From clements at galaxyproject.org Tue Jun 4 15:27:34 2013 From: clements at galaxyproject.org (Dave Clements) Date: Tue, 4 Jun 2013 12:27:34 -0700 Subject: [BiO BB] GCC2013 Regular Registration Closes June 14 Message-ID: Hello all, This is the final registration reminder for the 2013 Galaxy Community Conference (GCC2013), being held in Oslo, 30 June through July 2. GCC2013 is a great opportunity to share best practices and network with other researchers who also facing the challenges of data-intensive biology. Registration closes June 14*, ten days from today. Register now and guarantee your spot in the Training Day sessions you want to take.* *Registration is still a bargain with the full 3-day registration starting at ~ ?165 for post-docs and students (that is just ?55 per day). The program features 15 Training Day sessions in 5 tracks on 12 different topics, 25 Talks on topics ranging from Reproducibility to Exploiting Galaxy , 23 Posters (and counting), 2 Lightning Talk sessions, and a end-of-conference event at an historic venue high above Oslo. Ser frem til ? se deg i Oslo! GCC2013 Organizing Committee PS: Please help get the word out . * Not June 7, as had been stated earlier in several places. -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ From cannataro at unicz.it Sun Jun 9 18:52:28 2013 From: cannataro at unicz.it (Mario Cannataro) Date: Mon, 10 Jun 2013 00:52:28 +0200 (CEST) Subject: [BiO BB] ACM-BCB 2nd Workshop on Parallel and Cloud-based Bioinformatics and Biomedicine (ParBio) In-Reply-To: <98ffa7905c49afd30a50480d1812b59f.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> <057ca61063d2df86dbfedb3f33fe06f8.squirrel@email.unicz.it> <29b4f0ef371de5adb52505f83a1d153a.squirrel@email.unicz.it> <8a9b80c485a3eac1ad09c3134eb1841d.squirrel@email.unicz.it> <5ef1e4bd7aebe7bd69da47a45ee9d058.squirrel@email.unicz.it> <8e6a0eaa020399bfb82507040c017757.squirrel@email.unicz.it> <98ffa7905c49afd30a50480d1812b59f.squirrel@email.unicz.it> Message-ID: I apologize for any cross-posting of this announcement. ===================================================================== 2nd International Workshop on Parallel and Cloud-based Bioinformatics and Biomedicine (ParBio) http://staff.icar.cnr.it/cannataro/parbio2013/ held in conjunction with ACM BCB 2013 - ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics September 22-25, 2013 Washington DC, USA http://www.cse.buffalo.edu/ACM-BCB2013/ ===================================================================== DEADLINE EXTENDED TO: JUNE 18, 2013 ===================================================================== * * * 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 2013 welcomes original submissions that have not been published and that are not under review by another conference or journal. Papers should not exceed 10 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=parbio2013). IMPORTANT DATES Paper submission: June 18, 2013 (Deadline Extended) Notifications sent to authors: July 15, 2013 Camera-ready papers due: August 1, 2013 Conference: September 22-25, 2013 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 Krakow PL and University of Amsterdam NL 6. Rajkumar Buyya, University of Melbourne, Melbourne, Australia 7. Umit Catalyurek, The Ohio State University, USA 8. Tim Clark, Harvard Medical School, USA 9. Giuseppe Di Fatta, University of Reading, UK 10. Werner Dubitzky, University of Ulster, UK 11. Ananth Y. Grama, Purdue University, USA 12. Concettina Guerra, University of Padova, Italy 13. Pietro Hiram Guzzi, University Magna Gr?cia of Catanzaro, Italy 14. Vicente Hern?ndez, Univ. Polit?cnica de Valencia, Spain 15. Pilar Herrero, Universidad Politecnica de Madrid, Madrid, Spain 16. Kamer Kaya, The Ohio State University, USA 17. Maria Mirto, University of Salento, Italy 18. Salvatore Orlando, University of Venezia, Italy 19. Maria S. Perez, Universidad Politecnica de Madrid, Madrid, Spain 20. Richard Sinnott, University of Melbourne, Melbourne, Australia 21. Fabrizio Silvestri, ISTI-CNR, Italy 22. Tony Solomonides, University of West of England, Bristol, UK 23. Roberto Tagliaferri, University of Salerno, Italy 24. Paolo Trunfio, University of Calabria, Italy 25. Albert Zomaya, University of Sydney, Australia