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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 03 Mar '05

03 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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FW: [BioInformatics Group] NETTAB 2005 Workshop on Workflows management in bioinformatics, Naples, October 2005
by Angulo, David 26 Feb '05

26 Feb '05

FYI David S. Angulo Faculty College of Computer Science, Telecommunications and Information Science DePaul University dangulo(a)cti.depaul.edu > -----Original Message----- > From: Paolo Romano [mailto:paolo@ist.unige.it] > Sent: Friday, February 25, 2005 10:39 AM > To: BioInformaticsGroup(a)yahoogroups.com > Subject: [BioInformatics Group] NETTAB 2005 Workshop on Workflows > management in bioinformatics, Naples, October 2005 > > > > Dear all, > > Do you have any plans for next october? > NETTAB 2005 is being announced. > > NETTAB 2005 Workshop on: > > Workflows management: > new abilities for the biological information overflow > > 5-7 October, 2005, > Second University of Naples, Naples, Italy > > http://www.nettab.org/2005/ > > This is the fifth in a series of workshops that intend to introduce > and discuss some of the most innovative and promising network tools > and applications in bioinformatics. > > The NETTAB 2005 workshop is focused on: > "Workflows management: new abilities for the biological information > overflow". > > It is well known that bioinformatics has to cope with one of the hugest > amount of information in all knowledge domains. This does not only include > biological sequences and structures, but also and increasingly microarray > data, metabolic pathways, interaction maps, gene networks. > Moreover, there is an exponential increase of this information (e.g., DNA > sequences increased more than 10% during last three months), so that it > won't be locally manageable soon. > > This huge amount of data is also largely distributed over the network, has > heterogeneous data structures and information systems and, often, even a > different semantics. The same heterogeneicity applies to the many > available > softwares. > > Moreover, the biomedical research domain is one of the fastest evoluting > research areas. New hypothesis and knowledges are accumulated daily, often > leading to new data and elaboration needs. User needs are often very > peculiar, > deeply different from one application domain to another. In this frame, > the > development of general purpose applications is difficult, both for the > different users' needs and the quickly accumulating knowledges, and > limited > to essential tools. > > Biological information is made available to researchers through web sites. > Biologists connect to many sites and switch among them to submit and > retrieve > preliminar and intermediate data. Final achievements are often the result > of a manual integration activity. The huge amount of information makes its > access un-exhaustive and inefficient and requires the development of > complex > searching and retrieval softwares. They can be developed to perform this > integration activity, provided that they are taught the semantics of the > information, how to link data and how to pipe retrieval and analysis > steps. > > According to the Workflow Management Coalition, a workflow is "a > computerized > facilitation or automation of a business process, in whole or part". > Its main goal is the implemention of data analysis processes in > standardized > environments. Its main advantages relates to: > > - effectiveness: being an automatic procedure, it frees the bioscientist > from > repetitive interactions with the web and it supports good practice, > - reproducibility: analysis can be replicated over time, > - reusability: intermediate results can be reused, > - traceability: the workflow is carried out in a transparent analysis > environment. > > Advantages of changing current biological information management from a > human-oriented to a machine-oriented approach are therefore clear. Machine > orientation is quickly improving, both as to technologies and tools and as > to its diffusion in the biomedical domain. Many Web Services have been > implemented, even by some of the most important network service Institute, > such as EBI and NCBI. Technologies related to registries of biological web > services and related implementation are also emerging, e.g. bioMOBY. > > It is therefore not surprising that implementation of workflows management > software already started. In recent years, we had Biopipe, an add-on to > bioperl for pipelines management, GPipe, an extension of the Pise > interface, > and, especially, Taverna, the most well known workflow management tool > that > is being developed within MyGrid project. And many others are coming. > > You can have a look at the presentation of the NETTAB 2005 workshop given > by Paolo Romano at the end of the NETTAB 2004 workshop in Camerino. > See http://www.nettab.org/2005/IntroductionToNETTAB05.pps . > > Best regards. > > On behalf of the Organizing Committee > Paolo Romano > -- > Paolo Romano (paolo.romano(a)istge.it) > National Cancer Research Institute > Largo Rosanna Benzi, 10, I-16132, Genova, Italy > Tel: +39-010-5737-288 Fax: +39-010-5737-295 > > > > ------------------------ Yahoo! Groups Sponsor --------------------~--> > What would our lives be like without music, dance, and theater? > Donate or volunteer in the arts today at Network for Good! > http://us.click.yahoo.com/TzSHvD/SOnJAA/79vVAA/efDslB/TM > --------------------------------------------------------------------~-> > > > Yahoo! Groups Links > > <*> To visit your group on the web, go to: > http://groups.yahoo.com/group/BioInformaticsGroup/ > > <*> To unsubscribe from this group, send an email to: > BioInformaticsGroup-unsubscribe(a)yahoogroups.com > > <*> Your use of Yahoo! Groups is subject to: > http://docs.yahoo.com/info/terms/ > > >

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FW: RE: New industrial user communities for GGF?
by Angulo, David 20 Jan '05

20 Jan '05

Dear all: I don't know anything about this conference, but I thought I'd pass it on. If anyone knows anything, feel free to post information to the list (or send to me directly). Thanks. Dave Dave Angulo Faculty DePaul School of Computer Science, Telecommunications, and Information Science dangulo(a)cti.depaul.edu 312-362-5041 <http://www.ud.com/> <http://www.ud.com/company/> <http://www.ud.com/solutions/> <http://www.ud.com/industries/> <http://www.ud.com/services/> <http://www.ud.com/partners/> <http://www.ud.com/rescenter/> Overview <http://www.ud.com/conference05/> Registration <https://www.ud.com/contact/registration.htm> Agenda <http://www.ud.com/conference05/aag.htm> Speakers <http://www.ud.com/conference05/speakers.htm> Sponsorships <http://www.ud.com/conference05/sponsors.htm> Not In Life Sciences? <http://www.ud.com/conference05/lifesciences.htm> <https://www.ud.com/contact/registration.htm> United Devices is proud to announce the 2005 Life Sciences Grid Conference -- a 2-day event focused on how grid computing is playing a critical role and delivering proven business benefits in Life Sciences. Join United Devices, our customers & partners, industry experts, and Life Sciences executives and scientists for a comprehensive look at what Life Sciences companies are doing with grid today - and tomorrow. UD'05 will provide attendees with an inside view of how grids are being used - and delivering value - across the Pharma business. What makes this conference a Do-Not-Miss Occasion? Real: We've got real customers talking about actual problems being solved by grid technology. Specific: Our sessions are focused and specific - we dive deep & deliver more value. Practical: Learn about strategies relevant to you - and leave with more than a hotel brochure. New: You'll hear it here first! Exclusive looks at cutting-edge grid uses (topics include human genomics and FDA compliance). Timely: Grids are expanding rapidly throughout Life Sciences - now's the time to understand how they can benefit you. You'll participate in discussions and workshops with professionals using grid in a variety of ways. You'll also have the chance to interact with application vendors, analysts and other experts. At UD'05, new and experienced grid users will join colleagues and industry experts for: 1. Business Value Presentations by Top Pharmas 2. Application Focus Sessions: Who's using grid - and how - for what benefit? 3. Ask the Expert: Submit questions after registration to be answered by our panel of experts 4. Technical Workshops: How your colleagues are interacting with grid technology Download a Conference brochure. <http://www.ud.com/conference05/ud05_brochure.pdf> Get more information about sponsoring this event. <http://www.ud.com/conference05/sponsors.htm> Space is limited -- Register today! <https://www.ud.com/contact/registration.htm> Who should attend: * CFOs, CIOs & CEOs interested in hearing about cost-saving solutions and proven, predictable ROI from grid * IT Managers who need real, proven technology solutions to virtualize, aggregate and manage their infrastructure * End Users of Life Sciences Applications from R&D to Sales & Marketing who want to connect with colleagues using grid <http://www.ud.com/conference05/> > Conference Brochure <http://www.ud.com/conference05/ud05_brochure.pdf> > Zurich Marriot Details <http://marriotthotels.ch/property/propertyPage/zrhdt> > Map and Transportation <http://marriotthotels.ch/property/mapandnearbyairports/default.mi?marsh aCode=zrhdt> Sponsored by: <http://welcome.hp.com/country/us/en/welcome.html> Keynote Addresses <http://www.ud.com/conference05/aag.htm> David Neilson, Johnson & Johnson Prof. Manuel Peitsch, Novartis Speakers From <http://www.ud.com/conference05/speakers.htm> GSK Johnson & Johnson Novartis HP Accelrys Schrodinger Tripos Gartner 451 Group Global Medical Forum Foundation Institute for Systems Biology University of Basel <http://www.ud.com/conference05/> Copyright (c) 1999-2005 United Devices. All Rights Reserved.

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GridWay development release
by Eduardo Huedo Cuesta 17 Jan '05

17 Jan '05

Dear LSG-RG colleagues, Below you will find the official announcement of the GridWay framework release. You can find some use cases in http://www.gridway.org/usecases.php, including a Bioinformatics application for protein structure prediction and thermodynamic analysis. Don't hesitate to check the rest of the web site and download the software. Best regards, Eduardo Huedo ======================================================================== GRIDWAY PROJECT TO RELEASE GRIDWAY 4.0 DEVELOPMENT RELEASE The GridWay Team is proud to announce the development release of GW4.0, which incorporates improved functionality and robustness for interacting with the Globus Toolkit services. More information and download at http://www.gridway.org All components developed as part of the GridWay framework are released as "open source" under the GPL license to encourage innovation and pass full freedom to our users. BENEFITS The GridWay framework provides a submission agent that incorporates the runtime mechanisms needed for transparently executing jobs in a Globus-based Grid. Its modular architecture for job adaptation to a dynamic environment offers the following benefits: - Easy to deploy: GridWay is a client tool that does not require new services, apart from Globus basic services. - Easy to extend and adapt: GridWay modules allow its communication with the Grid services available in a given testbed. In fact, it could be used as a building block for much more complex service-oriented. - Easy to use: It is not bounded to a specific class of application generated by a given programming environment, which extends its application range and allows reusing of existing software. - Easy to scale: Its decentralized architecture gives the possibility of boosting scalability. REQUIREMENTS GridWay framework does not require new system software to be installed in the Grid resources apart from Globus Toolkit services. The framework is currently functional on any Grid testbed based on the Globus Toolkit. The client computer must reach the following requirements: - UNIX-like Operating System (i.e. Linux) - A running Globus installation, version 2.4-3.9.3 GridWay uses the following Globus Toolkit services: - Pre-WS and WS GRAM - GridFTP - MDS, when necessary by the Resource Selector FEATURES The GridWay framework offers the following functionality: - Unix-like: GridWay uses commands very similar to those found on Unix systems and resource management systems like PBS or SGE. - Job control: With GridWay you can submit, kill, migrate, watch and wait for jobs. Also, you can submit an array of jobs. - Error detection: GridWay automatically detects when a job has failed, and allows the user to abort, retry o migrate it to a new machine. - Log information: Most relevant information about the jobs can be obtained in the several log files that GridWay generates. - Programming: DRMAA subset support to develop distributed applications. -- ************************************************** Eduardo Huedo Cuesta Laboratorio de Computación Avanzada, Simulación y Aplicaciones Telemáticas Centro de Astrobiología (CSIC-INTA) Ctra. de Ajalvir Km 4 28850 Torrejón de Ardoz, Madrid Spain Tel: +34 91 520 64 28 Fax: +34 91 520 10 74 Email: huedoce(a)inta.es Web: http://www.cab.inta.es/~huedoce **************************************************

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INTERNATIONAL SYMPOSIUM ON WEB SERVICES FOR COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
by Carole Goble 04 Jan '05

04 Jan '05

*Call for Presentations* <>INTERNATIONAL SYMPOSIUM *ON** WEB SERVICES FOR COMPUTATIONAL BIOLOGY **AND BIOINFORMATICS* *May 26 & 27, 2005 **Sponsored by Sun Microsystems** Organized by Virginia Bioinformatics Institute (VBI)* *At Virginia Polytechnic Institute and State University** Location: Virginia Bioinformatics Institute Conference Facilities** Donaldson Brown Hotel & Conference Center*<>* Blacksburg, Virginia *The deadline for submission of the Call for Presentations is January 31, 2005. Please feel free to forward this message. This Call is soliciting presentations for the* /International Symposium on Web Services for Computational Biology and Bioinformatics/. *An increasing number of groups are providing access to data and computational resources through web services. Through providing this access, challenges can occur for hardware, software, and system management, which need to be resolved for web services to be successful. Also, the number of deployed web applications in the field of Computational Biology is increasing; thereby, leading to scientific results generated through the use of distributed resources.** We are looking for contributions in the following areas: * Architecture (SGE, Portals Architectures, Open Grid) * Technical Issues (Scheduling, Economics/Accounting/Cost Recovery, Security) * Web Service-Based Applications * Scientific Results Using Web Service-Based Applications The expected length of each presentation will be 30 minutes. If you would like to present, please provide the following information: * Title of Presentation// * Abstract (300 words)// * Contact Information // * Short Biography (150 words or less)// * Audio/Visual Requirements// The deadline for submission of the Call for Presentations is January 31, 2005. Please send your information or questions to *webconference(a)vbi.vt.edu* <mailto:webconference@vbi.vt.edu>. All applicants will be notified of acceptance of their presentation by February 28, 2005.

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