March 2011 - sem-grd - lists.ogf.org

HiBB 2011 Euro-Par Workshop on High Performance Bioinformatics and Biomedicine
by Mario Cannataro 31 Mar '11

31 Mar '11

I apologize for any cross-posting of this announcement. ===================================================================== 2nd International Workshop on High Performance Bioinformatics and Biomedicine (HiBB) August 30th 2011, Bordeaux, France HiBB 2011 http://staff.icar.cnr.it/cannataro/hibb2011/ held in conjunction with Euro-Par 2011 Bordeaux, France August 29th - September 2nd, 2011 http://europar2011.bordeaux.inria.fr/ ===================================================================== * * * CALL FOR PAPERS * * * ===================================================================== High-throughput technologies (e.g. microarray and mass spectrometry) and clinical diagnostic tools (e.g. medical imaging) are producing an increasing amount of experimental and clinical data. In such a scenario, large scale databases and bioinformatics tools are key tools for organizing and exploring biological and biomedical data with the aim to discover new knowledge in biology and medicine. High-performance computing may play an important role in many phases of life sciences research, from raw data management and processing, to data analysis and integration, till data exploration and visualization. In particular, at the raw data layer, Grid infrastructures may offer the huge data storage needed to store experimental and biomedical data, while parallel computing can be used for basic pre-processing (e.g. parallel BLAST) and for more advanced analysis (e.g. parallel data mining). In such a scenario, novel parallel architectures (e.g. e.g. CELL processors, GPUs, FPGA, hybrid CPU/FPGA) coupled with emerging programming models may overcome the limits posed by conventional computers to the mining and exploration of large amounts of data. At an higher layer, emerging biomedical applications need to use in a coordinated way both bioinformatics tools, biological data banks and patients clinical data, that require seamless integration, privacy preservation and controlled sharing. Service Oriented Architectures and semantic technologies, such as ontologies, may allow the building and deployment of the so called collaboratories, where experimental research may be conducted by remote scientists in a collaborative way. The goal of HiBB is to bring together scientists in the fields of high performance computing, computational biology and medicine to discuss, among the others, the organization of large scale biological and biomedical databases and the parallel implementation of bioinformatics algorithms and biomedical applications. 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 applications of parallel and high performance computing to biology and medicine. Topics of interest include, but are not limited to: - Large scale biological and biomedical databases - Data integration and ontologies in biology and medicine - Parallel bioinformatics algorithms - Parallel visualization and exploration of biomedical data - Parallel visualization and analysis of biomedical images - Computing environments for large scale collaboration - Scientific workflows in bioinformatics and biomedicine - (Web) Services for bioinformatics and biomedicine - Grid Computing for bioinformatics and biomedicine - Peer-To-Peer Computing for bioinformatics and biomedicine - Emerging architectures and programming models (e.g. Cell, GPUs) for bioinformatics and biomedicine - Parallel processing of bio-signals - Modeling and simulation of complex biological processes PROGRAM The workshop will take place on August, 30th. It is scheduled as full-day. The program is not available yet. PAPER SUBMISSION, REGISTRATION AND PUBLICATION We invite original previously unpublished contributions. Submission implies that at least one author will register for the workshops at Euro-Par 2011 and present the paper in the workshop session, if accepted. Full papers should not exceed 10 pages in the Springer LNCS style (http://www.springer.com/computer/lncs?SGWID=0-164-6-793341-0) Paper submission has to be performed by using the HiBB EasyChair submission server (https://www.easychair.org/conferences/?conf=hibb2011) In case of problems, authors may send their manuscript in PDF to the workshop chair: cannataro AT unicz.it. Papers accepted for publication must also be supplied in source form (Latex or Word). All accepted and presented papers will be included in the Workshops proceedings, that will be published in a separate Springer LNCS Euro-Par 2010 Workshop volume after the conference. Deadline for submitting camera Authors of accepted papers will be required to sign up a Springer copyright form. JOURNAL SPECIAL ISSUE At the end of the workshop, we plan to invite the best 4-6 papers of the workshop for a special section on an international journal. IMPORTANT DATES Full papers submission: June 6, 2011 Decision Notification: July 15, 2011 Final papers due: August 5, 2011 Workshop session: August 30, 2011 Final review comments: October 1, 2011 Camera ready papers for EuroPar Workshop Proceedings: October 15, 2011 WORKSHOP ORGANIZER Mario Cannataro, University Magna Græcia of Catanzaro, Italy PROGRAM COMMITTEE (TO BE CONFIRMED) 1. Pratul K. Agarwal, Oak Ridge National Laboratory, USA 2. David A. Bader, College of Computing, Georgia University of Technology, USA 3. Ignacio Blanquer; Universidad Politécnica de Valencia, Valencia, Spain 4. Daniela Calvetti, Case Western Reserve University, USA 5. Werner Dubitzky, University of Ulster, UK 6. Ananth Y. Grama, Purdue University, USA 7. Concettina Guerra, University of Padova, Italy 8. Vicente Hernández, Univ. Politécnica de Valencia, Spain 9. Salvatore Orlando, University of Venezia, Italy 10. Omer F. Rana, Cardiff University, UK 11. Richard Sinnott; National e-Science Centre, University of Glasgow, Glasgow, United Kingdom 12. Fabrizio Silvestri, ISTI-CNR, Italy 13. Erkki Somersalo, Case Western Reserve University, USA 14. Paolo Trunfio, University of Calabria, Italy 15. 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 Græcia" of Catanzaro, Viale Europa (Località Germaneto), 88100 CATANZARO, ITALY, Tel: 0961-369 4100, Fax: 0961-369 4073/4090, Email: cannataro(a)unicz.it, Web: http://bioingegneria.unicz.it/~cannataro/ ****************************************

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Final CfP: 5th Int. Workshop on Modular Ontologies (WoMO 2011)
by Thomas Schneider 29 Mar '11

29 Mar '11

======================================================== 5th Int. Workshop on Modular Ontologies (WoMO) Ljubljana, Slovenia, August 8-12, 2011 held in conjunction with ESSLLI 2011 --- Last Call for Papers --- ======================================================== EXTENDED+FINAL Submission deadline: April 15, 2011 ======================================================== http://www.informatik.uni-bremen.de/~okutz/womo5 INVITED SPEAKERS: Stefano Borgo (Laboratory of Applied Ontology, Trento, Italy) Modularity in foundational ontologies Stefan Schulz (Medical University Graz, Austria) "Modularity Aspects in Biomedical Ontologies" Michael Zakharyaschev (Birkbeck College London, UK) Logical approaches to modularity (Topics are tentative.) MODULARITY, as studied for many years in software engineering, allows mechanisms for easy and flexible reuse, generalization, structuring, maintenance, design patterns, and comprehension. Applied to ontology engineering, modularity is central not only to reduce the complexity of understanding ontologies, but also to facilitate ontology maintenance and ontology reasoning. Recent research on ontology modularity shows substantial progress in foundations of modularity, techniques of modularization and modular development, distributed reasoning and empirical evaluation. These results provide a foundation for ongoing multi-disciplinary research and development. The workshop follows a series of successful events that have been an excellent venue for practitioners and researchers to discuss latest work and current problems, and is this time organised as a satellite workshop of ESSLLI 2011 (week 2, see http://esslli2011.ijs.si/?p=306 ), following an introductory ESSLLI course on notions of modularity in ontologies (week 1, see http://esslli2011.ijs.si/?p=310 ). TOPICS include, but are not limited to: - What is Modularity: Kinds of modules and their properties; modules vs. contexts; design patterns; granularity of representation; - Logical/Foundational Studies: Conservativity and syntactic approximations for modules; modular ontology languages; reconciling inconsistencies across modules; formal structuring of modules; networks of ontologies; heterogeneity; - Algorithmic Approaches: distributed reasoning; modularization and module extraction; (selective) sharing and re-using, linking and importing; hiding and privacy; evaluation of modularization approaches; complexity of reasoning; reasoners or implemented systems; - Applications: Semantic Web; life sciences; bio-ontologies; natural language processing; ontologies of space and time; ambient intelligence; collaborative ontology development; etc. The workshop is open to all members of the ESSLLI community. Workshop speakers will be required to register for the Summer School; however, they will be able to register at a reduced rate to be determined by the Local Organizers. Participants can attend any other ESSLLI courses and workshops of their choice. IMPORTANT DATES (Updated) Paper Submission: April 15, 2011 Notification: May 23, 2011 Camera ready: June 6, 2011 Workshop: August 8-12, 2011 SUBMISSION GUIDELINES: The workshop welcomes submission of high quality original and previously unpublished papers. Contributions should not exceed 13 pages in length and must be formatted according to IOS Press style (see http://www.iospress.nl/authco/instruction_crc.html ). Contributions should be prepared in PDF format and submitted not later than April 15, 2011, through the EasyChair Submission System (see http://www.easychair.org/conferences/?conf=womo2011 ). Info: In the LaTeX template, please comment the following line for compatibility. %\usepackage[mtplusscr,mtbold]{mathtime} Submitted papers will be peer-reviewed by members of the program committee. Accepted papers may be extended up to 16 pages and will be published as chapters in an IOS Press book in the series 'Frontiers in Artificial Intelligence and Applications'. (Find the WoMO 2010 proceedings here http://www.booksonline.iospress.nl/Content/View.aspx?piid=16268 ) WORKSHOP CO-CHAIRS: Oliver Kutz (Research Center on Spatial Cognition (SFB/TR 8), Bremen, Germany) Thomas Schneider (Saarland University, Saarbruecken, Germany) PROGRAM COMMITTEE: Jie Bao (Rensselaer Polytechnic Institute, Troy, NY, USA) Simon Colton (Imperial College, London, UK) Melanie Courtot (BC Cancer Care & Research, Vancouver, Canada) Bernardo Cuenca Grau (University of Oxford, UK) Faezeh Ensan (University of New Brunswick, Canada) Fred Freitas (Federal University of Pernambuco, Brazil) Silvio Ghilardi (University of Milan, Italy) Janna Hastings (European Bioinformatics Institute, Cambridge, UK) Robert Hoehndorf (University of Cambridge, UK) Joana Hois (University of Bremen, Germany) C. Maria Keet (University of KwaZulu-Natal, Durban, South Africa) Roman Kontchakov (Birkbeck College, London, UK) Frank Loebe (University of Leipzig, Germany) Till Mossakowski (German Research Center for Artificial Intelligence, Bremen, Germany) Leo Obrst (MITRE, McLean, VA, USA) Bijan Parsia (University of Manchester, UK) Daniel Pokrywczynski (University of Liverpool, UK) Anne Schlicht (University of Mannheim, Germany) Marco Schorlemmer (Artificial Intelligence Research Institute, Barcelona, Spain) Andrei Tamilin (FBK-IRST, Trento, Italy) Dirk Walther (Polytechnic University of Madrid, Spain)

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4th CfP: 5th Int. Workshop on Modular Ontologies (WoMO 2011)
by Thomas Schneider 07 Mar '11

07 Mar '11

======================================================== 5th Int. Workshop on Modular Ontologies (WoMO) Ljubljana, Slovenia, August 8-12, 2011 held in conjunction with ESSLLI 2011 --- Fourth Call for Papers --- ======================================================== Submission deadline: April 1, 2011 ======================================================== http://www.informatik.uni-bremen.de/~okutz/womo5 INVITED SPEAKERS: Stefano Borgo (Laboratory of Applied Ontology, Trento, Italy) Modularity in foundational ontologies Stefan Schulz (Medical University Graz, Austria) "Modularity Aspects in Biomedical Ontologies" Michael Zakharyaschev (Birkbeck College London, UK) Logical approaches to modularity (Topics are tentative.) MODULARITY, as studied for many years in software engineering, allows mechanisms for easy and flexible reuse, generalization, structuring, maintenance, design patterns, and comprehension. Applied to ontology engineering, modularity is central not only to reduce the complexity of understanding ontologies, but also to facilitate ontology maintenance and ontology reasoning. Recent research on ontology modularity shows substantial progress in foundations of modularity, techniques of modularization and modular development, distributed reasoning and empirical evaluation. These results provide a foundation for ongoing multi-disciplinary research and development. The workshop follows a series of successful events that have been an excellent venue for practitioners and researchers to discuss latest work and current problems, and is this time organised as a satellite workshop of ESSLLI 2011 (week 2, see http://esslli2011.ijs.si/?p=306 ), following an introductory ESSLLI course on notions of modularity in ontologies (week 1, see http://esslli2011.ijs.si/?p=310 ). TOPICS include, but are not limited to: - What is Modularity: Kinds of modules and their properties; modules vs. contexts; design patterns; granularity of representation; - Logical/Foundational Studies: Conservativity and syntactic approximations for modules; modular ontology languages; reconciling inconsistencies across modules; formal structuring of modules; networks of ontologies; heterogeneity; - Algorithmic Approaches: distributed reasoning; modularization and module extraction; (selective) sharing and re-using, linking and importing; hiding and privacy; evaluation of modularization approaches; complexity of reasoning; reasoners or implemented systems; - Applications: Semantic Web; life sciences; bio-ontologies; natural language processing; ontologies of space and time; ambient intelligence; collaborative ontology development; etc. The workshop is open to all members of the ESSLLI community. Workshop speakers will be required to register for the Summer School; however, they will be able to register at a reduced rate to be determined by the Local Organizers. Participants can attend any other ESSLLI courses and workshops of their choice. IMPORTANT DATES (Updated) Paper Submission: April 1, 2011 Notification: May 2, 2011 Camera ready: June 1, 2011 Workshop: August 8-12, 2011 SUBMISSION GUIDELINES: The workshop welcomes submission of high quality original and previously unpublished papers. Contributions should not exceed 13 pages in length and must be formatted according to IOS Press style (see http://www.iospress.nl/authco/instruction_crc.html ). Contributions should be prepared in PDF format and submitted not later than April 1, 2011, through the EasyChair Submission System (see http://www.easychair.org/conferences/?conf=womo2011 ). Submitted papers will be peer-reviewed by members of the program committee. Accepted papers may be extended up to 16 pages and will be published as chapters in an IOS Press book in the series 'Frontiers in Artificial Intelligence and Applications'. (Find the WoMO 2010 proceedings here http://www.booksonline.iospress.nl/Content/View.aspx?piid=16268 ) WORKSHOP CO-CHAIRS: Oliver Kutz (Research Center on Spatial Cognition (SFB/TR 8), Bremen, Germany) Thomas Schneider (Saarland University, Saarbruecken, Germany) PROGRAM COMMITTEE: Jie Bao (Rensselaer Polytechnic Institute, Troy, NY, USA) Simon Colton (Imperial College, London, UK) Melanie Courtot (BC Cancer Care & Research, Vancouver, Canada) Bernardo Cuenca Grau (University of Oxford, UK) Faezeh Ensan (University of New Brunswick, Canada) Fred Freitas (Federal University of Pernambuco, Brazil) Silvio Ghilardi (University of Milan, Italy) Janna Hastings (European Bioinformatics Institute, Cambridge, UK) Robert Hoehndorf (University of Cambridge, UK) Joana Hois (University of Bremen, Germany) C. Maria Keet (University of KwaZulu-Natal, Durban, South Africa) Roman Kontchakov (Birkbeck College, London, UK) Frank Loebe (University of Leipzig, Germany) Till Mossakowski (German Research Center for Artificial Intelligence, Bremen, Germany) Leo Obrst (MITRE, McLean, VA, USA) Bijan Parsia (University of Manchester, UK) Daniel Pokrywczynski (University of Liverpool, UK) Anne Schlicht (University of Mannheim, Germany) Marco Schorlemmer (Artificial Intelligence Research Institute, Barcelona, Spain) Andrei Tamilin (FBK-IRST, Trento, Italy) Dirk Walther (Polytechnic University of Madrid, Spain) ---------------------------------------------------------------------- Dr. Thomas Schneider Universität Bremen, FB 03 MZH, Raum 3100 Postfach 330440 28334 Bremen Germany +49 421 218-64432 http://www.informatik.uni-bremen.de/~ts/ ----------------------------------------------------------------------

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