From ivanoe.defalco from na.icar.cnr.it Thu Dec 4 04:53:46 2008 From: ivanoe.defalco from na.icar.cnr.it (Ivanoe De Falco) Date: Thu Dec 4 12:31:36 2008 Subject: [Computational-biology] BADS 2009 - call for papers Message-ID: <4937A8AA.7060700@na.icar.cnr.it> (Apologies if you have received this more than once) ********************** CALL FOR PAPERS ********************** Workshop on Bio-Inspired Algorithms for Distributed Systems (BADS) http://bads.icar.cnr.it email: bads@icar.cnr.it June 19, 2009 In association with ICAC 2009 the 6th IEEE International Conference on Autonomic Computing & Communications June 15-19, 2009 **** IMPORTANT DATES **** January 31, 2009: Submission of Papers March 15, 2009: Notification of Acceptance/ Rejection April 06, 2009: Submission of Camera-Ready Copies June 19, 2009: Workshop Takes Place **** PUBLICATION **** The workshop proceedings will be published by ACM along with the proceedings of the other ICAC workshops, and distributed at the conference. **** JOURNAL SPECIAL ISSUE **** Selected papers will be invited to a special issue of the journal Future Generation Computer Systems, Elsevier (approved). **** SCOPE **** Currently used computer systems are characterized by an ever growing complexity and a pronounced distributed nature. While the use of centralized or hierarchical architectures and algorithms has been dominant so far, they are now becoming impractical because they have poor scalability and fault-tolerance characteristics. Decentralized architectures and algorithms, for example P2P and Grid systems, are increasingly popular, but they need new types of algorithms to be efficiently managed. Bio-inspired algorithms are proving effective, since they can solve hard parallel and distributed computational problems through the interaction of multiple agents. The behaviour of agents is often inspired by a number of biological systems, including ant colonies, bird flocking, honey bees, bacteria, and many more. The solution of a problem can emerge from the activity of "intelligent" agents that perform complex functionalities or from the interaction of a large number of very simple agents, in the so called "swarm intelligence" systems. These kinds of techniques feature fault-tolerant and self-adaptive behaviours that help to boost the autonomic nature of distributed systems. Such techniques are sometimes "evolutionary", as they can exploit genetic rules for the selection and the recombination of candidate solutions. Bio-inspired algorithms and systems are routinely applied to hard and large problems in a variety of areas. Some examples are optimization problems solved with genetic algorithms, routing strategies inspired by honey bee behaviour, resource discovery and data mining computations in Grid and P2P frameworks achieved by ant-inspired algorithms, and so on. The workshop aims to gather scientists, engineers, and practitioners to share and exchange their experiences, discuss challenges, and report state-of-the-art and in-progress research on Bio-Inspired Algorithms and Systems. **** AREAS OF INTEREST **** In this workshop we are interested in the exploitation of bio-inspired algorithms and systems to support the effective design and efficient implementation of distributed systems. The topics of interest include (but are not limited to): * Bio-inspired algorithms for parallel and distributed computing * Bio-inspired algorithms for P2P and Grid systems * Bio-inspired techniques for the construction and management of distributed systems * Parallel and distributed techniques of Swarm Intelligence: ant colonies, flock of birds, etc.. * Parallel and distributed evolutionary algorithms * High performance tools for bio-inspired algorithms and systems * Application of bio-inspired algorithms to routing, resource discovery, scheduling in parallel and distributed systems * Bio-inspired algorithms for data mining, bioinformatics, etc. **** ORGANIZING COMMITTEE **** Gianluigi Folino, ICAR-CNR, Italy, folino@icar.cnr.it Natalio Krasnogor, University of Nottingham, UK, nxk@cs.nott.ac.uk Carlo Mastroianni, ICAR-CNR, Italy, mastroianni@icar.cnr.it Franco Zambonelli, Universita' di Modena e Reggio Emilia, Italy, franco.zambonelli@unimore.it **** INTERNATIONAL PROGRAM COMMITTEE **** Ivanoe De Falco, ICAR-CNR, Italy Marios Dikaiakos, University of Cyprus Giovanna Di Marzo, University of London, UK Marco Dorigo, Universit? Libre de Bruxelles, Belgium Agostino Forestiero, ICAR-CNR, Italy Paraskevi Fragopoulou, FORTH-ICS, Greece Elena Marchiori, Radboud University, Netherlands. Antonio Nebro Urbaneja, Universidad de M?laga, Spain Muaz Niazi, Foundation University of Islamabad, Pakistan Giuseppe Nicosia, Universit? di Catania, Italy Gauthier Picard, ?cole Nationale Sup?rieure des Mines de Saint?tienne, France Omer Rana, Cardiff University, UK Giandomenico Spezzano, ICAR-CNR, Italy Ian Taylor, Cardiff University, UK Marco Tomassini, University of Lausanne, Switzerland **** WEB SITE AND CONTACT E-MAIL **** http://bads.icar.cnr.it email: bads@icar.cnr.it **** SUBMISSION GUIDELINES **** Original papers (a maximum of 8 pages in length) are invited. Please follow the formatting instructions that will be posted at the web site. The call is open to all members of the Autonomic Computing and Distributed Systems communities. All manuscripts will be reviewed by at least 3 members of the International Program Committee and judged on merits including correctness, originality, technical strength, quality of presentation, and relevance to the conference themes. At least one author of each accepted submission must attend the workshop. From frederic.fleche from gmail.com Mon Dec 8 17:22:38 2008 From: frederic.fleche from gmail.com (Fred) Date: Mon Dec 8 22:12:12 2008 Subject: [Computational-biology] Google get Bioinformatician connected Message-ID: Dear all, We are very delighted, at Bioinformatics.fr, to let you know that we successfully set up Google Friend Connect on Bioinformatics.fr website. That means that all people from the bioinformatics world will be able to be connected to each other and share any kind of useful information related to Bioinformatics. Up to now you can comment/review all available bioinformatics databases/web servers/links/blogs/books listed. You can also give a review of your bioinformatics degree if you are proud of it. You can also promote any kind of Bioinformatics News and Tools on the "Bioinformatics Wall" available at http://www.bioinformatics.fr And in a near futur you will ba able to add your resume and tell other what field(s) of Bioinformatics are you interested/efficient in. Don't waste time and join us to be part the Bioinformatics Networks. You can Log in using an account you've already have at Google, Yahoo, AIM or OPENID Use this link to join us : http://www.bioinformatics.fr/?psinvite=ALRopfVOq2t9-yPrOqEDK8vgzCrRgH6ddAAwkQubEJrl4b9oqvZktC0v0R-XCZqOqX8YXxGy7FWGbu5ytxO-85ayixCS78z5jw Cheers, Fred From tavares from fe.up.pt Wed Dec 10 07:20:09 2008 From: tavares from fe.up.pt (tavares@fe.up.pt) Date: Wed Dec 10 11:51:07 2008 Subject: [Computational-biology] EURASIP JASP - Special issue on Image Processing and Analysis in Biomechanics - Announce & Call for papers Message-ID: <6e3b58c1-a752-4c76-b8c4-66d8196bb108@r36g2000prf.googlegroups.com> ------------------------------------------------------------------------------------------------------------------------------------------ (Apologies for cross-posting) EURASIP Journal on Advances in Signal Processing Special issue on Image Processing and Analysis in Biomechanics http://www.hindawi.com/journals/asp/si/ipab.html Announce and Call for papers We would appreciate if you could distribute this information by your colleagues and co-workers. ------------------------------------------------------------------------------------------------------------------------------------------ Dear Colleague, A critical component for true realistic biomechanical analysis and simulations is to obtain accurately, from images, the geometric data and the behavior of the desired structures. For that, the use of automatic, efficient, and robust techniques of image processing and analysis is mandatory. The main objective of this Special Issue, of the EURASIP Journal on Advances in Signal Processing, on Image Processing and Analysis in Biomechanics is to bring together recent advances in the related fields (not limited to): - Signal processing in biomechanical applications; - Data interpolation, registration, acquisition and compression in biomechanics; - Segmentation of objects in images for biomechanical applications; - 3D reconstruction of objects from images for biomechanical applications; - 2D/3D tracking and object analysis in images for biomechanical applications; - 3D vision in biomechanics; - Biomechanical applications involving image processing and analysis algorithms; - Virtual reality in biomechanics; - Software development for image processing and analysis in biomechanics. Submission Instructions & Important Dates: Authors should follow the journal manuscript format (http:// www.hindawi.com/journals/asp/) and submit their manuscript through the journal Manuscript Tracking System (http://mts.hindawi.com/), according to the following timetable: - Manuscript Due: May 1, 2009; - First Round of Reviews: August 1, 2009; - Publication Date: November 1, 2009. Lead Guest Editor Jo?o Manuel R. S. Tavares, University of Porto, Portugal (tavares@fe.up.pt) Guest Editor R. M. Natal Jorge, University of Porto, Portugal (rnatal@fe.up.pt) From staffa from niehs.nih.gov Thu Dec 11 10:28:30 2008 From: staffa from niehs.nih.gov (Staffa, Nick (NIH/NIEHS) [C]) Date: Thu Dec 11 12:09:37 2008 Subject: [Computational-biology] RE: [Info-gcg] Other: Re - GCG non-support In-Reply-To: <20081103121427.E74728@epsilon.bio.fsu.edu> References: <46B1AEA8.2040308@ebi.ac.uk><20070802081845.D3246@epsilon.bio.fsu.edu><46B2F2E3.4020305@ebi.ac.uk><20070803131050.H7747@epsilon.bio.fsu.edu><1186251135.996351.149470@g12g2000prg.googlegroups.com><46B721F0.8050407@ebi.ac.uk><7930EE6CD7CA354D93B444D0433C061103A8C70D@NIHCESMLBX6.nih.gov><46B83135.7050107@ebi.ac.uk> <20081103121427.E74728@epsilon.bio.fsu.edu> Message-ID: <7930EE6CD7CA354D93B444D0433C061106848CD6@NIHCESMLBX6.nih.gov> I've heard that the legal cost is a measly $70,000. Can we find 70 people to put up $1000? Or 140 to put up $500? Or........ Accelrys is being very wimpy about this; They should give the thing away and let the chips fall where they may. Nickolas G. Staffa, Jr. Ph.D. Telephone: 919-316-4569 (NIEHS: 6-4569) Scientific Computing Support Group NIEHS E-WITS Contract National Institute of Environmental Health Sciences National Institutes of Health Research Triangle Park, North Carolina > -----Original Message----- > From: Steve Thompson [mailto:stevet@bio.fsu.edu] > Sent: Monday, November 03, 2008 3:56 PM > To: Peter Rice > Cc: mol-evol@magpie.bio.indiana.edu; evoldir@evol.biology.McMaster.CA; > bio-soft@magpie.bio.indiana.edu; info-gcg@magpie.bio.indiana.edu; comp- > bio@magpie.bio.indiana.edu > Subject: [Info-gcg] Other: Re - GCG non-support > > Hi Peter - > > I'm picking back up on an old thread from summer 2007 re. the Acclerys GCG > 'retirement.' Since that time several developments, only a few positive > in my opinion, have clarified the situation. > > One - my online petition at www.petitiononline.com was very successful > (http://bio.fsu.edu/~stevet/Accelrys_petition.pdf) in gathering > signatures, almost 200 in a month, and in fostering international > exposure, as the BioInform article from April 2008 attests > (http://bio.fsu.edu/~stevet/BioInformGCG.pdf). But Accelrys remains > committed to not releasing any GCG code, due to exhorbiant and without > profit legal expense. So be it and understood - we tried. > > Two - Accelryrs did distirbute the 'perpetual' licenses to all valid > license holders that were entitled to it, as I announced in this forum > April 2008, and they worked great, even across multiple nodes in a > cluster. Thany you Accelrys. However . . . > > Three - We (FSU) upgraded our Linux cluster that supports GCG and many > other bioinformatics tools to CentOS version 5. Unfortunately, almost > half of the GCG package now fails due to unresolvable library conflicts > (as I warned would happen - unfortunately sooner than I had hoped). Our > systems operations folk initially thought they could fix this but the > solution has remained ellusive. The affected programs are all the oldest > 'legacy' programs in the package, although some longtime GCG pragrams like > Pearson's FastA package remain viable. > > Four - SeqLab continues to operate just fine, but without access to many > of the analytic tools of the package, its usefullness is quite impacted, > though I still think it's one of the best multiple sequence alignment > editors around. This is where you come back in Peter. It may seem odd to > ask, but the need is actually larger now that so much of the package no > longer works in an Enterprise (or CentOS) Linux version 5 environment. > I'm sure that I am not alone in this situation. So here goes - I've asked > it many time before, and I've begun to do the work myself starting with > PlotCon, but has anybody built SeqLab extension configuration files to > launch EMBOSS programs? > > Cheers - Steve > Steven M. Thompson > A C T G stevet@bio.fsu.edu > \-/ > http://bio.fsu.edu/~stevet/cv.html > /\ > /--| FSU SCS / BioInfo 4U > /---/ > |--/ Florida State University School > of > \-/ Computational Science > /\ > /--\ 1st floor DIRAC 150G > |---\ Tallahassee, Florida > \---\ 32306-4120 > \--| 850-644-4490 > \-/ > /\ 2538 Winnwood Circle > /--\ Valdosta, Georgia > /---| 31601-7953 > |--/ 229-249-9751 > > _______________________________________________ > Info-gcg mailing list > Info-gcg@net.bio.net > http://www.bio.net/biomail/listinfo/info-gcg From masulli from disi.unige.it Tue Dec 16 12:36:46 2008 From: masulli from disi.unige.it (Francesco Masulli) Date: Tue Dec 16 13:38:58 2008 Subject: [Computational-biology] Call for Papers - IJCNN 2009 - Special Session on Soft Computing tools for Bioinformatics (Jan 5 2009 NEW deadline) Message-ID: <200812161836.48283.masulli@disi.unige.it> [apologies for multiple posts] deadline post-poned to Jan 5 2009 ----------------------------------------------------------------------------------------------------------------- CALL FOR PAPERS - Special Session on Soft Computing tools for Bioinformatics at International Joint Conference on Neural Networks (IJCNN 2009) sponsored by SIG on Bioinformatics of the International Neural Network Society (INNS) Location: Westin PeachTree Hotel, Atlanta, Georgia, USA, June 14-19 2009 Conference Web Site: http://cnd.memphis.edu/ijcnn2009/ Special Session Web Site: http://www.disi.unige.it/person/MasulliF/conferences/IJCNN2009-SS.html Description and Scope: The body of information surrounding molecular and genomic experiments and clinical investigations is rapidly growing as the magnitude and rate of applications involving large-scale high-throughput technologies are ever-increasing. Bioinformatic data mining efforts now range from more recent methods including miRNA target identification and protein structure prediction to classical methods such as ANN and RBFN classification of DNA microarray gene expression data. Data fusion and integration are also gaining considerable attention for merging signals, features, images, and text data from multiple sensors together in order to understand influences of data components on early detection and diagnosis of disease. Altogether, bioinformatics has become a very promising multidisciplinary research area in the life sciences because results provide new insights for interpretation and establish new leads for deeper understanding. Each year there are numerous Soft Computing and Machine Learning algorithms introduced providing new examples of application in related fields (clustering, feature selection, text mining, signal and image processing, data visualization, etc.). This session will take stock in new soft computing methods for bioinformatic data mining in general, and Neural Network methods in particular. Topics: We welcome papers which present novel algorithms or refined classical methods for the analysis of high dimensional bioinformatic data sets. The target problems include but are not limited to: * Data integration and fusion * Ensemble techniques * Biological sequence identification * DNA/CGH/SNP/miRNA arrays * Gene regulatory and ontology networks * Protein-protein, protein-small molecule interactions * Protein structure prediction * Cellular metabolism and signaling * Pharmacogenomics and pharmacodynamics * Metabolic pathways * Signal processing * Unsupervised and supervised classification * Imaging/data visualization * Text mining methods * Biomarker selection Organizers: Alexandru Floares (1), Francesco Masulli (2,3), (1) Department of Artificial Intelligence Oncological Institute Cluj-Napoca 400015 Str. Republicii, Nr. 34-36, Cluj-Napoca Romania E-mail: alexandru.floares iocn.ro (2) DISI Dept. Computer and Information Sciences University of Genova Via Dodecaneso 35 16146 Genoa, Italy E-mail: masulli disi.unige.it (3) Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, 1900 N 12th Street Philadelphia, PA 19122, USA. Important dates: As soon as possibile: Inform by email the Special Session organizers of your willness to submit a paper Paper submission deadline: Jan 5, 2008 (&) Author notification of acceptance or rejection: Jan 30, 2009 Deadline for final paper re-submission: March 10, 2009 (&&) (&) Paper submission (deadline Dec 15, 2008): At http://cnd.memphis.edu/ijcnn2009/submission.html you'll find the Instruction for Authors and the link to the IJCNN 2009 submission site. While submitting, select Main research topic as "S04. SC Tools for Bioinformatics (Chairs: Francesco Masulli & Alexandru Floares)" only. Don't select any Additional rearch topics. After uploaded your paper on the IJCNN 2009 submission site, send by email to the special session organizers a copy of your paper. In the Subject of the email please specify: "Paper submitted to SS on Bioinformatics IJCNN09". (&&) Final Paper re-submission (deadline March 10, 2009): After re-uploaded your paper on the IJCNN 2009 submission site, send by email to the special session organizers a copy of your revised paper and a letter indicating in detail all changes made. In the Subject of the email please specify: "Paper submitted to SS on Bioinformatics IJCNN09 (revised)". -- <--------------------------------------------------------------------> Dr. Francesco Masulli Associate Professor of Computer Science DISI - Dept. Computer and Information Sciences University of Genova - Via Dodecaneso 35, 16146 Genoa - ITALY tel. +39 010 353 6604 fax. +39 010 353 6699 and Adjunct Associate Professor Center for Biotechnology - College of Science and Technology -Temple University - Philadelphia - PA, USA. email: masulli@disi.unige.it skype id: masulli url: http://www.disi.unige.it/person/MasulliF <--------------------------------------------------------------------> From mark.bathe from gmail.com Wed Dec 17 12:42:18 2008 From: mark.bathe from gmail.com (Mark Bathe) Date: Wed Dec 17 14:38:32 2008 Subject: [Computational-biology] Postdoctoral Research Position Opening at MIT Message-ID: <49493a12.1aab7e0a.55da.6f9f@mx.google.com> The Laboratory for Integrative Computational Cell Biology & Biophysics ( http://web.mit.edu/liccbb) in the Department of Biological Engineering at MIT has an immediate postdoctoral position opening in computational cell biology. The applicant should be proficient in C/C++ and MATLAB, ideally including the image processing, optimization, and statistics toolboxes. Experience with spatiotemporal image correlation spectroscopy, quantitative fluorescent speckle microscopy, particle tracking, and methods for inverse computational modeling of stochastic processes is highly desirable. The successful applicant will develop and apply such techniques to dynamic fluorescence microscopy data of cytoskeletal protein dynamics involved in fundamental cellular processes. Competitive salary and full benefits included. For more information please forward your CV and sample of recent publications to: Mark Bathe, Ph.D. mark.bathe@mit.edu Department of Biological Engineering Massachusetts Institute of Technology http://web.mit.edu/be/people/bathe.htm From ivanoe.defalco from na.icar.cnr.it Fri Dec 19 09:47:16 2008 From: ivanoe.defalco from na.icar.cnr.it (Ivanoe De Falco) Date: Fri Dec 19 10:36:14 2008 Subject: [Computational-biology] BADS 2009 - second call for papers Message-ID: <494BB3F4.6090702@na.icar.cnr.it> (Apologies for multiples copies) ********************** CALL FOR PAPERS ********************** BADS 2009 International Workshop on Bio-Inspired Algorithms for Distributed Systems http://bads.icar.cnr.it email: bads@icar.cnr.it Barcelona, Spain, June 19, 2009 In association with ICAC 2009 the 6th IEEE International Conference on Autonomic Computing & Communications Barcelona, Spain, June 15-19, 2009 **** IMPORTANT DATES **** January 31, 2009: Submission of Papers March 15, 2009: Notification of Acceptance/ Rejection April 06, 2009: Submission of Camera-Ready Copies June 19, 2009: Workshop Takes Place **** PUBLICATION **** The workshop proceedings will be published by ACM along with the proceedings of the other ICAC workshops, and distributed at the conference. **** JOURNAL SPECIAL ISSUE **** Selected papers will be invited to a special issue of the journal Future Generation Computer Systems, Elsevier (approved). **** SCOPE **** Currently used computer systems are characterized by an ever growing complexity and a pronounced distributed nature. While the use of centralized or hierarchical architectures and algorithms has been dominant so far, they are now becoming impractical because they have poor scalability and fault-tolerance characteristics. Decentralized architectures and algorithms, for example P2P and Grid systems, are increasingly popular, but they need new types of algorithms to be efficiently managed. Bio-inspired algorithms are proving effective, since they can solve hard parallel and distributed computational problems through the interaction of multiple agents. The behaviour of agents is often inspired by a number of biological systems, including ant colonies, bird flocking, honey bees, bacteria, and many more. The solution of a problem can emerge from the activity of "intelligent" agents that perform complex functionalities or from the interaction of a large number of very simple agents, in the so called "swarm intelligence" systems. These kinds of techniques feature fault-tolerant and self-adaptive behaviours that help to boost the autonomic nature of distributed systems. Such techniques are sometimes "evolutionary", as they can exploit genetic rules for the selection and the recombination of candidate solutions. Bio-inspired algorithms and systems are routinely applied to hard and large problems in a variety of areas. Some examples are optimization problems solved with genetic algorithms, routing strategies inspired by honey bee behaviour, resource discovery and data mining computations in Grid and P2P frameworks achieved by ant-inspired algorithms, and so on. The workshop aims to gather scientists, engineers, and practitioners to share and exchange their experiences, discuss challenges, and report state-of-the-art and in-progress research on Bio-Inspired Algorithms and Systems. **** AREAS OF INTEREST **** In this workshop we are interested in the exploitation of bio-inspired algorithms and systems to support the effective design and efficient implementation of distributed systems. The topics of interest include (but are not limited to): * Bio-inspired algorithms for parallel and distributed computing * Bio-inspired algorithms for P2P and Grid systems * Bio-inspired techniques for the construction and management of distributed systems * Parallel and distributed techniques of Swarm Intelligence: ant colonies, flock of birds, etc.. * Parallel and distributed evolutionary algorithms * High performance tools for bio-inspired algorithms and systems * Application of bio-inspired algorithms to routing, resource discovery, scheduling in parallel and distributed systems * Bio-inspired algorithms for data mining, bioinformatics, etc. **** ORGANIZING COMMITTEE **** Gianluigi Folino, ICAR-CNR, Italy, folino@icar.cnr.it Natalio Krasnogor, University of Nottingham, UK, nxk@cs.nott.ac.uk Carlo Mastroianni, ICAR-CNR, Italy, mastroianni@icar.cnr.it Franco Zambonelli, Universita' di Modena e Reggio Emilia, Italy, franco.zambonelli@unimore.it **** INTERNATIONAL PROGRAM COMMITTEE **** Ivanoe De Falco, ICAR-CNR, Italy Marios Dikaiakos, University of Cyprus Giovanna Di Marzo, University of London, UK Marco Dorigo, Universit? Libre de Bruxelles, Belgium Agostino Forestiero, ICAR-CNR, Italy Paraskevi Fragopoulou, FORTH-ICS, Greece Niloy Ganguly, Indian Institute of Technology, Kharagpur, India Yaohang Li, North Carolina A&T State University, USA Elena Marchiori, Radboud University, Netherlands Nicolas Monmarch?, Universit? de Tours, France Antonio Nebro Urbaneja, Universidad de M?laga, Spain Muaz Niazi, Foundation University of Islamabad, Pakistan Giuseppe Nicosia, Universit? di Catania, Italy Gauthier Picard, ?cole Nationale Sup?rieure des Mines de Saint?tienne, France Omer Rana, Cardiff University, UK Giandomenico Spezzano, ICAR-CNR, Italy Ian Taylor, Cardiff University, UK Marco Tomassini, University of Lausanne, Switzerland Paolo Trunfio, Universit? della Calabria, Italy Naoki Wakamiya, Osaka University, Japan **** WEB SITE AND CONTACT E-MAIL **** http://bads.icar.cnr.it email: bads@icar.cnr.it **** SUBMISSION GUIDELINES **** Original papers, no longer than 8 two-column pages (including figures and references), are invited. Please use the ACM format available at http://www.acm.org/sigs/pubs/proceed/template.html. The call is open to all members of the Autonomic Computing and Distributed Systems communities. All manuscripts will be peer-reviewed and judged on merits including correctness, originality, technical strength, quality of presentation, and relevance to the conference themes. At least one author of each accepted submission must attend the workshop. Further submission instructions will be posted at the workshop web site. From paolo.romano from istge.it Tue Dec 23 06:28:09 2008 From: paolo.romano from istge.it (Paolo Romano) Date: Tue Dec 23 14:26:53 2008 Subject: [Computational-biology] BITS '09: First announcement and preliminary Call for Papers Message-ID: <200812231141.mBNBf9lV011018@ibm43p.biotech.ist.unige.it> BITS 2009 Sixth Annual Meeting of the Italian Bioinformatics Society 18-20 March 2009, Genova http://bits09.istge.it/ First Announcement and Preliminary Call for Papers The Sixth Annual Meeting of the Bioinformatics Italian Society (BITS 2009) aims at presenting some of the hottest bioinformatics achievements, as well as a landscape of Italian bioinformatics research. It is also intended to allow young researchers to present their work in a collaborative and supporting atmosphere. BITS 2009 will include keynote lectures, oral communications, posters presentations and tutorials. Social activities will include a welcome reception, a guided tour of the historical city center of Genoa, one of the oldest towns in Italy, and the social dinner. Invited Speakers ? Alex Bateman, Sanger Institute, United Kingdom ? Peer Bork, EMBL, Heidelberg, Germany ? Rob Russel, EMBL, Heidelberg, Germany ? One more speaker to be confirmed Topics Submitted contributions should address novel bioinformatics methods, algorithms, databases, tools and applications for research and development in one or more of the following domains: - Genomics - Molecular Evolution - Protein structure and function - Proteomics - Transcriptomics - Gene expression - Biological Interaction Networks and Pathways - Systems Biology - In-silico drug design - Clinical Bioinformatics - Bio-ontologies This list is by no means exclusive of any further topics in the field of Bioinformatics. Deadlines - January 20, 2009: Oral communications submission - February 10, 2009: Posters submission - February 13, 2009: Early registration (reduced fee) Instructions Abstracts must be submitted through the BITS 2009 Abstracts submission form (soon available!). All abstracts must be written in English and structured in the following sections: Motivation, Methods, Results. Abstracts' length cannot be greater than 5,000 characters or 4,000 characters (spaces included) when a figure is also included. All accepted contributions will be published in the abstracts' book. Organizers are considering the possibility of identifying an internationally peer-reviewed journal to publish a Supplement including extended versions of best oral communications and posters as full papers. Scientific Committee + D. Bordo, National Cancer Research Institute of Genova + R. Casadio, University of Bologna + M.L. Chiusano, University of Naples + M. Helmer-Citterich, University of Rome "Tor Vergata" + F. Masulli, University of Genoa + L. Milanesi, ITB/CNR, Milan + M. Muselli, IEIIT/CNR, Genoa + E. Pizzi, National Institute of Health, Rome + G. Pesole, Univerity of Bari + P. Romano, National Cancer Research Institute of Genoa Organizing Committee + D. Bordo, National Cancer Research Institute of Genova + F. Masulli, University of Genoa + M. Muselli, IEIIT/CNR, Genoa + P. Romano, National Cancer Research Institute of Genoa Paolo Romano (paolo.romano@istge.it) Bioinformatics, National Cancer Research Institute (IST), Genova, Italy http://www.nettab.org/promano/ From heather from cs.man.ac.uk Mon Dec 29 12:26:52 2008 From: heather from cs.man.ac.uk (Heather Vincent) Date: Mon Dec 29 13:20:08 2008 Subject: [Computational-biology] Biocomputing course, March 2009 Message-ID: <4959085C.3060106@cs.man.ac.uk> Computational biology, or Biocomputing, is concerned with the development of methods for the efficient storage and processing of biological data. A large part of the work of computational biologists thus consists of the management and analysis of strings of characters. These strings may be nucleic acid or protein sequences, or their annotation. This online course, from The University of Manchester, introduces perl, for data processing, and database design. It is suitable for anyone with some experience in programming, who needs to extend their skills in application design. Our distance courses are delivered in a Virtual Learning Environment, which allows us to extend the classroom into the web. Each course, which is paced to suit those in full-time employment, runs over 16 teaching weeks. In this course, teaching and learning are focussed around tutor-supported group activities. Week 1 Introduction and software setup Week 2 The unix operating system Week 3 Data interchange and display Week 4 CGI and perl Weeks 5 to 9 perl project Weeks 10 and 11 Relational database design Week 12 The data:user interface Weeks 13 to 16 Database project You will find information on all our courses, including fees and a link to the online application form, here : http://octette.cs.man.ac.uk/bioinformatics/index.html If you have any questions, or need advice on the module options, please contact Heather.Vincent@manchester.ac.uk From mourad12345678 from yahoo.com Mon Dec 29 16:49:00 2008 From: mourad12345678 from yahoo.com (Mourad Elloumi) Date: Tue Dec 30 13:29:40 2008 Subject: [Computational-biology] DEXA'09 / BIOKDD'09 CfP Message-ID: <797016.19403.qm@web31507.mail.mud.yahoo.com> CALL FOR PAPERS Higher School of Sciences and Technologies of Tunis (Tunisia) And Faculty of Applied Sciences, Bucharest (Romania) Organize Biological Knowledge Discovery from Databases (BIOKDD'09) Workshop held in parallel with 20th International Conference on Database and Expert Systems Applications (DEXA'09) www.dexa.org University of Linz, Austria August 31 - September 4, 2009 With the development of Biology during the last decades, we are witnessing an exponential growth of both the volume and the complexity of biological databases. 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 much efforts on the accumulation of biological data in databases, we have now to focus as much efforts, and even more, on the analysis of these data. Analyzing this huge volume of biological data stored in databases is a challenging task because, not only, of its complexity and its multiple numerous correlated factors, but also, because of the continuous evolution of our understanding of the biological structural and evolutionary mechanisms. Knowledge Discovery from Databases (KDD) is a response to these new trends. You are invited to submit a draft paper in PDF format before February 28, 2009 via DEXA'09 ConfDriver. Papers should not exceed 5 pages in IEEE format www.ieee.org/web/publications/authors/transjnl/index.html All accepted papers will be published in the proceedings of DEXA’09 Workshops with IEEE CSP. One of the authors of an accepted paper must register to DEXA’09 conference and present the paper at BIOKDD’09 workshop. Program Committee: Mourad Elloumi, University of Tunis, Tunisia, (PC Chair) Cristian Toma, Politehnica University, Bucharest, Romania (PC Co-Chair) Jin-Kao Hao, University of Angers, France Beatrice Duval, University of Angers, France Abdelouahid Lyhyaoui. Abdelmalek Essaadi University, Tanger, Morocco El-Ghazali Talbi, University of Sciences and Techniques of Lille, France Xiangchao Gan, University of Oxford, UK Kathleen Steinhöfel, King's College London, UK Dragan Bosnacki, Eindhoven University of Technology, Netherlands Important Dates: Submission of Full Papers: February 28, 2009 Notification of Acceptance: May 10, 2009 Camera-ready Copies: May 31, 2009 From tavares from fe.up.pt Mon Dec 8 18:04:10 2008 From: tavares from fe.up.pt (tavares@fe.up.pt) Date: Sat Feb 7 17:12:55 2009 Subject: [Computational-biology] (no subject) Message-ID: <71dd6ddb-3f33-463a-982c-45adf5c349d4@g38g2000yqd.googlegroups.com> ------------------------------------------------------------------------------------------------------------------------------- (Apologies for cross-posting) Symposium on “Computational methods in image analysis” 10th US National Congress on Computational Mechanics (USNCCM X) Columbus, Ohio, USA, July 16-19, 2009 http://usnccm-10.eng.ohio-state.edu/ We would appreciate if you could distribute this information by your colleagues and co-workers. ------------------------------------------------------------------------------------------------------------------------------- Dear Colleague, Within the 10th US National Congress on Computational Mechanics (USNCCM X), to be held in Ohio, USA, in July 16-19, 2009, we are organizing the Symposium “Computational methods in image analysis”. Examples of some topics that will be considered in the symposium “Computational methods in image analysis” are: Image Analysis, Objects Modeling, Image Segmentation, Matching, Shape Reconstruction, Motion and Deformation Analysis, Objects Description and Registration, Medical imaging, Software Development for Image Analysis and Grid and High Performance Computing in Image Analysis. Due to your research activities in those fields, we would like to invite you to submit your work and participate in the Symposium “Computational methods in image analysis”. For instructions and submission, please access to the conference website at: http://usnccm-10.eng.ohio-state.edu/abstractsub.html Please note that, when submitting your work you should select the Symposium “2.18.4 Computational methods in image analysis”. Important dates: - January 31, 2009: Deadline for abstract submission; - March 1, 2009: Deadline and notification of abstract acceptance; - July 16-19, 2009: Congress Events. Kind regards, João Manuel R. S. Tavares (University of Porto, Portugal, tavares@fe.up.pt) Renato Natal Jorge (University of Porto, Portugal, rnatal@fe.up.pt) Yongjie Zhang (Carnegie Mellon University, USA, jessicaz@andrew.cmu.edu) Dinggang Shen (UNC-CH School of Medicine, USA, dgshen@med.unc.edu) (Symposium organizers) From tavares from fe.up.pt Tue Dec 23 09:21:58 2008 From: tavares from fe.up.pt (tavares@fe.up.pt) Date: Sat Feb 7 17:13:01 2009 Subject: [Computational-biology] (no subject) Message-ID: <21082d53-ed8c-47fb-92a4-50831bc8262b@i24g2000prf.googlegroups.com> ---------------------------------------------------------------------------------------------------------------------------------------- (Apologies for cross-posting) Symposium on “Visualization and Human-Computer” 3rd International Conference on Integrity, Reliability & Failure (IRF’2009) Faculty of Engineering, University of Porto, Porto – PORTUGAL, 20-24 July 2009 http://paginas.fe.up.pt/clme/IRF2009/index.htm (We would appreciate if you could distribute this information by your colleagues and co-workers.) ---------------------------------------------------------------------------------------------------------------------------------------- Dear Colleague, Within the 3rd International Conference on Integrity, Reliability & Failure (IRF’2009), to be held in FEUP, Porto, Portugal, in July 20-24, 2009, we are organizing the Symposium “Visualization and Human- Computer”. Examples of some topics that will be considered are: Scientific Data Visualization, Spatial Data in Visualization, Data Processing and Analysis, Information Visualization, Visualization Techniques, Large Data Visualization, Image Processing and Analysis, Hardware for Visualization, Human-Computer Interaction, Visual Analytics, Visual Data Mining and Knowledge Discovery, Human Perception, Interface Design, Evaluation and User Studies, Software Development, Grid and High Performance Computing, Applications in Engineering, Biomechanics, Bioinformatics, Bioimaging, Physical, Earth, Space, Environmental and Information Sciences. Due to your research activities in those fields, we would like to invite you to submit your work and participate in the Symposium “Visualization and Human-Computer”. For instructions and submission, please access to the conference website at: http://paginas.fe.up.pt/clme/IRF2009/index.htm Please note that, when submitting your work you should select the Symposium #7 “Visualization and Human-Computer”. Important dates: - February 28, 2009: Deadline for abstract submission; - March 21, 2009: Notification of abstract acceptance; - May 10, 2009: Receipt of Full Papers; - July 20-24, 2009: Conference Events. Kind regards, João Manuel R. S. Tavares (University of Porto, Portugal, tavares@fe.up.pt) Renato Natal Jorge (University of Porto, Portugal, rnatal@fe.up.pt) (Symposium organizers) From tavares from fe.up.pt Mon Dec 29 09:12:51 2008 From: tavares from fe.up.pt (tavares@fe.up.pt) Date: Sat Feb 7 17:13:05 2009 Subject: [Computational-biology] (no subject) Message-ID: <8c787410-1d77-4923-ad1f-26abe499e270@l33g2000pri.googlegroups.com> (Our apologies for cross-posting. We appreciate if you kindly distribute this information by your co- workers and colleagues.) ******************************************************************************************************* Symposium “Image Processing and Analysis” Int. Conf. on Computational & Experimental Engineering and Sciences 2009 (ICCES'09) Phuket, Thailand, 8-13 April 2009 http://icces.org/cgi-bin/ices09/pages/index ******************************************************************************************************* Dear Colleague, Within the International Conference on Computational & Experimental Engineering and Sciences 2009 (ICCES'09), to be held in Phuket, Thailand, in 8-13 April 2009, we are organizing the Symposium “Image Processing and Analysis”. Examples of some topics that will be considered in that symposium are: Image restoring, Description, Compression, Segmentation and Description; Objects tracking, Matching, Reconstruction and Registration; Visualization Enhance; Simulation and Animation; Software Development for Image Processing and Analysis; Grid Computing in Image Processing and Analysis; Applications of Image Processing and Analysis. Due to your research activities in those fields, we would like to invite you to submit your work and participate in the Symposium “Image Processing and Analysis”. Important dates and Instructions: - 1 Jan 2009: Deadline for abstract submission; - 10 Jan 2009: End of abstract selection. For instructions and submission, please access to the conference website at: http://icces.org/cgi-bin/ices09/pages/index. Instructions for authors are available at: http://icces.org/cgi-bin/ices09/pages/guide. Please note, when submitting your work you should choose the Symposium “Image Processing and Analysis”. If you intend to submit your work please notify as soon as possible the main organizer of your intention (tavares@fe.up.pt); The organizers are preparing a special issue of the International Journal Computer Modeling in Engineering & Sciences (CMES), ISSN: 1526-1492, dedicated to the Symposium “Image Processing and Analysis” with extended papers of the works presented in the ICCES'09. With kind regards, The Organizers, João Manuel R. S. Tavares (tavares@fe.up.pt) (main organizer) Faculty of Engineering of University of Porto, Porto, Portugal Yongjie (Jessica) Zhan (jessicaz@andrew.cmu.edu) Carnegie Mellon University, Pittsburgh, USA Maria João M. Vasconcelos (maria.vasconcelos@fe.up.pt) Faculty of Engineering of University of Porto, Porto, Portugal