From cannataro at unicz.it Mon Jun 4 07:47:52 2012 From: cannataro at unicz.it (Mario Cannataro) Date: Mon, 4 Jun 2012 13:47:52 +0200 (CEST) Subject: [BiO BB] ACM-BCB Workshop on Parallel and Cloud-based Bioinformatics and Biomedicine (ParBio) In-Reply-To: <2bfa571d2421ca5842919c2d8038f74e.squirrel@email.unicz.it> References: <49488aa30fce78e7e8b644f2b6443229.squirrel@email.unicz.it> <0b90f151c841a8029f34aa95146d4a02.squirrel@email.unicz.it> <637f7d51898906671cc8ef02e2be2ccc.squirrel@email.unicz.it> <2bfa571d2421ca5842919c2d8038f74e.squirrel@email.unicz.it> Message-ID: <057ca61063d2df86dbfedb3f33fe06f8.squirrel@email.unicz.it> I apologize for any cross-posting of this announcement. ===================================================================== 1st International Workshop on Parallel and Cloud-based Bioinformatics and Biomedicine (ParBio) http://staff.icar.cnr.it/cannataro/parbio2012/ held in conjunction with ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB) October 7-10, 2012 Orlando, Florida, USA http://www.cse.buffalo.edu/ACM-BCB2012/ ===================================================================== * * * CALL FOR PAPERS * * * ===================================================================== Due to the availability of high-throughput platforms (e.g. next generation sequencing, microarray and mass spectrometry) and clinical diagnostic tools (e.g. medical imaging), a recent trend in Bioinformatics and Biomedicine is the increasing production of experimental and clinical data. Considering the complex analysis pipeline of the biomedical research, the bottleneck is more and more moving toward the storage, integration, and analysis of experimental data, as well as their correlation and integration with publicly available data banks. While Parallel Computing and Grid Computing may offer the computational power and the storage to face this overwhelming availability of data, Cloud Computing is a key technology to hide the complexity of computing infrastructures, to reduce the cost of the data analysis task, and especially to change the overall model of biomedical research and health provision. Grid infrastructures may offer the data storage needed to store the huge experimental and biomedical data, while parallel computing can be used for basic pre-processing (e.g. parallel BLAST, mpiBLAST) and for more advanced analysis (e.g. parallel data mining). In such a scenario, novel parallel architectures (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. On the other hand, these technologies yet require great investments by biomedical and clinical institutions and are based on a traditional model where users often need to be aware and face different management problems, such as hardware and software management, data storage, software ownership, and not scalable costs (different professional-level applications in the biomedical domain have high starting costs that prevent many small laboratories to use them). The Cloud Computing technology, that is able to offer scalable costs and increased reachability, availability and easiness of application use, and also the possibility to enforce collaboration among scientists, is already changing the business model in different domains and now it starts to be used also in the bioinformatics (see for instance the recent JCVI Cloud Bio-Linux initiative) and biomedical domains. However, many problems remain to be solved, such as availability and safety of the data, privacy-related issues, availability of software platforms for rapid deployment, execution and billing of biomedical applications. The goal of ParBio is to bring together scientists in the fields of high performance and cloud computing, computational biology and medicine, to discuss, among the others, the organization of large scale biological and biomedical databases, the parallel/service-based implementation of bioinformatics and biomedical applications, and problems and opportunities of moving biomedical and health applications on the cloud. The workshop will focus on research issues, problems and opportunities of moving biomedical and health applications on the cloud, as well as on the opportunity to define guidelines and minimum requirements for a Biomedical Cloud. Moreover, the workshop will discuss about parallel and distributed management and analysis of molecular and clinical data, that more and more need to be integrated and analysed in a joint way. TOPICS OF INTEREST The main themes and research topics will regard the applications of parallel and high performance computing to biology and medicine, as well as Cloud Computing opportunities and problems for bioinformatics and biomedical applications - Large scale biological and biomedical databases - Data integration and ontologies in biology and medicine - Integration and analysis of molecular and clinical data - Parallel bioinformatics algorithms - Parallel visualization and exploration of omics and clinical data - Parallel visualization and analysis of biomedical images - Computing environments for large scale collaboration - Scientific workflows in bioinformatics and biomedicine - Emerging architectures and programming models for bioinformatics and biomedicine - Parallel processing of bio-signals - Modeling and simulation of complex biological processes - Cloud Computing for bioinformatics and biomedicine - Cloud Computing for health systems - Privacy issues for Cloud-based biomedical applications - (Web) Services for bioinformatics and biomedicine - Grid Computing for bioinformatics and biomedicine - Peer-To-Peer Computing for bioinformatics and biomedicine PROGRAM The workshop will take place on (To Be Announced). It is scheduled as full-day. The program is not available yet. PAPER SUBMISSION, REGISTRATION AND PUBLICATION ParBio 2012 welcomes original submissions that have not been published and that are not under review by another conference or journal. Papers should not exceed 8 pages in ACM template on 8.5 x 11 inch paper (see ACM templates - http://www.acm.org/sigs/publications/proceedings-templates). All submissions will be evaluated on their originality, technical soundness, significance, presentation, and interest to the conference attendees. Submission implies the willingness of at least one of the authors to register and present the work associated with the paper submitted. All submitted papers will be reviewed by ParBio?s technical program committee. All accepted papers of registered authors will be included in the workshop proceedings published by ACM digital libraries. Authors of selected papers may be invited to adapt their papers for their publication in several journals. Authors of accepted papers will be required to submit an online ACM Copyright Form. Authors will be contacted by ACM requesting this information. Authors should submit papers using the Easy Chair System (https://www.easychair.org/conferences/?conf=parbio2012). IMPORTANT DATES Paper submission: July 8, 2012 Notifications sent to authors: August 8, 2012 Camera-ready papers due: August 16, 2012 Conference: October 7-10, 2012 WORKSHOP ORGANIZER Mario Cannataro, University Magna Gr?cia of Catanzaro, Italy PROVISIONAL 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 Polit?cnica de Valencia, Valencia, Spain 4. Vincent Breton, CNRS/IN2P3, LPC Clermont-Ferrand, France 5. Marian Bubak; AGH University of Science and Technology, Krak?w, Poland 6. Rajkumar Buyya, University of Melbourne, Melbourne, Australia 7. Tim Clark, Harvard Medical School, USA 8. Giuseppe Di Fatta, University of Reading, UK 9. Werner Dubitzky, University of Ulster, UK 10. Ananth Y. Grama, Purdue University, USA 11. Concettina Guerra, University of Padova, Italy 12. Pietro Hiram Guzzi, University Magna Gr?cia of Catanzaro, Italy 13. Vicente Hern?ndez, Univ. Polit?cnica de Valencia, Spain 14. Pilar Herrero, Universidad Politecnica de Madrid, Madrid, Spain 15. Maria Mirto, University of Salento, Italy 16. Salvatore Orlando, University of Venezia, Italy 17. Maria S. Perez, Universidad Politecnica de Madrid, Madrid, Spain 18. Richard Sinnott, University of Melbourne, Melbourne, Australia 19. Fabrizio Silvestri, ISTI-CNR, Italy 20. Tony Solomonides, University of West of England, Bristol, UK 21. Roberto Tagliaferri, University of Salerno, Italy 22. Paolo Trunfio, University of Calabria, Italy 23. Albert Zomaya, University of Sydney, Australia --------------------------------------------------------------------------------- 5x1000 Sostieni la Ricerca e le iniziative dell'Universit? degli Studi Magna Graecia di Catanzaro. Apponi la tua firma nel riquadro della dichiarazione dei redditi alla voce "Finanziamento agli enti della ricerca scientifica e della universit?", sia che si tratti del Modello 730, del Modello Unico 2012 oppure del CUD 2012. Trascrivi il codice fiscale dell'Universit?: 97026980793 From hlapp at gmx.net Mon Jun 11 18:31:21 2012 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon, 11 Jun 2012 18:31:21 -0400 Subject: [BiO BB] Last reminder: Deadline for iEvoBio Challenge Competitions is approaching Message-ID: <3B92635E-8140-465C-A9C1-5B3ADDBB26C6@gmx.net> The deadline for submissions to the yearly iEvoBio Challenge is June 25, 2012, and is rapidly approaching! This is our last reminder. This year?s theme is "Synthesizing Phylogenies," and further information on criteria for challenge entries, how to submit them, and award amount can be found at http://ievobio.org/challenge.html. Also, Biomatters Ltd is running the Geneious Challenge alongside iEvoBio?s competition. The goal of this challenge is to develop a new and exciting visualization or analysis plugin to Geneious Pro, using the public API. See http://ievobio.org/geneious_challenge.html for more information. The deadline for this competition is also June 25. More details about the iEvoBio conference and program are available at http://ievobio.org. You can also find continuous updates on the conference's Twitter feed at http://twitter.com/iEvoBio and Google+ page, or subscribe to the low-traffic iEvoBio announcements mailing list at http://groups.google.com/group/ievobio-announce. iEvoBio 2012 is sponsored by the US National Evolutionary Synthesis Center (NESCent) and by Biomatters Ltd., in partnership with the Society for the Study of Evolution (SSE) and the Society of Systematic Biologists (SSB). The iEvoBio 2012 Organizing Committee: Hilmar Lapp, US National Evolutionary Synthesis Center (chair) Robert Beiko, Dalhousie University Nico Cellinese, University of Florida Robert Guralnick, University of Colorado at Boulder Rebecca Kao, Denver Botanic Gardens Ellinor Michel, Natural History Museum, London Nadia Talent, Royal Ontario Museum Andrea Thomer, University of Illinois at Urbana-Champaign From clements at galaxyproject.org Sun Jun 10 13:31:42 2012 From: clements at galaxyproject.org (Dave Clements) Date: Sun, 10 Jun 2012 10:31:42 -0700 Subject: [BiO BB] GCC2012 Early Registration ENDS THIS MONDAY JUNE 11 In-Reply-To: References: Message-ID: Hello all, Just a *final* reminder that early registration for the 2012 Galaxy Community Conference (GCC2012) *closes on Monday June 11 (*which is probably* today* when you read this*)*. Registering early saves 36 to 42% on registration costs, and allows you to sign up for the GCC2012 Training Dayand book discounted conference lodging *before they fill up*. *Register today . * GCC2012 will be held July 25-27, in Chicago, Illinois, United States. This year GCC2012 features a full day of tutorial sessionswith 3 parallel tracks, each featuring four, 90 minute workshops and covering 10 different topic, including the newly added Variant and SNP Analsys, RNA-Seq Analysis, and Galaxy Code Architecture sessions. The two-day main meetingincludes over 25 talks by Galaxy community members and Galaxy developers addressing the challenges of integrating, analyzing, and sharing the diverse and very large datasets that are now typical in biomedical research. GCC2012 is an opportunity to share best practices with, and learn from, a large community of researchers and support staff who are facing the challenges of data-intensive biology. Galaxy is an open web-based platform for data intensive biomedical researchthat is widely used and deployed at research organizations of all sizes around the world. See you in Chicago! Dave Clements, on behalf of the GCC2012 Organizing Committee Links: http://galaxyproject.org/GCC2012 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ From german.terrazas at nottingham.ac.uk Mon Jun 11 15:44:10 2012 From: german.terrazas at nottingham.ac.uk (German Terrazas Angulo) Date: Mon, 11 Jun 2012 20:44:10 +0100 Subject: [BiO BB] ICARIS 2012 Last Call for Abstracts/Posters/Oral Presentations: June 15th, 2012 Message-ID: <4FD64A8A.6020600@nottingham.ac.uk> CALL FOR ABSTRACTS, SHORT PRESENTATIONS & POSTERS *Apologies for cross-posting* The 11th International Conference on Artificial Immune Systems 28-31 August 2012 Taormina, Italy http://www.artificial-immune-systems.org/icaris/2012/ http://www.artificial-immune-systems.org/icaris/2012/submission.php http://www.artificial-immune-systems.org/icaris/2012/submission_abstract.php IMPORTANT DATES: * Abstract/Poster/Short Presentation Submission deadline: June 15th, 2012 * Notification of acceptance: June 20th, 2012 ** ICARIS 2012 is divided into two main tracks: 1) Computational Immunology, Immunoinformatics, Theoretical Immunology, & Systems Immunology 2) Immunological Computation, Immune-inspired Engineering, Immune-inspired Heuristics *** all abstracts for oral or poster presentation can be submitted in both tracks **** participants of accepted abstracts at ICARIS 2012 can submit their extended versions to the special issue on Natural Computing journal ***** Plenary Speakers: - Piero Mastroeni, University of Cambridge, UK - Stephanie Forrest, University of New Mexico, USA ****** Tutorial Speaker: - Christian Blum, Universitat Politecnica de Catalunya, Spain - Heiko Muller, Italian Institute of Technology - Center of Genomic Science, Italy - Luca Zammataro, Italian Institute of Technology - Center of Genomic Science, Italy ******* Panel "The future of Computational Immunology, Immunoinformatics, Theoretical Immunology and Systems Immunology" - Hugues Bersini, Universit? Libre de Bruxelles, Belgium - Chang-Zheng Chen, Stanford University, USA - Marc Thilo Figge, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Kn?ll-Institute, Germany (TBC) - Stephanie Forrest, New Mexico University & SFI, USA - Koichi Kobayashi, Harvard University - Harvard Medical School, USA - Oliver Kohlbacher, University of T?bingen, Germany (TBC) - Melanie Moses, University of New Mexico, USA - Guido Poli, Division of Immunology, Transplantation and Infectious Diseases, Vita-Salute San Raffaele University School of Medicine & San Raffaele Scientific Institute, Milan, Italy - Alex Sette, La Jolla Institute for Allergy & Immunology, La Jolla, USA (TBC) - Veronique Thomas-Vaslin, Universit? Pierre et Marie Curie, Paris, France - Jon Timmis, University of York, UK - Elisa Vicenzi, Division of Immunology, Transplantation and Infectious Diseases San Raffaele Scientific Institute, Milan, Italy More Speakers to be Announced! We look forward to welcoming you to Taormina in August 2012! C. Coello Coello, J. Greensmith, N. Krasnogor, P. Lio', G. Nicosia, M. Pavone. This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. From jeff at bioinformatics.org Fri Jun 15 16:17:37 2012 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Fri, 15 Jun 2012 16:17:37 -0400 Subject: [BiO BB] New Course: Introduction to DNA and Protein Sequence Analysis Message-ID: <4FDB9861.4020001@bioinformatics.org> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- BI101 Introduction to DNA and Protein Sequence Analysis June 25-29, 2012 Live, Online at Bioinformatics.Org http://www.bioinformatics.org/wiki/BI101 -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- OBJECTIVES: This course teaches the individual how to analyze DNA and protein sequences using computer software. Topics to be covered include description of sequence alignments, search, formats, and various command line tools such as BLAST, FASTA, HMMER and editing software such as Geneious, Jalview, etc. INSTRUCTOR: Shailender Nagpal SYLLABUS: The course is divided into 4 sessions, roughly 1-1.5 hours each. Homework assignments will involve running computationally intensive tools. Session 1: Fundamentals of DNA and protein alphabets, representations, patterns, structures and annotations Session 2: DNA and protein sequence alignments: local, global and multiple; demonstration of tools to perform these alignments Session 3: Sequence database searches using BLAST, FASTA and SSEARCH Session 4: Additional DNA sequence analysis applications, such as gene finding, genome annotation and assembly Lecture schedule: Monday through Thursday, 16:00-17:30 GMT REGISTRATION: http://www.bioinformatics.org/edu/ACTG FOR MORE INFORMATION: http://www.bioinformatics.org/wiki/BI101_Introduction_to_DNA_and_Protein_Sequence_Analysis Or contact: edu at bioinformatics.org Cheers, Jeff -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 978 621 8258 -- From conference at cewit.org Thu Jun 21 12:50:20 2012 From: conference at cewit.org (CEWIT Conference) Date: Thu, 21 Jun 2012 12:50:20 -0400 Subject: [BiO BB] (Mailing List Submission) Call for Papers - CEWIT2012 - Songdo, Incheon, Korea - November 5 and 6, 2012 Message-ID: The 9th International Conference & Expo on Emerging Technologies for a Smarter World (CEWIT2012) Songdo, Incheon, Korea November 5 and 6, 2012 Scope of the Conference We cordially invite you to submit your contribution to the 9th International Conference & Expo on Emerging Technologies for a Smarter World (CEWIT2012). Originally known as the International Conference on Cutting-Edge Wireless & Information Technologies, this conference is organized by the Center of Excellence in Wireless and Information Technology (CEWIT) in the United States and CEWIT Korea. CEWIT2012 is the premier international forum on the applications of emerging technologies in infrastructure, healthcare, and energy, which are three of the most critical components of a smarter global environment. Specific topics of interest include, but are not limited to, the following: Area 1 ? Research on Emerging Technologies - Wireless Sensor Networks - Intelligent Sensors/Devices - Pervasive Computing - Mobile Platforms - Intelligent Service Robots - Cyber Security - Collaborative Signal/Image Processing - Web 3.0 Area 2 ? Cloud Computing - Cloud Infrastructure Management - Cloud Infrastructure Security - Cloud Interoperability - Cloud Benchmarking - Trust and Policy Management in the Clouds - Mobility and Clouds - Cloud Efficiency and Energy - Cloud-Centric Regulatory Compliance Area 3 ? Visual Computing - Immersive Interface - Tiled Displays - Advanced Medical Imaging - 3D Technology - Human Computer Interaction - Multimedia Information Management - IPTV Technologies - GPU Clustering Area 4 ? Wireless Medicine and Health Technologies - Personal Medical Devices - Advanced Medical Imaging - Computer-Aided Diagnostics - Wireless Telemedicine - Implantable Sensors - Noninvasive Health Monitoring - Teleradiology - Medication Adherence - Asset Tracking and Monitoring Area 5 ? Smart Grid & Smart Energy - Distributed Sensor Networks for Smart Grid - Advanced Metering Infrastructure - Grid Management & Visualization - Energy Efficient Computing - Securing the Smart Grid - Advanced Sensor and RFID Technologies - Smart Grid Interoperability - Simulation and Modeling Area 6 ? Smart Infrastructure/Ubiquitous Cities - Securing the Transportation Infrastructure - Transportation Infrastructure Sensing - Transportation Infrastructure Management & Optimization - Traffic Simulation & Visualization - Interaction between Vehicles and the Environment - Broadband Access Anywhere - Integrated Management Technology for Ubiquitous City Area 7 ? Big Data - Model Driven Data Analysis - Visual Analytics - Data Mining in Business Intelligence - Text Mining & Sentiment Analysis - Biomedical and Healthcare Informatics - Scalable Visual Search, Monitoring and Surveillance - Distributed Robotics and Real-Time Data Analytics Submission Guidelines The CEWIT2012 conference is primarily interested in serving as a venue for the discussion of technical contributions highlighting end-to-end technical solutions, applications and systems, even if available only in prototype form. Therefore, we strongly encourage authors to submit abstracts (up to two pages) describing their contributions in an application-oriented context. Abstracts will be evaluated by conference program committee members and external reviewers. Submissions will be judged on validity, originality, technical strength, practical significance, quality of presentation, and relevance to the conference topics. We encourage submissions from a variety of fields where in-depth application-centric ideas addressing important challenges related to the conference theme are discussed. Please submit your abstract electronically at www.cewit.org. Authors of accepted abstracts will be required to submit a full paper to be included in the conference proceedings. Please follow the formatting instructions provided on our website. Important Dates Abstract Submission Deadline: July 15, 2012 Notification of Acceptance: August 15, 2012 Camera-Ready Paper & Presentation Materials: September 15, 2012 Contact Information For more information about CEWIT2012, please visit www.cewit.org or www.cewit.re.kr, or contact the conference program committee co-chairs: Dr. Rong Zhao +1 631-632-4633 conference at cewit.stonybrook.edu Dr. SeonJoo Kim +82 32-626-1210 conference at cewit.re.kr Venue CEWIT2012 will be held at SUNY Korea, located on the Songdo Global University Campus (SGUC) in the Incheon Free Economic Zone (IFEZ), Incheon City, which is one hour west of Seoul. Through mutual efforts between Stony Brook University, a flagship campus of the State University of New York (SUNY) system, and the Republic of Korea, SUNY Korea was established to bring American-style education to Asia. The recently opened SGUC offers state-of-the-art facilities designed by world-renowned architects. For more information about SUNY Korea, SGUC, and the City of Songdo, please visit www.sunykorea.ac.kr, www.sguc.co.kr/eng/index.jsp, and www.songdo.com. The CEWIT2012 conference is technically sponsored by the IEEE. Peer reviewed conference papers will be included in the IEEE Xplore online database and cited in EI. From clement at cs.byu.edu Wed Jun 27 18:48:41 2012 From: clement at cs.byu.edu (Mark Clement) Date: Wed, 27 Jun 2012 16:48:41 -0600 Subject: [BiO BB] Call For Papers BIOT2012 Message-ID: Call For Papers 9th Annual Biotechnology and Bioinformatics Symposium October 25-26, 2012. Provo, Utah, USA http://biotconf.org/ We invite you to submit original research papers on topics related to the general area of bioinformatics and biotechnology to the 9th Annual Biotechnology and Bioinformatics Symposium (BIOT-2012) held at Brigham Young University, Provo, Utah on October 25 and 26, 2012. We solicit research and survey papers in the areas of cancer research, genome sequencing and annotation, functional and computational genomics, transcriptomics, and other computational biology and bioinformatics topics. Important Dates: Submission deadline for full papers and 2-3 page abstracts (for oral presentation): July 10, 2012. Acceptance decision: August 22, 2012. Final extended abstracts for papers due after revision: September 12, 2012. Symposium date: October 25 and 26, 2012. Thank you. Quinn Snell and Mark Clement Program Co-Chairs