August 2010 - BBClist - maillist.psb.ugent.be

[ECCB10] Benelux Fellowships - LAST CHANCE FELLOWSHIPS - DEADLINE SUNDAY SEPTEMBER 5
by Yves Moreau 30 Aug '10

30 Aug '10

Dear Colleagues, We have been quite successful in attracting participants to European Conference on Computational Biology 2010 with currently over 600 registered participants and 420 posters. This gives us a last chance to further support participation by bioinformaticians from the Benelux. We can offer several fellowships in the form of a discount registration rate of €100 for the conference. As you probably know, this year's European Conference on Computational Biology will act as the yearly Benelux Bioinformatics Conference. It is a unique opportunity to show internationally how active our bioinformatics community is, and for all research teams to put their work in the spotlight. The Benelux Bioinformatics Conference has always attracted numerous researchers from our bioinformatics community. ECCB10 will be a major scientific event happening "next door" - a not-to-be-missed opportunity! Conditions of the fellowships are the following: * The fellowship covers only the main conference * Attendance to the tutorials and workshops is not included (but possible at the registration rate of €100) * Attendance to the conference banquet is not included * Fellows MUST be currently affiliated to a Benelux institution * ISCB membership is not required * Fellows MUST submit a late-breaking poster (http://www.eccb10.org/index.php/guidelines/late-breaking-posters - web site is still open) and present their poster at the meeting * Fellows can be requested to perform 4 to 8 hours of volunteering work for the conference Priority will be given to PhD students over postdocs. Fellowships will partly be awarded on the basis of the number of registered members of the lab. For application, send an email to info(a)eccb10.org with "[ECCB10] Benelux Fellowships" as the subject and containing the following information by SUNDAY SEPTEMBER 5. * Full Name * Affiliation (including department/lab) * Name of advisor * Tentative poster title Looking forward to meeting you in September, Yves Moreau - ECCB10 Conference Chair for the ECCB10 Local Organizing Committee

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poste de Maître de Conférences - Paris Sud
by Jacques van Helden 25 Aug '10

25 Aug '10

Begin forwarded message: From: Xavier Vekemans <xavier.vekemans(a)univ-lille1.fr> Date: 25 August 2010 16:28:59 CEST To: jvhelden(a)ulb.ac.be, Philippe Baret <Philippe.Baret(a)uclouvain.be>, Olivier Hardy <ohardy(a)ulb.ac.be> Cc: Christine Dillmann <dillmann(a)moulon.inra.fr> Subject: Re: poste MC au moulon Chers collègues, voici une annonce de poste de Maitres de Conférences en biomathématiques à l'Université de Paris Sud (Orsay), pour transmission à d'éventuels intéressés. L'ouverture du poste est au printemps 2011 pour recrutement en septembre 2011 mais la procédure en France demande l'obtention d'une qualification nécessitant une inscription sur la liste de qualification avant fin octobre 2010. Au plaisir de vous revoir à une prochaine occasion, amicalement, Xavier > > Assistant professor position : Modelling in Evolutionary System's Biology > > Assistant professor position in biomathematics at the University of Paris-Sud, France : Modelling in Evolutionary System's Biology. > > We are looking for a population geneticist with a strong background in mathematics or physics, or a mathematician or a physician with a strong knowledge in Biology. The research work will be on system's biology, at the interface between math and biology, to better understand the evolution of biological networks. The candidate will teachTeaching will be in mathematics, biostatistics and bioinformatics at the licence and master level for biology students of the University of Paris-Sud. The candidate will join the GQF team at the UMR du Moulon (http://www.moulon.inra.fr) > > The position should be opened in spring 2011. Applicants NEED to be qualified by the French ministry of Research and Education as follows : > > Deadline for the qualification = October 2010 > Informations about the procedure: > https://www.galaxie.enseignementsup-recherche.gouv.fr/ensup/candidats.html > Application for the qualification: > https://galaxie.enseignementsup-recherche.gouv.fr/antares/can/index.jsp > > > Foreign applications are welcome. Please contact-us before September 2010. We will help you with the qualification and application procedures. > > > Contact : Christine Dillmann, dillmann(a)moulon.inra.fr > > >

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[ECCB10] Call for Late-Breaking Posters & Early Registration Deadline - August 20
by Sylvain Brohée 17 Aug '10

17 Aug '10

=== Apologies for multiple postings - Please distribute widely within your lab === Dear Colleague, Due to numerous requests, we open now a brief call for late-breaking poster abstracts. Take advantage of this final opportunity to present your work at ECCB10. Be quick as the submission deadline is August 20, 2010, only two weeks from now. Note that this deadline also corresponds to the early registration deadline, so that you can still benefit from a favorable registration rate. === LATE-BREAKING ABSTRACT SUBMISSION DEADLINE: August 20, 2010 === www.eccb10.org The European Conference on Computational Biology (ECCB10) will be held on September 26-29, 2010 in Ghent, Belgium. ECCB10 is the key European computational biology event in 2010 uniting scientists working in a broad range of disciplines, including bioinformatics, computational biology, medicine, biology, and systems biology. This year we have had a record number of 215 manuscript submissions and we have accepted 392 poster abstracts. We are thus looking forward to a fruitful scientific meeting. Ghent is one of Europe's most exciting medieval settings, a glorious eclectic city with spectacular buildings and a vivid cultural experience (National Geographic Traveler recently ranked it 3rd best historic place to visit internationally). Ghent is directly accessible by train from Brussels airport. The conference venue is highly convenient and located in a beautiful park within the city center. We invite you to submit posters in any area of computational biology and bioinformatics. Topics of interest include, but are not limited to * Sequence analysis, alignment, and next-generation sequencing * Comparative genomics, phylogeny, and evolution * Protein & nucleotide structure * Annotation and prediction of molecular function * Gene regulation and transcriptomics * Text mining, ontologies, and databases * Protein interactions, molecular networks, and systems biology * Genomic medicine * Other bioinformatics applications Posters, representing condensed descriptions of ongoing work, will be displayed during the meeting. Posters should describe original, interesting, and solid scientific content that is relevant to bioinformatics and computational biology. See the Guidelines at http://www.eccb10.org/index.php/guidelines/late-breaking-posters and and submit your abstract at http://www.eccb10.org/index.php/component/submission/. At least one of the authors of the poster will have to attend the meeting. Late-breaking posters will be available through the conference web site and indexed in the program book, but they will NOT be available on the conference CD because of the production schedule. The presenting author of each poster must register for the conference by the early registration deadline of August 20, 2010 for the abstract to be included in the program book and on the conference web site. We kindly request that you forward this announcement to the members of your team. We look forward to welcoming you to Ghent. The ECCB10 Organizing Committee www.eccb10.org ECCB10 KEY DATES * Late-breaking abstract submission deadline - August 20, 2010 * Early registration deadline - August 20, 2010 * Workshop and tutorials - Sunday September 26, 2010 * Conference opening - Sunday evening, September 26, 2010 * Main conference (proceedings, posters, and industry/demo track) - September 26-29, 2010 UNSUBSCRIBE - If you do not wish to receive further announcements for ECCB10, please reply to info(a)eccb10.org with UNSUBSCRIBE in the subject heading.

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MLSB 2010 - call for posters and rgistration
by Simon Rogers 16 Aug '10

16 Aug '10

******************* Call for Posters/Registration ********************** MLSB 2010 The Fourth International Workshop on Machine Learning in Systems Biology 15-16 October 2010, Edinburgh, Scotland *********************************************************************** http://mlsb10.ijs.si/ (apologies for multiple postings) ** REGISTRATION IS NOW OPEN: ttp://tinyurl.com/2cp7xwc ** MOTIVATION Molecular biology and all the biomedical sciences are undergoing a true revolution as a result of the emergence and growing impact of a series of new disciplines/tools sharing the "-omics" suffix in their name. These include in particular genomics, transcriptomics, proteomics and metabolomics, devoted respectively to the examination of the entire systems of genes, transcripts, proteins and metabolites present in a given cell or tissue type. The availability of these new, highly effective tools for biological exploration is dramatically changing the way one performs research in at least two respects. First, the amount of available experimental data is not a limiting factor any more; on the contrary, there is a plethora of it. Given the research question, the challenge has shifted towards identifying the relevant pieces of information and making sense out of it (a "data mining" issue). Second, rather than focus on components in isolation, we can now try to understand how biological systems behave as a result of the integration and interaction between the individual components that one can now monitor simultaneously (so called "systems biology"). Taking advantage of this wealth of "genomic" information has become a conditio sine qua non for whoever ambitions to remain competitive in molecular biology and in the biomedical sciences in general. Machine learning naturally appears as one of the main drivers of progress in this context, where most of the targets of interest deal with complex structured objects: sequences, 2D and 3D structures or interaction networks. At the same time bioinformatics and systems biology have already induced significant new developments of general interest in machine learning, for example in the context of learning with structured data, graph inference, semi-supervised learning, system identification, and novel combinations of optimization and learning algorithms. The Workshop is organized as "core - event" of Pattern Analysis, Statistical Modelling and Computational Learning - Network of Excellence 2 (PASCAL 2, http://www.pascal-network.org/) OBJECTIVE The aim of this workshop is to contribute to the cross-fertilization between the research in machine learning methods and their applications to systems biology (i.e., complex biological and medical questions) by bringing together method developers and experimentalists. We encourage submissions bringing forward methods for discovering complex structures (e.g. interaction networks, molecule structures) and methods supporting genome-wide data analysis. LOCATION AND CO-LOCATION The workshop will take place 15-16 October 2010 at the Edinburgh International Conference Centre and the Informatics Forum of the University of Edinburgh. It will be part of the wokshop program of ICSB 2010, The 11th International Conference on Systems Biology (11-14 OCT 2010, http://www.icsb2010.org.uk/) POSTER SUBMISSION INSTRUCTIONS We invite you to submit an abstract of up to 4 pages (minimum 1 page) describing new or recently published (2010) results, formatted according to the Springer Lecture Notes in Computer Science style. Each extended abstract must be submitted online via the Easychair submission system: http://www.easychair.org/conferences/?conf=mlsb10 KEY DATES 30th September: Poster submission deadline. REGISTRATION IS NOW OPEN: ttp://tinyurl.com/2cp7xwc TOPICS A non-exhaustive list of topics suitable for this workshop is given below: Methods Machine learning algorithms Bayesian methods Data integration/fusion Feature/subspace selection Clustering Biclustering/association rules Kernel methods Probabilistic inference Structured output prediction Systems identification Graph inference, completion, smoothing Semi-supervised learning Applications Sequence annotation Gene expression and post-transcriptional regulation Inference of gene regulation networks Gene prediction and whole genome association studies Metabolic pathway modeling Signaling networks Systems biology approaches to biomarker identification Rational drug design methods Metabolic reconstruction Protein function and structure prediction Protein-protein interaction networks Synthetic biology INVITED SPEAKERS (confirmed) Florence d'Alche Buc, Universite d'Evry-Val d'Essonne, Evry, France Nir Friedman, The Hebrew University of Jerusalem, Jerusalem, Israel Ursula Kummer, BIOQUANT, University of Heidelberg, Germany Hans Lehrach, Max Planck Institute for Molecular Genetics, Berlin, Germany Vebjorn Ljosa, The Broad Institute of MIT and Harvard, USA MLSB10 PROGRAM CHAIRS Saöo Dûeroski, Jozef Stefan Institute, Ljubljana, Slovenia Simon Rogers, University of Glasgow, UK Guido Sanguinetti, University of Sheffield/University of Edinburgh, UK SCIENTIFIC PROGRAM COMMITTEE (tentative) Florence d'AlchÈ-Buc, University of Evry, France Paolo Frasconi, Universit‡ degli Studi di Firenze, Italy Cesare Furlanello, Fondazione Bruno Kessler, Trento, Italy Pierre Geurts, University of LiËge, Belgium Mark Girolami, University of Glasgow, UK Dirk Husmeier, Biomathematics & Statistics Scotland, UK Samuel Kaski, Helsinki University of Technology, Finland Ross D. King, Aberystwyth University, UK Neil Lawrence, University of Manchester, UK Elena Marchiori, Vrije Universiteit Amsterdam, The Netherlands Yves Moreau, Katholieke Universiteit Leuven, Belgium William Stafford Noble, University of Washington, USA Gunnar R‰tsch, FML, Max Planck Society, T¸bingen Juho Rousu, University of Helsinki, Finland CÈline Rouveirol, University of Paris XIII, France Yvan Saeys, University of Gent, Belgium Ljupco Todorovski, University of Ljubljana, Slovenia Koji Tsuda, Max Planck Institute, Tuebingen Jean-Philippe Vert, Ecole des Mines, France Louis Wehenkel, University of LiËge, Belgium Jean-Daniel Zucker, University of Paris XIII, France Blaz Zupan, University of Ljubljana, Slovenia LOCAL ORGANIZATION Fiona Clark, University of Edinburgh, UK Dragi Kocev, Jozef Stefan Institute, Ljubljana, Slovenia (webmaster) -- Dr Simon Rogers Lecturer in Inference School of Computing Science University of Glasgow simon.rogers(a)glasgow.ac.uk skype: sdrogersskype The University of Glasgow, charity number SC004401

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ESCS1 Early Registration Aug 20 - Late Poster Aug 16
by Thomas Abeel 10 Aug '10

10 Aug '10

Dear Colleagues, The first European Student Council Symposium (ESCS1) will be held on September 26, 2010 in Ghent, Belgium, as a satellite meeting of the European Conference on Computational Biology (ECCB). You can register to the student symposium even if you do not attend ECCB. It only costs 100 euros, but will be 150 euros after the early registration deadline. The Student Symposium accepts late poster submissions till August 16, with notification on August 18. We actively encourage you to submit work you are presenting at ECCB to the Student Symposium as well. === LATE POSTER DEADLINE: Aug 16, 2010 === http://escs.iscbsc.org/abstract-submission === EARLY REGISTRATION DEADLINE: Aug 20, 2010 === http://escs.iscbsc.org/registration The program is available on our website and includes: - a keynote presentation by Yves Van de Peer about Generating hypotheses for molecular biology through (top-down) systems biology - a soft skill workshop on the use of theatre skills for presenting - student presentations from abstract submissions - a poster session See http://escs.iscbsc.org/program Looking forward to seeing you in Belgium! Magali Michaut ESCS1 chair Thomas Abeel ESCS1 co-chair

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PhD research studentship: improving patient treatment at the intensive care unit using data mining techniques
by Tim Van den Bulcke 10 Aug '10

10 Aug '10

Dear BBC member, please feel free to circulate this ad amongst potential candidates. Beste regards, Tim. _____________________________________ ir. Tim Van den Bulcke, PhD project leader i-ICT *UZA - Universitair Ziekenhuis Antwerpen* Directie ICT Wilrijkstraat 10 2650 Edegem T +32 (0)3 821 52 85 F +32 (0)3 821 44 30 E tim.van.den.bulcke(a)uza.be W www.uza.be _____________________________________

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post-doc & PhD positions in Glasgow, UK
by Anton Feenstra 09 Aug '10

09 Aug '10

------------------------------------------------------------------------------- Two post-doctoral positions and three PhD studentships available in bioinformatics and mathematical biology within the theoretical microbiology group of the School of Engineering at the University of Glasgow In the theoretical microbiology group at the University of Glasgow we have pioneered the application of theoretical ecology to microbial communities in environmental engineering contexts. Prof. Sloan (head of group) was the first to apply neutral theory to model the assembly of these communities. In addition Dr Christopher Quince has developed novel algorithms and software for the analysis of next generation sequencing data from these communities. Consequently we have been very successful in obtaining funding from UK research councils (BBSRC, EPSRC) andindustrial sponsors (Unilever). This has allowed us to embark on the ambitious project of integrating genomics data into mathematical community models. We have five positions available to work on aspects of this project (one Unilever funded PDRA, one EPSRC funded PDRA, and three PhD studentships). General enquiries can be addressed to Dr Christopher Quince (quince(a)civil.gla.ac.uk) ------------------------------------------------------------------------------- Research Associate in Bioinformatics Ref: 00130-3 Salary: Grade 6 £25,751 - £28,983 / Grade 7 £31,671 - £35,646 We are recruiting for a three-year postdoctoral position to develop new software tools and statistics for the analysis of genomics data from microbial communities. You will use ideas from machine learning and Bayesian statistics to further improve these algorithms and extend them to new sequencing formats and data types. In particular we will address the challenging problem of better assembly methods for metagenomics data. Linking function to taxonomic identity will be a priority. You will also closely integrate with the research funder, Unilever, applying these tools to their human associated microbiomics data sets and assist in installation of tools on-site. This is a unique opportunity for a candidate with excellent computational, mathematical and statistical skills to apply their knowledge to a wider field and within a broader context including application in a commercial environment. A good PhD in a numerical subject e.g. bioinformatics, computer science, mathematics, statistics, theoretical physics or machine learning is essential. Experience analysing biological sequence data would be an advantage. Please contact Dr Christopher Quince with queries (quince(a)civil.gla.ac.uk) Apply online at www.glasgow.ac.uk/jobs Closing Date: 30th July 2010 (late applicants should contact Dr Quince directly by e-mail) ------------------------------------------------------------------------------- Research Associate in Mathematical Modelling of Microbial Communities  Ref: 00126-2 Salary: Grade 6 £25,751 – £28,983/ Grade 7 £31,671 – £35,646 per annum A three-year EPSRC funded postdoctoral position in computational microbiology is available in the Department of Civil Engineering University of Glasgow. The researcher will form integrate data from new genomics methods into mathematical models of microbial communities. The long-term goal of the research will be improved wastewater treatment and microbial fuel cell (MFC) technologies. We will develop stochastic individual level models of microbial communities using ideas from neutral theory. The mathematical analysis of these models will be performed in conjunction with Dr Todd Parsons (U. of Penn.). Bayesian statistics will be used to link these models to the genomics data. International applicants from any area of science or engineering with a doctorate and the necessary computational and quantitative skills are invited to apply but knowledge of any of the following would be an advantage: Bayesian statistics, bioinformatics, machine learning, microbial ecology, neutral theory, numerical solution of PDEs or SDEs, software programming, and stochastic models. The appointment is for three years. The preferred start date is 1st October 2010 but earlier or later dates are possible. Apply online at www.glasgow.ac.uk/jobs Closing date: 20th August 2010. ------------------------------------------------------------------------------- PhD Studentship in Metagenomics of the Human Microbiome available 1st October 2010 at the University of Glasgow Supervisors: Dr Christopher Quince, Prof. William Sloan, and Dr David Taylor (Unilever) An exciting four-year PhD studentship is available under the BBSRC Industrial CASE scheme in the Department of Civil Engineering at the University of Glasgow. The objectives of this studentship are to develop improved statistical tools for the analysis of metagenomics data from human associated microbial communities. The successful candidate will have a good (2:1 or above or equivalent) MSc or undergraduate degree in bioinformatics, engineering, mathematics, physics, statistics or other numerical subject. Biology students will be accepted if they can demonstrate sufficient quantitative skills. The PhD studentship will provide a tax free stipend at the rate of £16,590 per annum. The preferred start date is 1st October 2010 but other start dates may be possible. The studentship is open only to applicants from the UK and the European Union who fulfill residency requirements. Full details are available from: http://www.jobs.ac.uk/job/ABI075/phd-studentship/ Please contact Dr Christopher Quince with queries or applications (quince(a)civil.gla.ac.uk) ------------------------------------------------------------------------------- PhD Studentship in Microbial Biodiversity available 1st October 2010 at the University of Glasgow Supervisors: Prof. William Sloan and Dr Christopher Quince A four-year Unilever funded PhD studentship is available in the Department of Civil Engineering at the University of Glasgow. The aim is to map and develop models for the biodiversity of bacteria on the human skin. The successful candidate will have a good or expected good (2:1 or above or equivalent) MSc or undergraduate degree in Engineering, Mathematics, Physics, Theoretical Ecology, or other mathematical subject. The ideal candidate should be an enthusiastic and self-motivated person with good organisational and interpersonal skills. The PhD studentship will provide a generous stipend of £16,590 per annum (likely to be reviewed annually). The start date is 1st October 2010. The studentship is open to UK, EU and international applicants but it will only fully fund fees at UK or EU student rates. Full details are available from: http://www.jobs.ac.uk/job/ABI077/phd-studentship-in-microbial-biodiversity Please contact Prof William Sloan with queries or applications (sloan(a)civil.gla.ac.uk) ------------------------------------------------------------------------------- PhD Studentship in Mathematical Ecology University of Glasgow Supervisors: Prof. William Sloan and Dr Mary Lunn A three-year EPSRC funded studentship is available in the Department of Civil Engineering at the University of Glasgow A three-year EPSRC funded PhD studentship is available in the Department of Civil Engineering at the University of Glasgow. The aim is to develop a mathematical model of the dynamics of groups of microbes that underpin many industrial processes like the treatment of waste. This is a burgeoning field of research with many unanswered questions where international reputations can be made quickly. Therefore, it represents a unique opportunity for a gifted numerate scientist to launch a high profile research career. The successful candidate will have a good or expected good (2:1 or above or equivalent) MSc or undergraduate degree in Engineering, Mathematics, Physics, Theoretical Ecology, or other mathematical subject. The ideal candidate should be an enthusiastic and self-motivated person with good organisational and interpersonal skills. The PhD studentship will provide a stipend at the standard EPSRC rate of £13,290 per annum (likely to be reviewed annually to take into account part of the inflationary rise in maintenance costs). The preferred start date is before 1st October 2010. The studentship is open to applicants from the UK and the EU. In order to qualify for the stipend EU students must satisfy the eligibility requirements as outlined by EPSRC. http://www.jobs.ac.uk/job/ABI074/phd-studentship-in-mathematical-ecology/ Please contact Prof William Sloan with queries or applications (sloan(a)civil.gla.ac.uk) ------------------------------------------------------------------------------- _______________________________________________ soft-matter mailing list soft-matter(a)lists.leeds.ac.uk http://lists.leeds.ac.uk/mailman/listinfo/soft-matter -- Sanne Abeln s.abeln(a)few.vu.nl Assistant Professor - VU University Amsterdam www.few.vu.nl/~abeln Treasurer - Prelude Foundation www.preludefund.org

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[Fwd: [bioinfo] launch of R/Bioconductor Cloud Computing web-service]
by Eric Bonnet 08 Aug '10

08 Aug '10

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GMOD Europe 2010, 13-16 Sept, Cambridge, UK
by Dave Clements 05 Aug '10

05 Aug '10

GMOD Europe 2010 ================ 13-16 September 2010 Cambridge, UK http://gmod.org/wiki/GMOD_Europe_2010 We are pleased to announce GMOD Europe 2010, four days of GMOD events being held 13-16 September 2010, at the University of Cambridge. GMOD Europe 2010 includes: 1) GMOD Community Meeting, Monday & Tuesday: Project updates, developer and user presentations and best practices, project direction. 2) GMOD Satellite Meetings, Wednesday: Special interest groups where GMOD community members meet to discuss specific topics of interest. 3) InterMine Workshop, Wednesday: A one day workshop on installing, configuring and using the InterMine biological data warehouse system. 4) BioMart Workshop, Thursday: A one day workshop on using the BioMart biological data warehouse system, including accessing data through APIs. Registration is now open for these events. There is a £50 registration fee for the GMOD Meeting to cover catered lunches and other expenses. Registration for all other events is free, but required, as space is limited. These events are open to all: GMOD users, developers, prospective users, biologists, and computer scientists. See http://gmod.org/wiki/January_2010_GMOD_Meeting for an idea of what goes on at GMOD meetings, GMOD is a collection of interoperable open source software components for managing, visualizing and annotating biological data. GMOD incorporates many widely used tools, including GBrowse and JBrowse for genome browsing, InterMine and BioMart for data mining, Galaxy and Ergatis for workflow, Chado for data management, GBrowse_syn and CMap for comparative genomics, plus many other tools (Apollo, MAKER, Pathway Tools, Textpresso, ...). GMOD is also an active community of researchers and developers addressing common challenges in exploiting their data. If you are struggling to fully exploit your data then please consider attending GMOD Europe 2010. Please let us know if you have any questions, and we hope to see you in Cambridge. Thanks, Scott Cain and Dave Clements -- http://gmod.org/wiki/GMOD_News <http://gmod.org/wiki/GMOD_News>http://gmod.org/wiki/GMOD_Evo_Hackathon http://gmod.org/wiki/GMOD_Europe_2010 http://gmod.org/wiki/Help_Desk_Feedback

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Postdoc position exome sequencing
by AHC van Kampen 03 Aug '10

03 Aug '10

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