From sandra.gesing at uni-tuebingen.de Mon Jan 2 09:33:18 2012 From: sandra.gesing at uni-tuebingen.de (Sandra Gesing) Date: Mon, 02 Jan 2012 15:33:18 +0100 Subject: [BiO BB] IWSG-Life 2012 - Deadline extension Message-ID: <20120102153318.10403devl0zo2vji@webmail.uni-tuebingen.de> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx IWSG-Life 2012 (4th International Workshop on Science Gateways for Life Sciences) Workshop Website: http://iwsg-life.org/2012 Date: 23-25 May 2012 Place: Amsterdam, The Netherlands Important dates: The deadline for paper/abstract submission: 30 January 2012 Notification of acceptance: 14 February 2012 Submission of camera ready papers: 19 March 2012 The workshop will take place in conjunction with the Healthgrid Conference 2012 (http://amsterdam2012.healthgrid.org/) and featuring EGI.eu. xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx Scope: IWSG-Life'12 will bring together scientists from the field of life sciences, bioinformatics and computer science. The aim is to exchange experience, formulate ideas and introduce up-to-date technological advances in molecular and systems biology in the context of Science Gateways. We invite the submission of papers related to various aspects of molecular and systems biology and Science Gateways/Portals. Suggested topics include, but are not limited to: * Management of biological high-throughput data * Modeling protein-carbohydrate recognition * Machine learning for computational immunomics * Molecular simulations for drug discovery * Portal technology and portal construction methods * Usage models and gateway tools for life sciences * Security aspects of Science Gateways for life sciences * Usability studies of life sciences portals/gateways * Workflows and service composition for life sciences * Service discovery and ontologies for life sciences * Tools for managing grid and cloud portability * Integration of life sciences with e-infrastructures * Demonstrations/ success stories Call for papers There are three alternatives for researchers to present their work: talks, lightning talks, and demonstration sessions. Submission of a full paper may result in a talk, submission of an abstract may result in an lightning talk or a demonstration. Additionally, attendees are invited to participate in a structured discussion facilitated by EGI.eu and an open discussion at the end of the workshop. *Accepted full papers will be published in PubMed-listed proceedings together with the proceedings of the Healthgrid Conference 2012.* Full papers All full papers will be double-blind peer reviewed and evaluated on quality and relevance. All submissions are held in confidentiality prior to publication in the proceedings. Presenters will be given a 20-minute time slot (plus 5 minutes for questions) to provide a summary and update to their work. Papers will be accepted electronically in PDF format only and are to be submitted through our EasyChair conference site at https://www.easychair.org/conferences/?conf=hgiwsg2012. They have to be formatted according to the layout style required by the IOSPress. Formatting requirements can be found at: http://www.iospress.nl/authco/instruction_crc.html. The paper length must not exceed ten pages and the papers must be written in clear and readable English. Every accepted submission must register and pay for at least one person. We expect one of the authors to attend the workshop and present the work. Abstracts Abstracts can be submitted for the lightning talk or for the demonstration sessions. Authors must indicate clearly which presentation format they are aiming for. All abstracts will be double-blind peer reviewed and evaluated on quality and relevance. Accepted lightning talk submissions will be given a 10-minute time slot (plus 5 minutes for questions) in an lightning talk session. Accepted demonstration submissions will be given a 10-minute time slot (plus 5 minutes for questions) in a demonstration session. Demonstrations will be given live to the workshop audience. Abstracts will be accepted electronically in PDF format only and are to be submitted through our EasyChair conference site at https://www.easychair.org/conferences/?conf=hgiwsg2012. The abstract length must not exceed 200 words and the abstracts must be written in clear and readably English. Every accepted submission must register and pay for at least one person. We expect one of the authors to attend the workshop and present the work. _______________________________________________ BBB mailing list BBB at www.bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb ----- Ende der weitergeleiteten Nachricht ----- From rwagner at faw.at Mon Jan 2 07:21:48 2012 From: rwagner at faw.at (Prof. Roland Wagner) Date: Mon, 02 Jan 2012 13:21:48 +0100 Subject: [BiO BB] ITBAM 2012 Call for Papers Message-ID: <4F01A15C.6010000@faw.at> Apologies in advance for multiple received copies of the CFP. Call for Papers - ITBAM '12 ******************************************** 3rd International Conference on Information Technology in Bio- and Medical Informatics - ITBAM 2012 Vienna, Austria September 3 - 7, 2012 ********************************************* Data intensive disciplines, such as life sciences and medicine, are promoting vivid research activities in the area of databases. Modern technologies, such as high-throughput mass-spectrometry and sequencing, micro-arrays, high-resolution imaging, etc. produce enormous and continuously increasing amounts of data. Huge public databases provide access to aggregated and consolidated information on genome and protein sequences, biological pathways, diseases, anatomy atlases, and scientific literature. There has never been more potentially available information to study biomedical systems, ranging from single cells to complete organisms. However, it is a non-trivial task to transform the vast amount of biomedical data into actionable information triggering scientific progress and supporting patient management. Major biomedical application scenarios for research in the database community include but are not limited to: . Systems biology . Genomics, proteomics, and metabolomics . Genome-wide association studies . Drug target discovery and personalized medicine . Neuroscience . Electronic patient records . Patient monitoring . Surgery planning and support . etc. Various emerging database technologies for coping with the challenges of these application scenarios have been developed and are an active area of research in information technology: . Administration of vast amounts of data . Integration of heterogeneous data sources . Federated and distributed databases . Data warehouses . Data mining techniques like classification, clustering, association rule mining, etc. . Decision support systems . Information and image retrieval . Signal processing and streaming databases . Privacy protection and data security . Data quality assurance . Process management and collaborative work . User interfaces and visualization . Interoperability and standardization . etc. Designing database technology to support applications in life sciences and medicine is an inspiring field of interdisciplinary research. The path from an idea to a practical application is often long and laborious, involving intensive interactions between experts in information technology, life sciences and the medical field. ITBAM accompanies and supports this path by providing an excellent venue for the exchange of ideas, fruitful discussion, and effective interaction among interdisciplinary researchers. In addition to the regular conference program featuring presentations of full and short research papers published in the proceedings, ITBAM encourages the submission of posters reporting work in progress. All accepted posters will be displayed during the whole event and abstracts will also be included in the proceedings. ******************************************************* IMPORTANT DATES . Submission of full papers (firm): March 12, 2012 . Notification of acceptance: May 14, 2012 . Submission of posters (firm): May 14, 2012 . Camera-ready copies due: June 15, 2012 ******************************************************* Paper Submission Details: Authors are invited to submit electronically original contributions or experience reports in English. The submitted manuscript should closely reflect the final paper as it will appear in the proceedings. . Paper submissions should not exceed 15 pages in LNCS format. Poster submissions are expected to consist of 1 page Abstract (http://www.springer.de/comp/lncs/authors.html). . Any submission that exceeds length limits or deviates from formatting requirements may be rejected without review. . For registration and electronic submission see: http://confdriver.ifs.tuwien.ac.at/ . The submission system will be open starting from January 2011. . Submitted papers will be carefully evaluated based on originality, significance, technical soundness, and clarity of exposition. . Duplicate submissions are not allowed. Authors are expected to agree to the following terms: "I understand that the paper being submitted must not overlap substantially with any other paper that I am a co-author of and that is currently submitted elsewhere. Furthermore, previously published papers with any overlap are cited prominently in this submission." Accepted Papers: All accepted conference papers will be published in "Lecture Notes in Computer Science" (LNCS) by Springer Verlag. Accepted full papers will be of 15 pages length, short papers 8 pages. Authors of accepted papers must sign a Springer copyright release form. For further inquiries, please contact the Conference Organisation Office (gabriela at dexa.org). GENERAL CHAIRPERSON: . Christian B?hm, University of Munich, Germany PROGRAM COMMITTEE CO-CHAIRPERSONS: . Sami Khuri, San Jos? State University, USA . Lenka Lhotska, Czech Technical University Prague, Czech Republic . M. Elena Renda, IIT - CNR, Pisa, Italy PROGRAM COMMITTEE: to be announced -- Univ. Prof. Dr. Roland Wagner Johannes Kepler Universit?t Linz A-4040 Linz Austria Europe Tel.: +43 676 84673210 Fax: +43 732 24689308 rrwagner at faw.at Director of the Institute of Applied Knowledgeprocessing (FAW) sec1: Monika Neubauer Tel.: +43 664 602468929 Fax.:+43 732 2468 9308 mneubauer at faw.uni-linz.ac.at http://www.faw.at http://www.dexa.org Director of the Institute "integriert studieren" (IS) Tel: +43 732 2468 9232Fax:+43 732 2468 9322 http://www.integriert-studieren.jku.at http://www.icchp.org Director of FAW GmbH Softwarepark 35 A-4232 Hagenberg Austria http://www.faw.at From maria.mirto at unisalento.it Wed Jan 4 05:58:41 2012 From: maria.mirto at unisalento.it (Maria Mirto) Date: Wed, 4 Jan 2012 11:58:41 +0100 Subject: [BiO BB] CFP - CBMS2012 - Special Track (ST-11) on Grid and Cloud Computing in Biomedicine and Life Sciences Message-ID: --- Apology for multiple posting --- ===================================================================== 25th IEEE International Symposium on COMPUTER-BASED MEDICAL SYSTEMS (CBMS 2012) Rome, Italy, 20-22 June 2012 5th Special Track on Grid and Cloud Computing in Biomedicine and Life Sciences http://datadog.unile.it/cbms2012 www.cbms2012.org ===================================================================== * * * CALL FOR PAPERS - Deadline January 15, 2012 * * * ===================================================================== Life sciences researchers routinely deal with large data to be analyzed by applications that need considerable computing power, including advanced parallel and distributed infrastructures, such as grids/clouds, clusters, and many-cores, multi-cores and FPGA architectures. Managing these data and optimizing the applications for these architectures is one of the challenges that must be tackled. High-throughput techniques for DNA sequencing, gene expression analysis, healthcare data analysis, etc., have led to an exponential increase in the volume of biological data, which in turn are geographically spread in several laboratories and data repositories. Other questions, such as climate change impact on the life sciences, and the disciplines to address them, are adding to the deluge of data: many prevalent human diseases are linked to climate fluctuations, from heat stress, cardiovascular mortality and respiratory illnesses due to heat waves, to altered transmission of infectious diseases and malnutrition connected to crop failures. Bringing together and correlating data among different and heterogeneous data sources will allow inference of new knowledge from these databases. There is a tremendous potential for end-users in many fields of life sciences, to routinely conduct large scale computations on distributed resources by using a combination of the following technologies: - Distributed middleware for connecting data/cluster computing centers: this includes grid computing middleware for users' authentication and accounting, remote job submission, resource scheduling/reservation, and data management; - Virtualization technologies capable of providing on demand application-specific execution environments: this involves a style of computing, cloud computing, in which on-demand resources are provided as a service over the Internet. Grid for the Life Sciences is an environment that allows sharing of resources, in which heterogeneous and dispersed health data as well as applications can be accessed by all users as a tailored information providing system according to their authorization. Cloud computing is emerging as a model for enabling convenient, on demand network access to a shared pool of configurable resources that can be rapidly provisioned and released with minimal management effort or service provider interaction. Institutions and medical professionals who frequently do not have enough storage and computing resources can manage their biomedical information through applications built on top of these types of services, accessing advanced computing infrastructures that they could not afford otherwise. While many companies, like Google, IBM, Amazon, and Microsoft, were early adopters of cloud computing, its application to biomedicine has been only recently proposed, mainly for bioinformatics applications. Several reviews and research papers have reported on these, while in contrast, applications in medical informatics have been infrequent. Now, medical applications are increasingly proposed and implemented, though reports are still scarce from a research and academic perspective. The main goal of the track is to exchange ideas and results related to on going grid and cloud computing research in Biomedicine, Life Sciences and correlated disciplines, such as Climate Change, that impact on human health, focusing on different aspects of middleware, technologies and applications. TOPICS OF INTEREST The topics of interest will include but will be not limited to: o Grid/cloud infrastructures, middleware and tools; o Grid/cloud applications: service and/or algorithm design and implementation; best practices related to solving large-scale problems on grid/cloud infrastructures; o Parallel algorithms using MPI or OpenMP; o Exploiting modern parallel architectures including FPGA, many-cores and multi-cores for parallel applications; o GPGPU parallel algorithms using OpenCL or CUDA; o Security and privacy preserving in grids/clouds; o Innovative approaches for the exploration, storage, processing, delivery and/or visualization of biomedical information; o Workflow Management Systems; o Scientific gateways and user environments; o Inferring new knowledge from databases by using data and text Mining methodologies and techniques; o Web services and cloud computing for biomedical applications: comparative studies; o Using biomedical ontologies for advanced cloud computing-based biomedical applications: requirements, experiences, limitations; o Real cases, testbeds and international projects facing (a) Biomedicine, bioinformatics and healthcare; (b) Climate change models and health challenges, etc.; (c) Applications for developing countries. PAPER SUBMISSION Papers should be submitted electronically using EasyChair online submission system. The papers must be prepared following the IEEE two-column format and should not exceed the length of 6 (six) Letter-sized pages. LaTeX or Microsoft Word templates can be used when preparing the papers. Please, note that only PDF format of submissions is allowed. Submission through EasyChair requires that an account in the system be created by a prospective author first. In order to create a new account, select the "I have no EasyChair account" option and follow the instructions given. When submitting, please, select the "Grid and Cloud Computing in Biomedicine and Life Sciences" special track. JOURNAL SPECIAL ISSUE After the workshop, selected papers may be invited for a special issue of an international journal or for an edited book. Selected papers (extended and revised versions) accepted on the previous editions of the workshop have been published on a special section of Briefings in Bioinformatics (Oxford University Press). IMPORTANT DATES Paper submission due January 15, 2012 Notification of acceptance March 15, 2012 Final camera-ready paper due April 10, 2012 Pre-registration deadline April 10, 2012 CBMS symposium days June 20-22 2012 TRACK CO-CHAIRS: * Giovanni Aloisio (University of Salento & CMCC, Lecce, Italy) * Maria Mirto (University of Salento & CMCC, Lecce, Italy) * Victor Maojo (Universidad Politecnica de Madrid, Spain) * Casimir A. Kulikowski (Rutgers University, New Brunswick, New Jersey, USA) * Tony Solomonides, Vice-President, HealthGrid, UK * Alfredo Tirado-Ramos, Emory University, Atlanta, USA PROGRAM COMMITTEE * Vincent Breton (CNRS/IN2P3, LPC Clermont-Ferrand, France) * Marian Bubak (AGH Krakow PL/ UvA Amsterdam NL) * Massimo Cafaro (University of Salento, Lecce, Italy) * Mario Cannataro (University "Magna Graecia" of Catanzaro, Italy) * Henri Casanova (University of Hawaii, USA) * Ewa Deelman (ISI/USC, USA) * Jack Dongarra (University of Tennessee, USA) * Geoffrey Fox (Indiana University, USA) * Vicente Hernandez (Universidad Politecnica de Valencia) * Dieter Kranzlmueller (Ludwing-Maximilian University Munich & Leibniz Supercomputing Centre Germany) * Mary Kratz (University of Michigan Medical School Information Services, USA) * Yannick Legre (MaatG / HealthGrid) * David Manset (University of Savoie, France, University West of England, UK, Maat G knowledge, Madrid, Spain) * Johan Montagnat (CNRS (I3S laboratory) France) * Silvia D. Olabarriaga (Academic Medical Center of the University of Amsterdam, The Netherlands) * Ashish Sharma (Emory University, Atlanta, USA) * Bruno Schulze, National Laboratory for Scientific Computing - LNCC, Brasil * Jonathan Silverstein (Computation Institute of the University of Chicago, USA) * Richard Sinnott (National e-Science Centre, Glasgow, UK) * Albert Zomaya (University of Sydney, Australia) ************************************************ PhD Maria Mirto Department of Innovation Engineering, University of Salento, Complesso Ecotekne, Edificio "Corpo O", Via per Monteroni, 73100 Lecce, Italy http://www.dii.unisalento.it Scientific Computing & Operations Division Euro Mediterranean Center for Climate Change (CMCC) Via Augusto Imperatore 16 - 73100 Lecce (Italy) http://www.cmcc.it/ office/mobile: +39 0832 297304 fax: +39 0832.297235 website: http://sara.unisalento.it/~mirto/ email: maria.mirto at unisalento.it ************************************************ From dan.bolser at gmail.com Fri Jan 6 06:59:13 2012 From: dan.bolser at gmail.com (Dan Bolser) Date: Fri, 6 Jan 2012 11:59:13 +0000 Subject: [BiO BB] Fwd: [SMW-devel] Fwd: MediaWiki Workshop: Preparing extensions for MediaWiki 1.19 - 1/13/2012 on #wikimedia-dev In-Reply-To: <4F06C979.2040208@semantic-mediawiki.org> References: <4F06C979.2040208@semantic-mediawiki.org> Message-ID: ---------- Forwarded message ---------- From: Markus Kr?tzsch Date: 6 January 2012 10:14 Subject: [SMW-devel] Fwd: MediaWiki Workshop: Preparing extensions for MediaWiki 1.19 - 1/13/2012 on #wikimedia-dev To: Semantic MediaWiki developers This might be interesting for extension developers on this list as well. Markus -------- Original Message -------- Subject: [Mediawiki-l] MediaWiki Workshop: Preparing extensions for MediaWiki 1.19 - 1/13/2012 on #wikimedia-dev Date: Thu, 5 Jan 2012 20:53:17 -0500 From: Gregory Varnum To: mediawiki-l at lists.wikimedia.org Greetings! Utilizing the model set by Wikimedia staff IRC office hours, MediaWiki.org's WikiProject Extensions is presenting our first MediaWiki Workshops for developers (volunteer and staff). ?Preparing extensions for MediaWiki 1.19 will be held on 13 January, 2012 at 19:00 UTC in IRC (#wikimedia-dev). This IRC workshop will be an opportunity to find out about changes in MediaWiki 1.19 that may require revisions to extensions or skins. Also an opportunity to ask MediaWiki developers questions regarding extension development. Everyone is invited to attend. ?Developers interested in serving as "extensions" or "MediaWiki 1.19" experts are encouraged to signup as participants at: http://www.mediawiki.org/wiki/Project:WikiProject_Extensions/MediaWiki_Workshops#MediaWiki_1.19_Experts If there's continued interest / demand, MediaWiki Workshops will typically last one hour, and happen no more than twice a month to present trainings, hold discussions and collaborate on community or WikiProject Extensions projects. Facilitators host the session to introduce any presenters, determine the order of questions, and generally helps to keep things going. Time of day will vary in order to offer people in different parts of the world the opportunity to participate. Future topics will likely include MediaWiki.org documentation, ResourceLouder orientation and workshops similar to our inaugural chat to prepare for each MediaWiki release. More information: http://www.mediawiki.org/wiki/Project:WikiProject_Extensions/MediaWiki_Workshops MediaWiki.org's WikiProject SysAdmins will also likely host similar MediaWiki Workshops to help third-party wiki system administrators. Stay tuned for more information, and chime in at: http://www.mediawiki.org/wiki/Project:WikiProject_SysAdmins/Ideas Look forward to seeing folks next Friday! ?Please feel free to forward this along to any interested folks. -greg aka varnent PS. Sorry if this is a duplicate - was having listserv problems earlier. ------- Gregory Varnum Lead Administrator, WikiQueer Lead, Aequalitas Project @GregVarnum fb.com/GregVarnum _______________________________________________ MediaWiki-l mailing list MediaWiki-l at lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/mediawiki-l ------------------------------------------------------------------------------ Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources to deliver seamless, secure access to virtual desktops. With this all-in-one solution, easily deploy virtual desktops for less than the cost of PCs and save 60% on VDI infrastructure costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox _______________________________________________ Semediawiki-devel mailing list Semediawiki-devel at lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/semediawiki-devel From ljgarcia at ebi.ac.uk Fri Jan 6 05:14:21 2012 From: ljgarcia at ebi.ac.uk (Leyla Garcia) Date: Fri, 06 Jan 2012 10:14:21 +0000 Subject: [BiO BB] Registrations for DAS Workshop 2012 In-Reply-To: References: Message-ID: <4F06C97D.6020700@ebi.ac.uk> --- Apology for multiple posting --- ===================================================================== DAS is currently being used to share annotations on genomes, protein alignments, structural and interaction information. If you are interested in sharing biological information the DAS workshop below may be of interest to you. Learn of and contribute to current developments in DAS such as: DAS in the cloud, DAS for Genotype Data, DAS searching, DAS for collaborative annotation projects, DAS alternative formats. Registration is open for the 2012 DAS workshop (27-29 February) at the Genome Campus, Hinxton UK. If you are interested in attending, please find out more by going to http://www.ebi.ac.uk/training/onsite/120227_DAS.html and register via the web link at the bottom of the page. This workshop will cater for novice to expert DAS users as each day is optional. Please register early as places will be limited. Registration closes 10 February 2012 - 12:00. If you are interested in giving a 15 minute talk on the second day please email Jonathan Warren using jonathan.warren at sanger.ac.uk Many thanks The Sanger/EBI DAS team. Jonathan Warren Senior Developer and DAS coordinator blog: http://biodasman.wordpress.com/ jw12 at sanger.ac.uk Ext: 2314 Telephone: 01223 492314 From gary.bader at utoronto.ca Sat Jan 7 20:16:53 2012 From: gary.bader at utoronto.ca (Gary Bader) Date: Sat, 7 Jan 2012 20:16:53 -0500 Subject: [BiO BB] NRNB Academy announcement References: Message-ID: <000EB037-2CE6-484A-8102-90958F803373@utoronto.ca> We are pleased to announce the official launch of NRNB Academy, an opportunity for anyone interested in open source development to work with the NRNB development team on network biology related tools and resources. The main goals of the NRNB Academy are to: * Provide participants with practical open source dev experience * Provide hobbyists and professionals with introductory projects * Promote development of scientific tools for network biology * Produce useful tools and resources for the research community How does it work? The NRNB Academy organizes and matches projects and participants, providing structure, guidelines and outreach. If you are familiar with the Google Summer of Code program, then you have the basic idea. The main difference is that NRNB Academy is a year-round program, accommodating students and non-students with flexible project dates ranging from 2 to 12 months. All projects are 100% unfunded, volunteer experiences. What is NRNB? The National Resource for Network Biology (nrnb.org) develops a freely available, open source suite of software technologies to enable network-based visualization, analysis, and biomedical discovery. NRNB is an NIH National Center for Research Resources (NCRR) Biomedical Technology Research Center (BTRC). If you tend to forget initials, just call it Narnby, as in, ?I just joined Narnby Academy!? To learn more and for details on how to participate, visit http://nrnb.org/academy.html. From jprudhomme at healthtech.com Wed Jan 11 10:28:04 2012 From: jprudhomme at healthtech.com (James Prudhomme) Date: Wed, 11 Jan 2012 10:28:04 -0500 Subject: [BiO BB] Integrated R&D Informatics & Knowledge Management Message-ID: <002101ccd075$9cc52aa0$d64f7fe0$@com> ** Please distribute this message to your colleagues. Thank you. ** CHI's Fourth Annual Integrated R&D Informatics & Knowledge Management (part of the Molecular Medicine Tri-Conference) February 21-23, 2012 Moscone North Convention Center, San Francisco, CA http://www.triconference.com.com/ird About the event: In the Pharmaceutical industry today, it is now critical to enable researchers to better predict outcomes and make good decisions. Developing integrated informatics systems and intelligent interfaces to support drug discovery and translational research continues to play a pivot role. Our fourth annual Integrated R&D Informatics & Knowledge Management will bring together thought leaders from across the life sciences to share their experiences dealing with moving large and complex data sets through public and private networks, the integration of disperse data streams and the correlation between pre-clinical observations and clinical outcomes. The integration of clinical and discovery data is key to translational research strategies in all major Pharma companies. We will present case studies on how to build an infrastructure to support translational research and medicine, dealing with complex clinical and translational data sets while allowing end users to ask complex questions. We will showcase innovative data analysis, visualization and informatics platforms and systems to support discovery, clinical and translational research. Examples of how to support secure collaboration between Pharma and academia to foster innovation will be presented, and informatics solutions to workflow management will also be featured. Conference topics: - Integration of Internal & External Data - Ontologies - Integrating & Accessing Non-Standard Public Data to Drive R&D - Workflow Project - Meeting the Informatics Needs to Support Biologics Development - Informatics for Translational Science Download a PDF brochure at http://www.triconference.com/mmtc_content.aspx?ekfrm=109217 Advance registration discounts are available until January 13. Register at https://chidb.com/register/2012/mmtc/reg.asp or call 781-972-5400. I hope to see you in San Francisco this coming February. James Prudhomme Cambridge Healthtech Institute 250 First Avenue, Suite 300 Needham, MA 02494 jprudhomme at healthtech.com From maria.mirto at unisalento.it Sun Jan 15 18:02:21 2012 From: maria.mirto at unisalento.it (Maria Mirto) Date: Mon, 16 Jan 2012 00:02:21 +0100 Subject: [BiO BB] Extended Deadline - CFP - CBMS2012 - Special Track (ST-11) on Grid and Cloud Computing in Biomedicine and Life Sciences Message-ID: <25F067EA-4005-428F-BEEE-81DCADDF99C3@unisalento.it> --- Apology for multiple posting --- ===================================================================== 25th IEEE International Symposium on COMPUTER-BASED MEDICAL SYSTEMS (CBMS 2012) Rome, Italy, 20-22 June 2012 5th Special Track on Grid and Cloud Computing in Biomedicine and Life Sciences http://datadog.unile.it/cbms2012 www.cbms2012.org ===================================================================== * * * CALL FOR PAPERS - Extended Deadline February 10, 2012 * * * ===================================================================== Life sciences researchers routinely deal with large data to be analyzed by applications that need considerable computing power, including advanced parallel and distributed infrastructures, such as grids/clouds, clusters, and many-cores, multi-cores and FPGA architectures. Managing these data and optimizing the applications for these architectures is one of the challenges that must be tackled. High-throughput techniques for DNA sequencing, gene expression analysis, healthcare data analysis, etc., have led to an exponential increase in the volume of biological data, which in turn are geographically spread in several laboratories and data repositories. Other questions, such as climate change impact on the life sciences, and the disciplines to address them, are adding to the deluge of data: many prevalent human diseases are linked to climate fluctuations, from heat stress, cardiovascular mortality and respiratory illnesses due to heat waves, to altered transmission of infectious diseases and malnutrition connected to crop failures. Bringing together and correlating data among different and heterogeneous data sources will allow inference of new knowledge from these databases. There is a tremendous potential for end-users in many fields of life sciences, to routinely conduct large scale computations on distributed resources by using a combination of the following technologies: - Distributed middleware for connecting data/cluster computing centers: this includes grid computing middleware for users' authentication and accounting, remote job submission, resource scheduling/reservation, and data management; - Virtualization technologies capable of providing on demand application-specific execution environments: this involves a style of computing, cloud computing, in which on-demand resources are provided as a service over the Internet. Grid for the Life Sciences is an environment that allows sharing of resources, in which heterogeneous and dispersed health data as well as applications can be accessed by all users as a tailored information providing system according to their authorization. Cloud computing is emerging as a model for enabling convenient, on demand network access to a shared pool of configurable resources that can be rapidly provisioned and released with minimal management effort or service provider interaction. Institutions and medical professionals who frequently do not have enough storage and computing resources can manage their biomedical information through applications built on top of these types of services, accessing advanced computing infrastructures that they could not afford otherwise. While many companies, like Google, IBM, Amazon, and Microsoft, were early adopters of cloud computing, its application to biomedicine has been only recently proposed, mainly for bioinformatics applications. Several reviews and research papers have reported on these, while in contrast, applications in medical informatics have been infrequent. Now, medical applications are increasingly proposed and implemented, though reports are still scarce from a research and academic perspective. The main goal of the track is to exchange ideas and results related to on going grid and cloud computing research in Biomedicine, Life Sciences and correlated disciplines, such as Climate Change, that impact on human health, focusing on different aspects of middleware, technologies and applications. TOPICS OF INTEREST The topics of interest will include but will be not limited to: o Grid/cloud infrastructures, middleware and tools; o Grid/cloud applications: service and/or algorithm design and implementation; best practices related to solving large-scale problems on grid/cloud infrastructures; o Parallel algorithms using MPI or OpenMP; o Exploiting modern parallel architectures including FPGA, many-cores and multi-cores for parallel applications; o GPGPU parallel algorithms using OpenCL or CUDA; o Security and privacy preserving in grids/clouds; o Innovative approaches for the exploration, storage, processing, delivery and/or visualization of biomedical information; o Workflow Management Systems; o Scientific gateways and user environments; o Inferring new knowledge from databases by using data and text Mining methodologies and techniques; o Web services and cloud computing for biomedical applications: comparative studies; o Using biomedical ontologies for advanced cloud computing-based biomedical applications: requirements, experiences, limitations; o Real cases, testbeds and international projects facing (a) Biomedicine, bioinformatics and healthcare; (b) Climate change models and health challenges, etc.; (c) Applications for developing countries. PAPER SUBMISSION Papers should be submitted electronically using EasyChair online submission system. The papers must be prepared following the IEEE two-column format and should not exceed the length of 6 (six) Letter-sized pages. LaTeX or Microsoft Word templates can be used when preparing the papers. Please, note that only PDF format of submissions is allowed. Submission through EasyChair requires that an account in the system be created by a prospective author first. In order to create a new account, select the "I have no EasyChair account" option and follow the instructions given. When submitting, please, select the "Grid and Cloud Computing in Biomedicine and Life Sciences" special track. JOURNAL SPECIAL ISSUE After the workshop, selected papers may be invited for a special issue of an international journal or for an edited book. Selected papers (extended and revised versions) accepted on the previous editions of the workshop have been published on a special section of Briefings in Bioinformatics (Oxford University Press). IMPORTANT DATES Paper submission due January 15, 2012 Notification of acceptance March 15, 2012 Final camera-ready paper due April 10, 2012 Pre-registration deadline April 10, 2012 CBMS symposium days June 20-22 2012 TRACK CO-CHAIRS: * Giovanni Aloisio (University of Salento & CMCC, Lecce, Italy) * Maria Mirto (University of Salento & CMCC, Lecce, Italy) * Victor Maojo (Universidad Politecnica de Madrid, Spain) * Casimir A. Kulikowski (Rutgers University, New Brunswick, New Jersey, USA) * Tony Solomonides, Vice-President, HealthGrid, UK * Alfredo Tirado-Ramos, Emory University, Atlanta, USA PROGRAM COMMITTEE * Ankica Babic (Link?ping University, Sweden) * Vincent Breton (CNRS/IN2P3, LPC Clermont-Ferrand, France) * Marian Bubak (AGH Krakow PL/ UvA Amsterdam NL) * Anca Bucur (Philips Research, The Netherlands) * Massimo Cafaro (University of Salento, Lecce, Italy) * Mario Cannataro (University "Magna Gr?cia" of Catanzaro, Italy) * Henri Casanova (University of Hawaii, USA) * Jose Crespo (Universidad Politecnica de Madrid, Spain) * Ewa Deelman (ISI/USC, USA) * Jack Dongarra (University of Tennessee, USA) * Julio Facelli (University of Utah, USA) * Geoffrey Fox (Indiana University, USA) * Miguel Garcia-Remesal (Universidad Politecnica de Madrid) * Leiguang T.J. Gong (Watson Research Center, IBM, USA) * Vicente Hernandez (Universidad Politecnica de Valencia) * Rada Hussein (Ministry of Telecommunications, Egypt) * Nikos Karacapidilis (University of Patras, Greece) * Dieter Kranzlmueller (Ludwing-Maximilian University Munich & Leibniz Supercomputing Centre Germany) * Mary Kratz (University of Michigan Medical School Information Services, USA) * Yannick Legre (MaatG / HealthGrid) * David Manset (University of Savoie, France, University West of England, UK, Maat G knowledge, Madrid, Spain) * Johan Montagnat (CNRS (I3S laboratory) France) * Silvia D. Olabarriaga (Academic Medical Center of the University of Amsterdam, The Netherlands) * Jose Luis Oliveira (University of Aveiro, Portugal) * Alejandro Pazos (University of A Coru?a, Spain) * David Perez-Rey (Universidad Politecnica de Madrid, Spain) * George Potamias (FORTH, Greece) * Stefan Rueping (Fraunhofer Institute, Germany) * Ashish Sharma (Emory University, Atlanta, USA) * Bruno Schulze (National Laboratory for Scientific Computing - LNCC, Brasil) * Jonathan Silverstein (Computation Institute of the University of Chicago, USA) * Richard Sinnott (National e-Science Centre, Glasgow, UK) * Albert Zomaya (University of Sydney, Australia) ************************************************ PhD Maria Mirto Department of Innovation Engineering, University of Salento, Complesso Ecotekne, Edificio "Corpo O", Via per Monteroni, 73100 Lecce, Italy http://www.dii.unisalento.it Scientific Computing & Operations Division Euro Mediterranean Center for Climate Change (CMCC) Via Augusto Imperatore 16 - 73100 Lecce (Italy) http://www.cmcc.it/ office/mobile: +39 0832 297304 fax: +39 0832.297235 website: http://sara.unisalento.it/~mirto/ email: maria.mirto at unisalento.it ************************************************ From luca at dmi.units.it Mon Jan 16 11:58:53 2012 From: luca at dmi.units.it (Luca Bortolussi) Date: Mon, 16 Jan 2012 16:58:53 +0000 Subject: [BiO BB] HSB2012 - first call for papers Message-ID: <4F14574D.1050904@dmi.units.it> [We apologize for the reception of multiple copies of this message] ********************************************************************* Call for Papers --- HSB 2012 First International Workshop on Hybrid Systems and Biology Newcasle upon Tyne, UK, September 3, 2012 Colocated with CONCUR 2012 http://hsb2012.units.it/ ********************************************************************* The goal of systems biology is to provide a system-level understanding of biological systems by unveiling their structure, dynamics and control methods. The intrinsic multi-scale nature of these systems, both in space, in organization levels, and in time, makes extremely difficult to model all of them in a uniform way, e.g. by means of differential equations or discrete stochastic processes. Furthermore such models are often not easily amenable to formal analysis and simulation at the organ or even the cell level is frequently impractical. Indeed, an important open problem is finding appropriate computational models that scale well for both the simulation and formal analysis of biological processes. Hybrid modeling techniques, combining discrete and continuous processes, are gaining more and more attention in systems biology, and they have been applied to successfully capture the behavior of several biological complex systems, ranging from genetic networks, biochemical reactions, signaling pathways and cardiac tissues electrophysiology. This workshop aims at collecting scientists working in the area of hybrid modeling applied to systems biology, in order to discuss about current achieved goals, current challenges and future possible developments. Topics of interest include, but are not limited to: * Hybrid models of biological systems (case studies of genetic, cellular networks, models of tissues, etc.) * Computational and mathematical analysis techniques for hybrid systems (i.e. reachability, model checking, abstract interpretation, bifurcation theory for hybrid dynamical systems, etc.), with applications in Systems Biology. * Hybrid system identification techniques (learning the model from the experimental data) * Efficient simulation techniques for hybrid systems. * Hybrid modeling languages for biological systems. * Hybrid systems coping with incomplete and uncertain information. * Sensitivity analysis for hybrid systems. * Behaviour-driven parameters identification for hybrid systems. * Analysis and simulation tools. We solicit the submission of unpublished results that address on both theoretical and applied aspects of hybrid modeling techniques in systems biology. The proceedings will be published in the Electronic Proceedings in Theoretical Computer Science (EPTCS) series. A special issue in a journal will be considered at the end of the workshop. Paper submission Full papers should be no more than 15 pages long, typesetted in the EPTCS-style. Electronic submissions of abstracts and of full-length papers (in PDF format), can be done through the online submission system: https://www.easychair.org/conferences/?conf=hsb2012 Important dates June 15, 2012 - Abstract submission deadline June 22, 2012 - Full paper submission deadline July 30, 2012 - Notification of paper acceptance August 7, 2012 - Camera-ready of accepted papers Program co-chairs Ezio Bartocci, University of Stony Brook, USA Luca Bortolussi, Univerity of Trieste, Italy Program committee Marco Antoniotti, University of Milano Bicocca Gregory Batt, INRIA Paris-Rocquencourt, France Alberto Casagrande, University of Trieste, Italy Edmund Clarke, Carnegie Mellon, USA Thao Dang, VERIMAG Lab, Grenoble, France Alexandre Donz?, VERIMAG Lab, Grenoble, France James R. Faeder, University of Pittsburgh, USA Jasmin Fisher, Microsoft Research, Cambridge, UK Vashti Galpin, University of Edinburgh, UK Colas Le Guernic, NYU, USA Oded Maler, VERIMAG Lab, Grenoble, France Emanuela Merelli, University of Camerino, Italy Bud Mishra, NYU, USA Carla Piazza, University of Udine, Italy Alberto Policriti, University of Udine, Italy Scott A. Smolka, University of Stony Brook, USA Gouhei Tanaka, University of Tokyo, Japan Verena Wolf, Saarland University, Germany Paolo Zuliani, Carnegie Mellon, USA From umeton at MIT.EDU Mon Jan 16 09:56:31 2012 From: umeton at MIT.EDU (Renato Umeton) Date: Mon, 16 Jan 2012 09:56:31 -0500 Subject: [BiO BB] ICARIS 2012 Call for Papers, Oral Presentations & Posters - 11th Int. Conf. on Artificial Immune Systems, August 28-31, 2012 Taormina, Italy Message-ID: <20120116095631.herorshwookoocs8@webmail.mit.edu> CALL FOR PAPERS, ORAL PRESENTATIONS & POSTERS *Apologies for cross-posting* The 11th International Conference on Artificial Immune Systems August 28-31, 2012 Taormina, Italy icaris2012 at dmi.unict.it http://www.artificial-immune-systems.org/icaris/2012/ https://www.easychair.org/conferences/?conf=icaris2012 http://www.artificial-immune-systems.org/icaris/2012/callForPapers.php Important Dates: Paper submission: 1st March 2012 Author notification: 15th May 2012 Paper final version: 15th June 2012 General Information: ICARIS 2012 aims to build on the success of previous years to provide a forum for AIS researchers in academia and industry to present and discuss their latest advances. In addition to peer-reviewed papers, ICARIS 2012 will present a range of plenary lectures and tutorials to inspire and facilitate both the computer scientists and immunologists in their work. ICARIS 2012 is divided into two main tracks: **28 and 29 August 2012: Computational Immunology & Immunoinformatics** http://www.artificial-immune-systems.org/icaris/2012/callForPapers.php (for Oral Presentations & Posters submission) **30 and 31 August 2012: Immunological Computation, Immune-inspired Engineering, Immune-inspired Heuristics** https://www.easychair.org/conferences/?conf=icaris2012 (for Full papers submission) http://www.artificial-immune-systems.org/icaris/2012/callForPapers.php (for Oral Presentations & Posters submission) **Track on Computational Immunology** This track aims is to attract researchers from computer science, information science, engineering, biomathematics, biomedicine, bioinformatics, systems biology, and immunology to share and exchange their knowledge of state-of-the-art research issues, methodologies, ideas, and challenges. Topics of interest include: * Immune modelling; * Structural Immunoinformatics; * Epitope analysis and prediction; * Analysis and prediction of MHC-peptide binding; * Databases and ontologies for Immunoinformatics; * Analysis and prediction of minor histocompatibility antigens; * Predictive models on organ transplantation; * Immunogenomics; * Vaccine design; * Multi-agent based models of immunity; * Gene networks and systems biology in immunity; * Allergenicity prediction. In this track, authors are requested to submit an abstract following the instructions on ICARIS 2012 website: http://www.artificial-immune-systems.org/icaris/2012/callForPapers.php The abstract submissions must be done no later than the submission deadline: 1 March 2012. All accepted abstracts will be published in a book of abstracts. Full versions of the best works on this track will be published in the Immunomics Research Journal and BMC Bioinformatics. **Track on Immunological Computation, Immune-inspired Engineering, Immune-inspired Heuristics** This track is for papers describing applications to computational and engineering problems, and theoretical aspects (e.g. mathematical modeling of algorithms, convergence analysis, empirical investigation into algorithm performance and complexity analysis) of AIS. For the first class, the problem domain should be clearly explained, detailing why it is challenging and why AIS are a suitable methodology to use. Experiments should be carefully explained, with the expectation that appropriate statistical analysis of results will be used to help draw conclusions. Where possible, the approach taken should be compared with alternative strategies. In order to appeal to the widest audience, theoretical papers must ensure that mathematical arguments and backgrounds are clearly presented, and the paper should also discuss the practical implications of any theoretical results. In this track authors may submit their manuscripts in two different ways: abstract paper, or regular paper (as in the past editions). * Abstract paper Authors must follow the instructions described on ICARIS 2012 website: http://www.artificial-immune-systems.org/icaris/2012/callForPapers.php * Regular paper All papers will undergo a double blind review process, and they should be no longer than fourteen (14) pages. Is recommended that authors name and affiliation should not appear on the paper. Authors are requested to submit a PDF file at the link https://www.easychair.org/conferences/?conf=icaris2012 following the formatting instructions at the Springer-Verlag LNCS site, no later than the submission deadline: 1 March 2012. All accepted papers, as for the previous editions, will be published in Springer's series Lecture Notes in Computer Science. The authors of best (regular) papers on this track will be invited to extend their work for publication in the Evolutionary Computation Journal - MIT Press (TBC). During the submission authors must make clear which stream the paper should to be considered for. We look forward to welcoming you to Taormina in August 2012. C. Coello Coello, J. Greensmith, N. Krasnogor, P. Lio', G. Nicosia, M. Pavone. From daniele.gianni at gmail.com Tue Jan 17 15:25:32 2012 From: daniele.gianni at gmail.com (Daniele Gianni) Date: Tue, 17 Jan 2012 21:25:32 +0100 Subject: [BiO BB] COMETS 2012 - 3rd IEEE Track on Collaborative Modeling and Simulation - Call for Papers Message-ID: (Please accept our apologies if you receive multiple copies of this message) ################################################################# IEEE WETICE 2012 3rd IEEE Track on Collaborative Modeling and Simulation (Comets 2012) in cooperation with AFIS (INCOSE France Chapter) MIMOS (Italian Association for M&S) CALL FOR PAPERS ################################################################# June 25-27, 2012, Toulouse (France) http://www.sel.uniroma2.it/comets12 ################################################################# # Papers Due: March 16, 2012 # Accepted papers will be published in the conference proceedings # by the IEEE Computer Society Press and indexed by EI. ################################################################# Modeling and Simulation (M&S) is increasingly becoming a central activity in the design of new systems and in the analysis of existing systems because it enables designers and researchers to investigate systems behavior through virtual representations. For this reason, M&S is gaining a primary role in many industrial and research fields, such as space, critical infrastructures, manufacturing, emergency management, biomedical systems and sustainable future. However, as the complexity of the investigated systems increases and the types of investigations widens, the cost of M&S activities increases for the more complex models and for the communications among a wider number and variety of M&S stakeholders (e.g., sub-domain experts, simulator users, simulator engineers, and final system users). To address the increasing costs of M&S activities, collaborative technologies must be introduced to support these activities by fostering the sharing and reuse of models, by facilitating the communications among M&S stakeholders, and more generally by integrating processes, tools and platforms. Aside from seeking applications of collaborative technologies to M&S activities, the track seeks innovative contributions that deal with the application of M&S practices to the design of collaborative environments. These environments are continuously becoming more complex, and therefore their design requires systematic approaches to meet the required quality of collaboration. This is important for two reasons: to reduce rework activities on the actual collaborative environment, and to maximize the productivity and the quality of the process the collaborative environment supports. M&S offers the methodologies and tools for such investigations and therefore it can be used to improve the quality of collaborative environments. A non?exhaustive list of topics of interest includes: * collaborative environments for M&S * collaborative Systems of Systems M&S * workflow modelling for collaborative environments and processes * agent-based M&S * collaborative distributed simulation * collaborative component-based M&S * net-centric M&S * web-based M&S * model sharing and reuse * model building and evaluation * modeling and simulation of business processes * modeling for collaboration * simulation-based performance evaluation of collaborative networks * model-driven simulation engineering * domain specific languages for the simulation of collaborative environments * domain specific languages for collaborative M&S * databases and repositories for M&S * distributed virtual environments * virtual research environment for M&S * collaborative DEVS M&S To stimulate creativity, however, the track maintains a wider scope and invites interested researchers to present contributions that offer original perspectives on collaboration and M&S. +++++++++++++++++++++++++++++++++++ On-Line Submissions and Publication +++++++++++++++++++++++++++++++++++ CoMetS'12 intends to bring together researchers and practitioners to discuss key issues, approaches, open problems, innovative applications and trends in the track research area. This year, we will accept submissions in two forms: (1) papers (2) poster and industrial presentations (1) Papers should contain original contributions not published or submitted elsewhere. Papers up to six pages (including figures, tables and references) can be submitted. Papers should follow the IEEE format, which is single spaced, two columns, 10 pt Times/Roman font. All submissions should be electronic (in PDF) and will be peer-reviewed by at least three program committee members. Accepted full papers will be included in the proceedings and published by the IEEE Computer Society Press (IEEE approval pending). Please note that at least one author for each accepted paper should register to attend WETICE 2012 (http://www.wetice.org) to have the paper published in the proceedings. (2) Posters should describe a practical, on-the-field, experience in any domain area using collaborative M&S. The poster submission requires the submission of an abstract for evaluation from the organizers. Accepted abstract must be followed by the submission of a poster which will be displayed at conference time. With the poster submission, a short (15 minutes) slot might be allocated for oral presentation illustrating the industrial case. The presentation may also include a live demo, but it should not include commercial details. Interested authors and participants may contact the organizers for expression of interests and content appropriateness at any time. Papers and posters can be submitted in PDF format at the submission site (https://www.easychair.org/conferences/?conf=comets2012), which is supported by the EasyChair conference management system. Please feel free to contact the track chairs (comets2012 at easychair.org) if you experience problems with the EasyChair Web site. +++++++++++++++ Important Dates +++++++++++++++ * Submission Deadline: March 16, 2012 * Notification to authors: April 16, 2012 * Camera Ready to IEEE: April 30, 2012 * Conference dates: June 25 - June 27, 2012 ++++++++++++++++++++ Organizing Committee ++++++++++++++++++++ * Andrea D'Ambrogio, University of Roma TorVergata, Italy * Daniele Gianni, European Space Agency, The Netherlands * Joachim Fuchs, European Space Agency, The Netherlands * Giuseppe Iazeolla, University of Roma TorVergata, Italy +++++++++++++++++ Program Committee +++++++++++++++++ * Santiago Balestrini, Georgia Institute of Technology, USA * Massimo Bandecchi, European Space Agency, The Netherlands * Joseph Giampapa, SEI, Carnegie Mellon University, USA * Alain Kerbrat, CollESys - AFIS, France * Axel Lehmann, Universitaet der Bundeswehr Muenchen, Germany * Cristiano Leorato, Rhea, The Netherlands * Steve McKeever, University of Oxford, UK * David Nickerson, Auckland Bioengineering Institute, NZ * Alfred Park, Oak Ridge National Laboratory, USA * Wolfgang Prinz, Fraunhofer FIT and RWTH Aachen, Germany * Jos? L. Risco-Martin, Universidad Complutense de Madrid, Spain * Jean-Francois Santucci, University of Corsica, France * Gabriel Wainer, Carleton University, Canada * Quirien Wijnand, European Space Agency, The Netherlands * Heming Zhang, Tsinghua University, China *** Contact Information *** Daniele Gianni (track co-chair) Email: danielegmail-comets at yahoo.it From mourad.elloumi at gmail.com Wed Jan 18 10:21:37 2012 From: mourad.elloumi at gmail.com (Mourad Elloumi) Date: Wed, 18 Jan 2012 16:21:37 +0100 Subject: [BiO BB] CfP : BIOKDD'12 - DEXA'12 Message-ID: *CALL FOR PAPERS* *3rd International Workshop on* *Biological **Knowledge Discovery and Data Mining** **(BIOKDD'12)* Held in parallel with *23rd International Conference on Database and * *Expert Systems Applications **(**DEXA?12**)* www.dexa.org Vienna, Austria *September 3 - 7, 2012* With the development of Molecular Biology during the last decades, we are witnessing an exponential growth of both the volume and the complexity of biological data. For example, the* Human Genome Project* provided the sequence of the 3 billion DNA bases that constitute the human genome. And, consequently, we are provided too with the sequences of about 100,000 proteins. Therefore, we are entering the post-genomic era: after having focused so many efforts on the accumulation of data, we have now to focus as much effort, and even more, on the analysis of these data. Analyzing this huge volume of data is a challenging task because, not only, of its complexity and its multiple and numerous correlated factors, but also, because of the continuous evolution of our understanding of the biological mechanisms. Classical approaches of biological data analysis are no longer efficient and produce only a very limited amount of information, compared to the numerous and complex biological mechanisms under study. From here comes the necessity to use computer tools and develop new *in silico* high performance approaches to support us in the analysis of biological data and, hence, to help us in our understanding of the correlations that exist between, on one hand, structures and functional patterns of biological sequences and, on the other hand, genetic and biochemical mechanisms. *Knowledge Discovery and Data Mining* (KDD) are a response to these new trends. Topics of BIOKDD'12 workshop include, but not limited to: *Data Preprocessing: *Biological Data* *Storage*, *Representation and Management (data warehouses, databases, sequences, trees, graphs, biological networks and pathways, ?), Biological Data *Cleaning* (errors removal, redundant data removal, completion of missing data, ?), *Feature* Extraction (motifs, subgraphs, ?), *Feature* Selection (filter approaches, wrapper approaches, hybrid approaches, embedded approaches, ?) *Data Mining: *Biological Data Regression (regression of biological sequences?), Biological data clustering/biclustering (microarray databiclustering, clustering/biclustering of biological sequences, ?), Biological Data Classification (classification of biological sequences?), Association Rules Learning from Biological Data, Text mining and Application to Biological Sequences, Web mining and Application to Biological Data, Parallel, Cloud and Grid Computing for Biological Data Mining *Data Postprocessing:* Biological Nuggets of Knowledge Filtering, Biological Nuggets of Knowledge Representation and Visualization, Biological Nuggets of Knowledge Evaluation* *(calculation of the classification error rate, evaluation of the association rules *via*numerical indicators, e.g. *measurements of interest*, ? ), Biological Nuggets of Knowledge Integration *PAPER SUBMISSION DETAILS: * Authors are invited to submit electronically original contributions in English. Submitted papers should not exceed 5 pages in IEEE format < www.ieee.org/web/publications/authors/transjnl/index.html<../../../Users/gwagner/AppData/Local/Temp/www.ieee.org/web/publications/authors/transjnl/index.html> >. All accepted papers will be published in the proceedings of DEXA?12 Workshops with IEEE CSP*. *One of the authors of an accepted paper must register to DEXA?12 conference and present the paper at BIOKDD?12 workshop. For paper registration and electronic submission see <* http://confdriver.ifs.tuwien.ac.at/dexa2012/*>, starting from January 2012. * * *IMPORTANT DATES: * Submission of abstracts: March 23, 2012 Submission of full papers: March 30, 2012 Notification of acceptance: May 18, 2012 Camera-ready copies due: May 25, 2012 *PROGRAM COMMITTEE:* Mourad Elloumi, LaTIC, University of Tunis, Tunisia (PC Chair) Costas S. Iliopoulos, King?s College London, UK Jason T. L. Wang, New Jersey Institute of Technology, USA Albert Y. Zomaya, The University of Sydney, Australia Mohammed S. Rahman, King?s College London, UK Daisuke Kihara, Purdue University, West Lafayette, IN, USA Alfredo Pulvirenti , University of Catania, Italy Jos? Luis Oliveira, University of Aveiro, Portugal Carlo Cattani, University of Salerno, Italy Shoba Ranganathan, University, Sydney, Australia Radha Krishna Murthy Karuturi, Genome Institute of Singapore, Singapore Solon P. Pissis, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany Adelaide Freitas, University of Aveiro, Portugal Fawzi Mhamdi, LaTIC, University of Tunis, Tunisia Wassim Ayadi, LaTIC, University of Tunis, Tunisia *** From eric_songhill at fastmail.fm Mon Jan 23 15:48:25 2012 From: eric_songhill at fastmail.fm (Eric Songhill) Date: Mon, 23 Jan 2012 12:48:25 -0800 Subject: [BiO BB] Understanding Pre-processing algorithms Message-ID: <1327351705.32760.140661027055189@webmail.messagingengine.com> Hi, I'm a newbie to the field of bioinformatics and I'm trying to learn about micro-arrays (e.g affymetrix genechip ) and about pre-processing algorithms. I understand that one of the most widely used algorithms for pre-processing is the RMA algorithm. This algorithm is the algorithm I'm trying to understand. It's supposed to have 3 steps ( background correction, normalization, summarization ). My question is what are the inputs and the outputs of such a pre-processing algorithm. Is the "input" data for a pre-processing algorithm a CEL file ?? Is this CEL file the file that the micro-array computer scanner returns as a result to the user ??? Is the CEL an image file viewable in an image viewer and if so where can I find sample CEL files ? And what is the output of the algorithm ? -- Eric Songhill eric_songhill at fastmail.fm -- http://www.fastmail.fm - A fast, anti-spam email service. From jprudhomme at healthtech.com Mon Jan 23 12:22:54 2012 From: jprudhomme at healthtech.com (James Prudhomme) Date: Mon, 23 Jan 2012 12:22:54 -0500 Subject: [BiO BB] Integrated R&D Informatics & Knowledge Management Message-ID: <004201ccd9f3$a446de90$ecd49bb0$@com> ** Please distribute this message to your colleagues. Thank you. ** CHI's Fourth Annual Integrated R&D Informatics & Knowledge Management (part of the Molecular Medicine Tri-Conference) February 21-23, 2012 Moscone North Convention Center, San Francisco, CA http://www.triconference.com.com/ird About the event: In the Pharmaceutical industry today, it is now critical to enable researchers to better predict outcomes and make good decisions. Developing integrated informatics systems and intelligent interfaces to support drug discovery and translational research continues to play a pivot role. Our fourth annual Integrated R&D Informatics & Knowledge Management will bring together thought leaders from across the life sciences to share their experiences dealing with moving large and complex data sets through public and private networks, the integration of disperse data streams and the correlation between pre-clinical observations and clinical outcomes. The integration of clinical and discovery data is key to translational research strategies in all major Pharma companies. We will present case studies on how to build an infrastructure to support translational research and medicine, dealing with complex clinical and translational data sets while allowing end users to ask complex questions. We will showcase innovative data analysis, visualization and informatics platforms and systems to support discovery, clinical and translational research. Examples of how to support secure collaboration between Pharma and academia to foster innovation will be presented, and informatics solutions to workflow management will also be featured. Conference topics: - Integration of Internal & External Data - Ontologies - Integrating & Accessing Non-Standard Public Data to Drive R&D - Workflow Project - Meeting the Informatics Needs to Support Biologics Development - Informatics for Translational Science Download a PDF brochure at http://www.triconference.com/mmtc_content.aspx?ekfrm=109217 Register at https://chidb.com/register/2012/mmtc/reg.asp or call 781-972-5400. I hope to see you in San Francisco this coming February. James Prudhomme Cambridge Healthtech Institute 250 First Avenue, Suite 300 Needham, MA 02494 jprudhomme at healthtech.com From cannataro at unicz.it Sun Jan 29 06:31:54 2012 From: cannataro at unicz.it (Mario Cannataro) Date: Sun, 29 Jan 2012 12:31:54 +0100 (CET) Subject: [BiO BB] Ext. Deadline ICCS 5th Workshop on Biomedical and Bioinformatics Challenges to Computer Science In-Reply-To: <2a8f79dd238a4472832705b8a1d95ca5.squirrel@email.unicz.it> References: <49488aa30fce78e7e8b644f2b6443229.squirrel@email.unicz.it> <0b90f151c841a8029f34aa95146d4a02.squirrel@email.unicz.it> <637f7d51898906671cc8ef02e2be2ccc.squirrel@email.unicz.it> <2a8f79dd238a4472832705b8a1d95ca5.squirrel@email.unicz.it> Message-ID: I apologize for any cross-posting of this announcement. ===================================================================== ICCS 2012 5th Workshop on Biomedical and Bioinformatics Challenges to Computer Science http://staff.icar.cnr.it/cannataro/iccs2012/ "Empowering Science through Computing" College of Information Science and Technology, University of Nebraska at Omaha Omaha, Nebraska, USA June 4 - June 6, 2012 http://www.iccs-meeting.org/ ===================================================================== * * * CALL FOR PAPERS - Deadline EXTENDED February 6, 2012 * * * ===================================================================== CALL FOR PAPERS Bioinformatics is providing the foundation for fast and reliable data analysis. Genomics, interactomics, proteomics, epidemiological, clinical and text mining applications have made essential progress through using bioinformatics tools. Standard tools are usually offered through the Web. This is no longer sufficient with more complex analysis and simulation tasks from emerging research fields like systems biology, image analysis, biomedical applications or data management. In recent years Grid and Web services based approaches have been developed to face the new challenges. Moreover, emerging life sciences applications need to use in a coordinated way both bioinformatics tools, biological data banks, and patient?s clinical data, that requires seamless integration, privacy preservation and controlled sharing. Previous workshops were held in Krak?w, Baton Rouge, Amsterdam and Singapore. This is the 5th edition of the workshop that was previously held, respectively, in Krak?w (2008), Baton Rouge (2009), Amsterdam (2010) and Singapore (2011). The Workshop on Biomedical and Bioinformatics Challenges to Computer Science will bring together scientists from computer and life sciences to discuss future directions of bioinformatics algorithms, applications, and data management. Questions to be looked at are whether wrapping existing algorithms, as Grid or Web service will be sufficient to cope with the more complex applications and the increasing volume of data to be processed or which applications would profit from being redeveloped as native parallel or distributed application. Furthermore, the use of novel parallel architectures and dedicated hardware to implement bioinformatics and biomedical algorithms will be discussed. TOPICS OF INTEREST The workshop is seeking original research papers presenting innovative solutions from parallel, distributed and Grid computing applied to bioinformatics algorithms, medical informatics and life sciences applications. Specifically we are interested in the following topics applied to bioinformatics, medicine, biology and life sciences: - sequence and structure bioinformatics - genomics, proteomics, interactomics - systems biology - biomedical image analysis - neuroimaging - biomedical simulation - data management - data integration - data visualization - workflow modelling - distributed biomedical applications - high performance computing - dedicated hardware and architectures - parallelisation techniques - service orientation - volunteer computing - peer-to-peer computing - Grid and Cloud Computing PAPER SUBMISSION AND PUBLICATION The submitted paper must be camera-ready and formatted according to the rules of Procedia Computer Science (http://www.elsevier.com/wps/find/journaldescription.cws_home/719435/description#description). Please use this file (http://www.iccs-meeting.org/iccs2012/procedia/ecrc-procs.zip) for a Latex template plus instructions and click here (http://www.iccs-meeting.org/iccs2012/procedia/ProcediaComputerScience_template.dot) for an MS word template file. Submission implies the willingness of at least one of the authors to register and present the paper. PostScript and source versions of your paper must be submitted electronically through the paper submission system (http://www.iccs-meeting.org/iccs2012/papers/upload.php) choosing the Workshop Biomedical and Bioinformatics Challenges to Computer Science. The copyright form (http://www.iccs-meeting.org/iccs2012/procedia/ProcediaComputerScience_copyrightform.doc) is only needed after the paper has been accepted for publication in the proceedings. Please, note that papers must not exceed ten pages in length, when typeset using the Procedia format. Dates of deadlines for draft paper submission (full paper), notification of acceptance, deadline for camera-ready paper submission and registration may be found in the Important Dates section of the ICCS Web site, except if otherwise specified on this workshop site. Papers must be based on unpublished, mature and original work and must be submitted to ICCS only. ICCS is an ERA 2010 A-ranked conference series. JOURNAL SPECIAL ISSUE After the workshop, selected papers may be invited for a special issue of the Journal of Computational Science. Selected papers (extended and revised version) accepted on the 1st edition of the workshop have been published on a special section of Future Generation Computer Systems, Elsevier. IMPORTANT DATES Full papers submission EXTENDED February 6, 2012 Notification of acceptance EXTENDED February 20, 2012 Camera ready papers March 1, 2012 Early registration opens February 15, 2012 Early registration closes April 15, 2012 Tutorials, wellcome reception June 3, 2012 Conference/Workshop sessions Monday June 4 - Wednesday June 6, 2012 WORKSHOP CO-ORGANIZERS Mario Cannataro, University Magna Gr?cia of Catanzaro, Italy Joakim Sundnes, Simula Research Laboratory, Norway Rodrigo Weber dos Santos, Federal University of Juiz de Fora, Brazil PROGRAM COMMITTEE (TO BE CONFIRMED) 1. Dave Angulo, DePaul University, Chicago, USA 2. Rui Brito, University of Coimbra, Portugal 3. Tim Clark, Harvard Medical School, USA 4. Giuseppe Di Fatta, University of Reading, UK 5. Werner Dubitzky, University of Ulster, UK 6. Christine Froidevaux, LRI-Bioinformatics Group - University Paris XI, Orsay, France 7. Alan Garny, University of Oxford, Department of Physiology, Anatomy & Genetics 8. Concettina Guerra, University of Padova, Italy 9. Pietro Hiram Guzzi, University Magna Gr?cia of Catanzaro, Italy 10. Ulrich Hansmann, Research Centre Juelich, Germany 11. Vicente Hern?ndez, Univ. Polit?cnica de Valencia, Spain 12. Pilar Herrero, Universidad Polit?cnica de Madrid, Madrid, Spain 13. Ela Hunt, SystemsX.ch, ETHZ, Switzerland 14. Glenn Terje Lines, Simula Research Laboratory, Norway 15. Marcelo Lobosco, Federal University of Juiz de Fora, Brazil 16. Uko Maran, University of Tartu, Estonia 17. Wagner Meira Jr., Federal University of Minas Gerais, Brazil 18. Maria Mirto, University of Salento, Italy 19. Hartmut Mix, University of Technology Dresden, Germany 20. Salvatore Orlando, University of Venezia, Italy 21. Mar?a S. P?rez, Universidad Polit?cnica de Madrid, Madrid, Spain 22. Gernot Plank, University of Graz, Austria 23. Omer F. Rana, Cardiff University, UK 24. Blanca Rodriguez, University of Oxford, UK 25. Luis Paulo da Silva Barra, Federal University of Juiz de Fora, Brazil 26. Fabrizio Silvestri, ISTI-CNR, Italy 27. Raymond Spiteri, University of Saskatchewan, Canada 28. Roberto Tagliaferri, University of Salerno, Italy 29. El-Ghazali Talbi, Universit? des Sciences et Technologies de Lille, France 30. Paolo Trunfio, University of Calabria, Italy 31. Pierangelo Veltri, University Magna Gr?cia of Catanzaro, Italy 32. Edward J. Vigmond, University of Calgary, Canada 33. Albert Zomaya, University of Sydney, Australia **************************************** New book release Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine, and Healthcare ISBN: 978-1-60566-374-6; 1,050 pp; May 2009 Published under Medical Information Science Reference an imprint of IGI Global http://www.igi-global.com/reference/details.asp?id=34292 Edited by: Mario Cannataro, University Magna Graecia of Catanzaro, Italy **************************************** Prof. Mario Cannataro, Informatics and Biomedical Engineering, University "Magna Gr?cia" of Catanzaro, Viale Europa (Localit? Germaneto), 88100 CATANZARO, ITALY, Tel: 0961-369 4100, Fax: 0961-369 4073/4090, Email: cannataro at unicz.it, Web: http://bioingegneria.unicz.it/~cannataro/ ****************************************