to present? It might not be my remit to put such questions as I'm not formally the LSG-RG anything, but the group needs to be more proactive if it is to be worthwhile. Rich ________________________________ From: owner-lsg-rg(a)ggf.org [mailto:owner-lsg-rg@ggf.org] On Behalf Of Richard Sinnott Sent: 16 February 2006 20:57 To: lsg-rg(a)ggf.org Subject: [lsg-rg] new impetus...?[MESSAGE NOT SCANNED] Hi Folks, it seems clear that there needs to be some more impetus to this group at GGF. Here are a couple of ideas which we might take forward/discuss. I'd welcome agreements/disagreements - silence is normally golden but not on email lists!!! Split into a healthGrid group and a life science group (here I'm thinking of a bioinformatics Grid) 1. Let us develop a real HealthGrid with folk who are interested in this area (I am one and we have already built various prototype systems accessing and using "representative" patient data sets using existing solutions across the NHS here in Scotland). 2. Let us develop a real life science Grid. We are interested in this and have bioinformatics data Grids and compute Grids already in place. Is this of interest? I think it will help to make this group have a goal. We might want to agree on the scope of these, e.g. whether we just want to look at exploring basic secure services for access to and usage of healthcare data sets, incorporating anonymisation and de-anonymisation scenarios, data linkage perhaps from patient records to imaging data etc. We are already working with advanced authorisation infrastructures using results from GGF standards groups such as AuthZ and ShibGrid. This group (in my humble opinion should be doing these kinds of things) if it is to be "GGF". If it isn't using GGF standards and technologies then one coule argue that it should be handled separately, e.g. through other conferences and workshops. What do folk think? Rich PS I am happy to provide more information on what we are up to at the National e-Science Centre, and am willing to lead/be involved in both of these Grid development activities if there is interest from folk that it should happen. Let's do stuff!

1 0

Call For Papers - ACM Crossroads Special Issue in Bioinformatics
by Angulo, David 28 Feb '06

28 Feb '06

Greetings, I am the guest editor of the ACM Crossroads special issue on Bioinformatics. ACM Crossroads is the largest and most popular college computing journal by and for computer science students, and sponsored by the premier computer science professional organization, the Association for Computing Machinery. We are looking for professional guest reviewers and editors from the academic community for this special issue on bioinformatics. If you have the time to spare to review 3-5 article submissions, please let us know. If you have a bit more time to help an accepted article through the editorial process, including content editing, that would also be greatly appreciated. In addition, we are calling for articles related to bioinformatics. We are hoping that you will pass this message along to any of your students who might be interested in submitting an article to Crossroads for this issue (both graduate and undergraduate students). Please also forward this on to your colleagues so that they can distribute it to their students. The "Call for Articles" is below... Thank you. If you have any questions, please don't hesitate to ask me or the Editor-in-Chief, Jerry Guo. Sincerely, David S. Angulo Faculty College of Computer Science, Telecommunications and Information Science DePaul University dangulo(a)cti.depaul.edu Jerry Guo Editor in Chief, ACM Crossroads Yale University ji.guo(a)yale.edu -- Call For Articles Crossroads, the Association for Computing Machinery Student Magazine Bioinformatics (Fall 2006) DUE DATE: 3 April 2006 SUBMISSION ADDRESS: http://www.acm.org/crossroads/submit/ INFORMATION: crossroads(a)acm.org http://www.acm.org/crossroads/doc/cfas/bio.html The Crossroads editorial staff invites authors to submit articles dealing with topics drawn from several areas pertaining to bioinformatics and computational biology. The following partial list of topics is provided to give prospective authors ideas for articles and is by no means exhaustive; other relevant topics will be considered. Papers that draw connections between two or more of these areas are especially welcome. * Genetic programming * Neural networks * Genomic and sequencing analysis * Evolutionary modeling * Data mining * Protein structure prediction * Modeling and simulations * Bioinformatic programs * Expression analysis * Bioinformatic ethics Articles should include a basic description of the kinds of problems being worked on, the state of the art of research, the state of the art of commercial applications, open problems, or future research/commercial development trends. Interviews with researchers; reviews of related books, software, videos, or conferences; and opinion columns on related issues are also welcome. We especially encourage both undergraduate and graduate students to submit articles. However, articles written or coauthored by professionals will also be considered. Crossroads articles should be written for a broad audience. They should be easily understandable by someone who has had only the most basic computer science instruction, and yet still be interesting to the advanced computer enthusiast. Articles longer than 6000 words will generally not be considered for publication. Feature articles should be between 1500 and 6000 words; reviews should be between 800 and 2000 words; and opinion columns should be between 800 and 3000 words. Articles should be written in a magazine style rather than a research paper style. In consideration of our diverse readership, authors should try to use language that is inclusive of people regardless of their gender, race, religion, nationality, or field of study. Additional writing guidelines and submission information are available online at the Crossroads web site (http://www.acm.org/crossroads/doc/information/writing.html) Crossroads is published both online and in print. We have a print circulation of about 20,000. All back issues are available for free on our website. Authors that have an article printed in Crossroads can receive complementary copies of the issue they were published in. All submissions should be formatted in XHTML or plain text format with all images at least 300 dpi, and submitted via http://www.acm.org/crossroads/submit/ Submissions are due April 3, 2006. They will be reviewed shortly thereafter and authors of accepted submissions will be notified within two to three weeks of the deadline. Prospective authors are invited to send email to the editors of Crossroads (crossroads(a)acm.org) indicating their intention to submit an article. In this way we can keep everyone informed of any changes in deadlines or formats and to make sure we have a good variety of articles. General questions should also be sent to the Crossroads editors.

2 1

Summer Fellowships for US undergraduates
by Angulo, David 24 Feb '06

24 Feb '06

Dear all: Below I have forwarded some information about a summer fellowship that is available to undergraduates interested in biology and computers - they MUST be US citizens or permanent residents. I would very much appreciate your help in soliciting good students for this summer. Please feel free to pass this on and to pass recommendations on to me. Thanks very much for your help. Dave The Biomedical Informatics Group at DePaul has a summer undergraduate research project in Bioinformatics and Grid computing. This group co-sponsors paid summer fellowships with the Illinois Bio-Grid, Argonne National Laboratory and the University of Chicago. The program will last for 10 weeks and will be conducted on-site in Chicago. Grid computing is a new field that utilizes geographically separated commodity computers as a virtual supercomputer. Students will have access to thousands of computers at the advanced computational facilities at Argonne National Laboratory and the Illinois Bio-Grid. Bioinformatics is a relatively new field of biological research involving computation. Areas include human genome research, simulations of biological and biochemical processes (such as cell membranes), and proteomics (e.g., protein folding simulations). This project will provide free summer housing and will pay $420 per week. More information on the project for Bioinformatics and Grid computing are available at http://reu.cti.depaul.edu or by contacting Dave Angulo at dangulo(a)cti.depaul.edu David S. Angulo Faculty College of Computer Science, Telecommunications and Information Science DePaul University dangulo(a)cti.depaul.edu

1 0

new impetus...?
by Richard Sinnott 16 Feb '06

16 Feb '06

Hi Folks, it seems clear that there needs to be some more impetus to this group at GGF. Here are a couple of ideas which we might take forward/discuss. I'd welcome agreements/disagreements - silence is normally golden but not on email lists!!! Split into a healthGrid group and a life science group (here I'm thinking of a bioinformatics Grid) 1. Let us develop a real HealthGrid with folk who are interested in this area (I am one and we have already built various prototype systems accessing and using "representative" patient data sets using existing solutions across the NHS here in Scotland). 2. Let us develop a real life science Grid. We are interested in this and have bioinformatics data Grids and compute Grids already in place. Is this of interest? I think it will help to make this group have a goal. We might want to agree on the scope of these, e.g. whether we just want to look at exploring basic secure services for access to and usage of healthcare data sets, incorporating anonymisation and de-anonymisation scenarios, data linkage perhaps from patient records to imaging data etc. We are already working with advanced authorisation infrastructures using results from GGF standards groups such as AuthZ and ShibGrid. This group (in my humble opinion should be doing these kinds of things) if it is to be "GGF". If it isn't using GGF standards and technologies then one coule argue that it should be handled separately, e.g. through other conferences and workshops. What do folk think? Rich PS I am happy to provide more information on what we are up to at the National e-Science Centre, and am willing to lead/be involved in both of these Grid development activities if there is interest from folk that it should happen. Let's do stuff!

2 3

minutes of LSG-RG meeting from GGF16
by Richard Sinnott 16 Feb '06

16 Feb '06

Hello All, attached are the minutes from the meeting that took place at GGF16 in Athens. Any comments from those who attended are welcomed (or those who didn't!?). I also attach the link to the caBIG security work that was mentioned at the meeting. https://cabig.nci.nih.gov/workspaces/Architecture/Security_Tech_Eval_White_… Cheers, Rich -- Dr Richard Sinnott (Professorial Research Fellow) Technical Director National e-Science Centre University of Glasgow, Glasgow G12 8QQ Tel: +44-(0)141-330-8606 Fax: -8625 Email: ros(a)dcs.gla.ac.uk

1 0