- BBClist - maillist.psb.ugent.be

Support Letter for BEDTools!!
by Stéphane Plaisance 11 May '11

11 May '11

Dear all, If you use BEDTools in your daily work, please consider supporting Aaron by following his instructions below. I am a great fan of BEDTools and find that Aaron greatly deserves this for all the time he saved me with BEDTools in the last years. Stephane Begin forwarded message: > From: bedtools-discuss+noreply(a)googlegroups.com > Date: 10 May 2011 23:53:00 GMT+02:00 > To: Digest Recipients <bedtools-discuss+digest(a)googlegroups.com> > Subject: [bedtools-discuss] Digest for bedtools-discuss(a)googlegroups.com - 2 Messages in 2 Topics > Reply-To: bedtools-discuss(a)googlegroups.com > > Today's Topic Summary > Group: http://groups.google.com/group/bedtools-discuss/topics > > BEDTools Needs Your Support! [1 Update] > Topic: BEDTools Needs Your Support! > Aaron Quinlan <aaronquinlan(a)gmail.com> May 09 10:26PM -0400 ^ > > Dear BEDTools User, > > Thus far, BEDTools has had no formal funding and has been supported by myself and a handful of talented and dedicated contributors. A primary goal of my new laboratory is to continue to improve, support and maintain these tools. More ambitiously, I intend to develop a suite of scalable and efficient algorithms for genome arithmetic (e.g., intersect, count, complement, subtract, merge) in order to accommodate the size and complexity of current and future genomic datasets. These new algorithms will be capable of interrogating multiple datasets at once (i.e., moving beyond pairwise comparisons), use less memory, exploit parallel computing architectures, and will have improved support for many more file formats. In turn, "BEDTools 2" will provide entirely new classes of tools for large-scale genomic analyses. > > In order to fulfill these goals, I am seeking NIH funding and I would like to ask for your help. If you find BEDTools to be at all useful in your research, I would like to ask you to write a brief letter of support. Your letter will be included as a supplement to the grant application and it will greatly improve the strength of the grant. > > If you would be willing to document your support of BEDTools, I ask that you: > > - Send an email directly to me (aaronquinlan(a)gmail.com) Please include your name and affiliation. > - Write a few sentences documenting: > . your support for the project > . how you use the tools > . what, if anything, you like about them. > . how they have benefited, improved, or expedited your research. > > Thanks so much in advance for your assistance - a couple of minutes writing an email of support will certainly help me immensely. > > If you know of other users that are not on the BEDTools list but might be interested in helping out, please pass this on. > > Sincerely, > Aaron > > Aaron Quinlan, Ph.D. > Assistant Professor > Department of Public Health Sciences > Center for Public Health Genomics > University of Virginia

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Bioinformatics PhD job opening at Radboud University Nijmegen Medical Centre
by Sacha van Hijum 08 May '11

08 May '11

Dear all, there is a job-opening for a bioinformatics PhD student at the Radboud University Nijmegen Medical Centre. For those interested, please see below for details. Best regards, Sacha van Hijum Job profile The PhD student will work in a multidisciplinary team with other scientists and medical doctors to discuss, plan and perform bioinformatics research in a highly stimulating environment. Work-place will be the Laboratory of Pediatric Infectious Diseases (Prof. dr. P. Hermans) and the Bacterial Genomics group (Dr. S. van Hijum). • Independently generate and analyze data • Present results at (inter)national scientific meetings and in international peer-reviewed journals Requirements • Msc degree in (molecular) life sciences, specializing in bioinformatics • Background in statistics and understanding of bioinformatics algorithms. Knowledge of Perl/Python and R is a plus • Preferably experience in microbiology, molecular biology and biochemistry • Fluent in English (speaking, reading and writing) • An independent and well-structured working style • Teamplayer and a strong motivation to succeed in scientific and translational research Organization unit Laboratory of Pediatric Infectious Diseases The Laboratory of Pediatric Infectious Diseases at Radboud University Nijmegen Medical Centre is an academic research lab in which scientists and medical doctors work closely together to conduct translational research on the pathogenesis, immunology, and epidemiology of pediatric respiratory tract infections. Our studies aim to increase the molecular and clinical understanding of the interactions occurring between host and pathogen during infection. This knowledge is used to design improved and novel diagnostic, therapeutic, and preventive strategies. The Laboratory of Pediatric Infectious Diseases participates in the Nijmegen Institute for Infection, Inflammation, and Immunity (N4i) and the Nijmegen Center for Molecular Life Science (NCMLS), with focus on basic science and its translation into pioneering treatments for disease. The innovations are advanced through technology platforms such as genomics, proteomics, and molecular imaging. The Laboratory of Pediatric Infectious Diseases works in close collaboration with the… Bacterial Genomics group Focus of the Bacterial Genomics group (Radboud University Nijmegen Medical Centre) is on the bioinformatics analysis of ~omics data of (consortia of) bacteria in the context of industrial fermentations, health and safety. The research involves (meta)genome sequencing and assembly, annotation, comparative genomics, RNA-seq, transcriptomics and multivariate analysis of ~omics datasets, all in relation to exploration and exploitation of the enormous microbial diversity that is found in Nature. The Bacterial Genomics group is part of the CMBI (Centre for Molecular and Biomolecular Informatics). The CMBI pursues a rigorous research program with topics ranging from computational small-molecule chemistry to bioinformatics. The CMBI is among the largest bioinformatics departments in the Netherlands producing dozens of high impact peer-reviewed publications each year. It consists of 4 research groups (Prof. Vriend, Prof. Huynen, Prof. de Vlieg and Dr. van Hijum) with strong connections with the NBiC, centre of excellence and the largest bioinformatics cluster in the Netherlands. Information Prof. dr. P.W.M. Hermans, head of the laboratory, (024) 3666406, P.Hermans(a)cukz.umcn.nl Dr. A.L. Zomer, bioinformatician, (024) 3651545, A.Zomer(a)cukz.umcn.nl Dr. S.A.F.T. van Hijum, group leader Bacterial Genomics (024) 3619389, svhijum(a)cmbi.ru.nl More information and online application via this link: http://www.umcn.nl/OVERUMCSTRADBOUD/WERKENBIJ/Pages/Vacature.aspx?VacatureN… -- Dr. Sacha van Hijum Group leader CMBI Bacterial Genomics Group leader Bioinformatics NIZO food research B.V. Bioinformatics coordinator Top Institute Food and Nutrition T: +31(0)318 659 570 F: +31(0)318 650 400 M: +31(0)624782895 E: sacha.vanhijum(a)nizo.nl or svhijum(a)cmbi.ru.nl P.O. Box 20, 6710 BA EDE, The Netherlands Kernhemseweg 2, 6718 ZB EDE, The Netherlands

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Ph.D. /Postdoc positions -ICT & computational research for health care -at IBBT -K.U.Leuven Future Health Department at ESAT
by mimi deprez 02 May '11

02 May '11

Dear members: The IBBT-K.U.Leuven Future Health Department has several job openings for Ph.D. and or postdocs in ICT and computational research for health care located at ESAT. All details can be found on www.kuleuven.be/ibbt/jobopenings <http://www.kuleuven.be/ibbt/jobopenings> or see below the detailed research topics. Positions focusing on genomics and next gen sequencing for translational medicine * Reporting of genome sequencing results in a clinical setting <https://phd.kuleuven.be/set/voorstel.php?id=2204&none=display> * Identification and visualization of structural variation in the human genome <https://phd.kuleuven.be/set/voorstel.php?id=2205&none=display> * High-performance data analytics for nextgeneration sequencing data analysis <https://phd.kuleuven.be/set/voorstel.php?id=2212&none=display> * Network analysis of analysis of disease phenotypes and drug responses <https://phd.kuleuven.be/set/voorstel.php?id=2213&none=display> * Federated and collaborative knowledge bases for genomic medicine <https://phd.kuleuven.be/set/voorstel.php?id=2195&none=display> Positions focusing on biomedical signal processing and hearing aids * Advanced algorithms for integrated EEG-fMRI data processing <https://phd.kuleuven.be/set/voorstel.php?id=2210&none=display> * Compressive Sensing for Biomedical Signals <https://phd.kuleuven.be/set/voorstel.php?id=2207&none=display> * Distributed Noise Reduction in Hearing Aids <https://phd.kuleuven.be/set/voorstel.php?id=2206&none=display> Positions focusing on data mining and biostatistics for pattern recognition, data analysis and data fusion * Policy Decision Support Systems to objectively evaluate care <https://phd.kuleuven.be/set/voorstel.php?id=2203&none=display> * Mass Spectrometry Imaging and Bioinformatics <https://phd.kuleuven.be/set/voorstel.php?id=2202&none=display> * Decision Support Systems for Cardiovascular Diseases <https://phd.kuleuven.be/set/voorstel.php?id=2208&none=display> * Analysis of multicentre data on the preoperative diagnosis of ovarian tumours based on standard and advanced prediction models <https://phd.kuleuven.be/set/voorstel.php?id=2209&none=display> * Biomedical text mining and network analysis for disease gene discovery <https://phd.kuleuven.be/set/voorstel.php?id=2211&none=display> For more information on these positions and requirements please contact inge.thijs(a)esat.kuleuven.be <mailto:inge.thijs@esat.kuleuven.be> or steven.vandeput(a)esat.kuleuven.be <mailto:steven.vandeput@esat.kuleuven.be> ** /The IBBT-K.U.Leuven Future Health Department is part of IBBT, the Institute for Broad Band Technology. IBBT aims to create a lasting and positive impact on society through ICT innovation. IBBT Future Health directs this innovation towards a healthy society, by developing information technologies for health care. To this end, IBBT Future Health combines pioneering research with market-driven R&D, creates synergies with stakeholders and engages in societal outreach. We indeed believe that the key to accessible and efficient health care lies in the cross-fertilization between research, technology and health care itself. IBBT Future Health joins the forces of 80 researchers in four K.U.Leuven research groups, and enables an interdisciplinary approach of innovative ICT for health care thanks to its multifaceted expertise, including data mining, bioinformatics, biomedical data processing, advanced image computing, the creation of e-learning environment, and user experience research. //More info at /www.kuleuven.be/ibbt <http://www.kuleuven.be/ibbt>. -- Mimi Deprez Project coordinator K.U.Leuven, ESAT/SCD (SISTA) Kasteelpark Arenberg 10 -- bus 2446 B-3001 Leuven, Belgium Tel. +32/16/32.85.55 Fax. +32/16/32.19.70 mimi.deprez(a)esat.kuleuven.be

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[DUTCH] Vacature Docent Moleculaire Biologie/Bio-informatica
by Bruggen Martijn van der 29 Apr '11

29 Apr '11

De Faculteit Techniek zoekt voor de campus in Nijmegen zo spoedig mogelijk een Docent Moleculaire Biologie/Bio-informatica 0,8-1,0 fte Standplaats: Nijmegen De Faculteit Techniek (FT) verzorgt de technische opleidingen van de HAN. Studenten volgen er competentiegericht onderwijs in moderne werkvormen en in diverse trajecten, zoals in voltijd, deeltijd en duaal. Ze worden opgeleid tot gekwalificeerde bachelors/ingenieurs in het specifieke beroepenveld. Medewerkers van de faculteit kunnen naast het leveren van een bijdrage aan het reguliere onderwijs, ook activiteiten verrichten voor post-hbo-, internationale en masteropleidingen, voor toegepaste onderzoeksopdrachten van én voor bedrijven en instellingen. Wat zijn uw werkzaamheden? U verzorgt competentiegericht onderwijs in het Nederlands en Engels voor alle studiejaren van de opleidingen Bio-informatica en Biologisch Laboratorium Onderwijs. U begeleidt leerprocessen (onder andere in de rol van tutor, expert en studieloopbaanbegeleider) en stages en afstudeeropdrachten, zowel in binnen- als buitenland. U past bestaand onderwijs aan en draagt bij aan de ontwikkeling van nieuw onderwijs. Eventueel voert u ook scholings- en onderzoeksactiviteiten uit voor externe relaties. Wat zijn uw kwaliteiten? U hebt een afgeronde gerichte opleiding, academisch denk- en werkniveau en passie voor onderwijs. U hebt gedegen kennis van en werkervaring in de moleculaire biologie en bio-informatica. Bij voorkeur hebt u ervaring met programmeren/scripting, bijvoorbeeld Python, Java of SQL. U bent communicatief en sociaal vaardig. U bent enthousiast en flexibel en resultaatgericht. Tot slot bent u collegiaal. Wat bieden wij u? Een interessante en afwisselende functie in een dynamische, informele werkomgeving. Aanstelling vindt plaats voor de duur van een jaar met uitzicht op een vast dienstverband. U wordt aangesteld in de functie van Docent niveau 1. Afhankelijk van uw ervaring bedraagt het bruto maandsalaris maximaal € 4.365,16 (cao-hbo schaal 11) bij een fulltime aanstelling. Het salaris is exclusief 8% vakantietoeslag en 8,3% eindejaarsuitkering. Daarnaast biedt de HAN goede voorzieningen op het vlak van pensioen, ziektekosten, scholingsfaciliteiten, mobiliteit en betaald ouderschapsverlof. Wilt u meer informatie? Voor meer informatie over deze functie kunt u contact opnemen met de heer C.W. van Verseveld, Directeur, T (024) 353 19 05. Hebt u belangstelling? Herkent u zich in bovenstaand profiel en voldoet u aan de eisen? Klik dan vóór 12 mei 2011 op de link onder aan deze advertentie om online te solliciteren. Sollicitaties die rechtstreeks naar de contactpersoon of op andere wijze worden verstuurd, worden niet in behandeling genomen. Wilt u meer informatie over de sollicitatieprocedure voor deze vacature, dan kunt u contact opnemen met mevrouw M. Geltink, Secretaresse P&O, T (026) 369 15 51. Link naar vacature: http://ssl1.peoplexs.com/Peoplexs22/CandidatesPortalNoLogin/Vacancy.cfm?Por… Link naar HAN vacatures: http://www.han.nl/start/corporate/werken-bij-de-han/vacatures/

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Meeting on Robust Methods, Antwerp
by Katrijn Van Deun 22 Apr '11

22 Apr '11

--- APOLOGIES FOR CROSS-POSTING--- Dear Colleagues, The Dutch/Flemish Classification Society (called VOC: http://www.voc.ac) organizes two scientific meetings per year. The 2011 Spring Meeting will be held on Friday May 13 in the centre of Antwerp and is on "Robust Methods". Keynote speakers are Stefan Van Aelst (Ghent University) and Marco Riani (Parma University). The program, including titles and abstracts of the presentations, is attached to this e-mail. Those who would like to participate are welcome and are kindly requested to register by sending an e-mail to meeting(a)voc.ac<mailto:meeting@voc.ac> with subject 'Registration Spring Meeting 2011' and including name and affiliation in the body of the e-mail. Participation is free, lunch is available for 10 Euros and must be requested upon registration. Registration deadline: May 10th. We hope to welcome you in Antwerp. Best wishes (also on behalf of Mark de Rooij, co-organizer of the meeting), Katrijn Van Deun

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PhD position in Statistics for Integrative Bioinformatics
by Martin van Vliet 18 Apr '11

18 Apr '11

PhD position in Statistics for Integrative Bioinformatics, The Netherlands Department/section: Epidemiology and Biostatistics, Division VI & Pathology, Division V Full details are available at: http://www.werkenbijvumc.nl/vacatures/D5.2011.00040/<http://www.rcog.org.uk/work-us/research-associate> General: The Biostatistics group (see http://www.vumc.nl/afdelingen/EB/ - in Dutch) at the VU University Medical Center has a very active group of statisticians working on high-dimensional data analysis. The group within the Department of Epidemiology & Biostatistics has close links to the Mathematics and Statistics Department of the VU University Amsterdam, as well as to both the Microarray Facility and the Department of Pathology of the VU University Medical Center. Within the Department of Pathology, the unit Molecular Pathology investigates the molecular changes involved in the development of cervical cancer. Ultimate aim of this research is the identification of potential therapeutic targets and molecular markers for population-based screening programs (see http://www.vumc.com/afdelingen/pathology/ - Research - Oncology) Project: The project aims to produce multivariate statistical models that describe the development of HPV-induced cervical cancer in vitro from a longitudinal experiment in which multiple molecular levels (DNA copy number, methylation, gene expression, and microRNA expression) of consecutive stages of a cell line model have been characterized in high-throughput fashion. The high-dimensionality of the information on and the dependency between the molecular levels make the inference of the molecular mechanisms underlying cervical cancer development a statistical challenge, which is to be tackled within this project. The project is a collaboration between the Department of Epidemiology & Biostatistics and the Unit Molecular Pathology, providing an optimal statistical and biological framework. Requirements: We are looking for a PhD student with an MSc in Statistics, Bioinformatics or a closely related discipline. Essentials are: good statistical knowledge enabling the development of new models and analysis tools, programming skills, the ability to explain complex ideas to biologists/non-specialists and an affinity with genetics and biology. Previous knowledge of any of the areas involved in the project (such as longitudinal models, multivariate statistics, high-dimensional data analysis) and of R programming are an advantage. The PhD student we are looking for has good communication skills and is flexible to work both with statisticians and biomedical researchers. The PhD student will participate in the PhD program of the VU Institute for Cancer and Immunology (V-ICI). Work conditions: The temporary employment will be for a period of 4 years. Salary and terms of employment will be in accordance with the CAO-Universtair medische centra of the Netherlands. Contact: For details about the project contents please contact - Wessel van Wieringen (PhD), Statistician, Dept of Epidemiology and Biostatistics, w.vanwieringen(a)vumc.nl<mailto:w.vanwieringen@vumc.nl>, tel: +31 20 444 1047 - Saskia Wilting (PhD), Biomedical researcher, Dept of Pathology, s.wilting(a)vumc.nl<mailto:s.wilting@vumc.nl>, tel: +31 20 444 8584

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[Dutch] Vacature Teamleider Applied Bioinformatics
by Datema, Erwin 08 Apr '11

08 Apr '11

Teamleider Applied Bioinformatics Vacaturenummer PSG-BIOS-0006 Regio Gelderland Onderdeel Plant Research International Functietype Leidinggevende functies Sluitingsdatum voor sollicitaties 20 April 2011 Wij zoeken een teamleider voor het team Applied Bioinformatics. De teamleider: • geeft inspirerende leiding aan een jong en enthousiast team; • is verantwoordelijk voor de omzet van het team en is zelf zeer actief in het verwerven en leiden van grote projecten; • is verantwoordelijk voor het succesvol functioneren van de team; zowel wetenschappelijk als financieel en personeel; • vertegenwoordigt het eigen team, de business-unit en PRI/PSG in externe contacten; • weet zich aan te passen aan veranderende situaties en aan een qua cultuur veranderende organisatie, is daar een voorloper in en weet de medewerkers hierin mee te krijgen; • geeft op een inspirerende wijze en met een duidelijke visie leiding aan het team (ca 8 vaste medewerkers, tijdelijke medewerkers en PhD studenten) en is daarbij verantwoordelijk voor de ontwikkeling van de medewerkers d.m.v. R&O-gesprekken en coaching; • is in staat om bij te dragen aan het vormgeven van een cultuur waarin zakelijkheid en menselijke betrokkenheid samengaan; • maakt deel uit van het MT van de business unit; • draagt bij aan de voorbereiding, ontwikkeling en uitvoering van het (meerjaren)business plan en strategisch personeelsplan van de business unit; • stimuleert samenwerkingsverbanden en kennisdeling over de teams en BU’s heen, in het bijzonder met de BU Plantenverdeling en Biometris en de leerstoelgroep Bioinformatica • gaat een duurzame relatie aan met (inter)nationale zaadbedrijven en geeft in samenwerking vorm aan de genoomgebaseerde veredeling van gewassen. Wij vragen • academisch werk- en denkniveau; gepromoveerd op het vakgebied van de BU; • zeer goede inhoudelijke kennis op de expertiseterreinen van het team: genoombioinformatica, vergelijkende genomics en systeembiologie; • in staat om één of meerdere van deze onderzoeksvelden als trekker vorm te geven; • een uitgebreid netwerk in dit marktsegment en een aantoonbaar trackrecord van wetenschappelijke publicaties en/of patenten; • ruime kennis van marktontwikkelingen op het gebied van genoombioinformatica, in staat nieuwe kansen te herkennen; • ervaring met het leidinggeven aan professionals in een kennis/projectorganisatie; • uitstekende communicatieve vaardigheden en empathisch vermogen • succesvol in het initiëren, acquireren, opzetten, begeleiden en uitvoeren van grote (internationale) onderzoeksprojecten; • competenties: samenwerkingsgerichtheid, omgevingsbewustzijn, coaching, initiatief, optreden, samenbindend leiderschap en durf; • Inzicht in de onderzoeksvelden en technologieën van de BU. Wij bieden Een uitdagende baan voor 32 - 36 uur per week, salaris max. € 5707 (schaal 13) en een uitstekend pakket aan overige arbeidsvoorwaarden. Aanstelling voor een jaar met uitzicht op verlenging. Informatie: Voor aanvullende informatie over deze vacature kunt u contact opnemen met Dr. A.J. Koops, Manager BU Bioscience, tel. 0317-480822, e-mail andries.koops(a)wur.nl Stuur uw sollicitatie niet naar de genoemde contactpersoon, maar solliciteer via de website. www.werkenbij.wur.nl/NL/<http://www.werkenbij.wur.nl/NL/> Wij zijn Plant Sciences Group De Plant Sciences Group is het samenwerkingsverband waarin Wageningen Universiteit en de onderzoeksinstituten Plant Research International (PRI) en Praktijkonderzoek Plant & Omgeving samenwerken op het gebied van plantgerelateerd onderzoek en onderwijs. De Plant Sciences Group is een onderdeel van Wageningen UR. Bioscience PRI bestaat uit vijf business units (BU), waaronder de BU Bioscience. Het onderzoek van de BU Bioscience is gericht op het beter begrijpen van de genetische, moleculaire en metabole processen in de plant, en het effect van plant inhoudsstoffen op mens en dier. Hierbij wordt gebruik gemaakt van state of the art faciliteiten zoals next-generation DNA sequencing, proteomics, metabolomics, microscopie en een bionanoreceptor-platform. Het onderzoek is gericht op het verbeteren van de kwaliteit en opbrengst van gewassen en de productie van inhoudsstoffen voor gebruik in voedsel, farmaca en chemieproducten. Bioscience heeft een vaste staf van ongeveer 60 medewerkers en een tijdelijke staf van gemiddeld 35 studenten, PhD’s en post-docs. De omzet is ongeveer €8.0 miljoen. Bioscience bestaat uit 4 teams: Plant Development Systems, Metabolic Regulation, Applied Genomics & Proteomics en Applied Bioinformatics (AB). De onderzoeksthema’s binnen het team AB zijn genoombioinformatica (genoom assemblage en -annotatie) en genome mining. Samen met de andere teams wordt gewerkt aan systeembiologie en bioinformatica van metabolomics en proteomics. Wageningen UR Wageningen Universiteit en Researchcentrum (Wageningen UR) is een internationaal toonaangevende kennisinstelling op het gebied van life sciences en duurzaamheid. Wij zoeken binnen ons domein gezonde voeding en leefomgeving naar antwoorden op vragen over maatschappelijke thema’s als duurzame voedselproductie, klimaatverandering en alternatieve energiebronnen. Dat doen we natuurlijk niet alleen. Om dit, ook internationaal, waar te maken werken we elke dag met 6500 mensen aan de kwaliteit van leven. Kijk voor meer informatie over werken bij Wageningen UR op www.werkenbij.wur.nl<http://www.werkenbij.wur.nl/>.

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NBIC PhD Course - Comparative Genomics: from evolution to function
by Celia van Gelder 08 Apr '11

08 Apr '11

NBIC PhD Course - Comparative Genomics: from evolution to function On June 27 - July 1, 2011 the NBIC PhD School organises the PhD Course 'Comparative Genomics: from evolution to function' in Utrecht. Course Lecturers: Berend Snel (coordinator), Martijn Huynen, Jaap Heringa Course Description Comparative genomics between species and types of data is pivotal for biology. The first two days we move "beyond blast": supersensitive homology searches, domain level analysis of protein evolution and interpretation of gene trees (levels of orthology). Based on this, the threeremaining days investigate: (1) functional and evolutionary consequence of (genome)duplications, (2) the evolution of interactions and complexes (3) the prediction and evolution of genomic regulatory elements. Target audience The course is intended for PhD and master students in bioinformatics, especially those interested in evolution or in comparing various genomics data between species. More information about the course, including information about the course programme, can be found on http://www.nbic.nl/index.php?id=638 . Enrolment information can be found at http://www.nbic.nl/education/nbic-phd-school/enrolment/. This course is part of the Education Programme of the NBIC PhD School. The PhD School is an initiative of NBIC together with a number of universities to organize high level education and training for PhD students in bioinformatics. More information about the latest developments of the NBIC PhD School can also be found on the NBIC website (www.nbic.nl -> Education -> NBIC PhD School). Best regards, Celia van Gelder Project leader Education NBIC -- Dr. Celia W.G. van Gelder Coordinator Education CMBI Projectleader Education NBIC tel. +31-(0)24-3666120 e-mail: C.vanGelder(a)cmbi.ru.nl websites: www.cmbi.ru.nl, www.nbic.nl Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre /NCMLS PO Box 9101, 6500 HB Nijmegen The Netherlands

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Ghent University: Tenure Track position in Statistical Genomics
by Stijn Vansteelandt 05 Apr '11

05 Apr '11

Ghent University invites applications for a full time tenure track position dedicated to research in Statistical Genomics. The position is funded by the Special Research Fund (BOF) as one of five tenure track positions in Bioinformatics launched at Ghent University as part of its Multidisciplinary Research Partnership in Bioinformatics `From Nucleotides to Networks' (N2N). This is an interdisciplinary field joining the expertise of scientists with different backgrounds to solve problems in (molecular) biology through computational means, which Ghent University has identified as one of their 5 areas of excellence. We seek an upcoming research leader with an outstanding scientific record in Statistical Genomics, motivated to play a major role in the high profile Multidisciplinary Research Partnership in Bioinformatics. The successful candidate is expected to engage in research related to one or more work packages identified by the partnership (www.nucleotides2networks.be) to 1) build streamlined pipelines to deal with increasingly large numbers of heterogeneous data, 2) integrate these data for further downstream analyses, 3) develop novel tools and approaches for systems biology (inferring and modeling biological networks), and 4) apply these tools and approaches to Sustainable Agriculture and Successful Aging. The successful candidate will be hosted within the Statistics research group at the Department of Applied Mathematics and Computer Science. The group is internationally recognized, primarily for its research on causal inference and robust statistics. More recently, the group has been developing closer ties with industry and government and develops targeted applied research, valorizing the academic work for innovation in society, through the consortium Stat-Gent CRESCENDO. This unit has its own scientific staff and operates across the university, in inter-faculty collaboration. The primary focus here is on life sciences, the analysis of electronic health records and genetics data. This position will initially be a five-year temporary appointment in a Tenure Track system dedicated to research, with a limited teaching load. The appointment will be made in the starting rank of assistant professor, with effect from 1 October 2011. Upon positive evaluation by the university board, the position will lead to a permanent position starting at the level of associate professor, at which point the teaching load may be revised. Profile: the candidate should: - Meet the degree requirements (PhD based on a doctoral thesis or equivalent recognised diploma), indicated in Article 83 of the Decree of 12 July 1991 concerning universities within the Flemish Community; the PhD or equivalent should have been obtained after 1 February 2004, but not later than 1 February 2009; - Candidates should hold a PhD with a doctoral thesis in sciences with a strong quantitative statistical component, by preference in Physical Sciences, including Statistics and Mathematics, Life Sciences, Bioscience engineering, or a degree recognized as equivalent; - Have carried out outstanding scientific research in Statistical Genomics, with corresponding research output; - Have strong didactic, communicative and organisational skills; - Have experience in generating research projects and/or coaching PhD students; - Have acquired international academic experience; The governing language at Ghent University is Dutch. However, research is primarily conducted in English. Persons who do not speak Dutch as a native language are very welcome to apply and are expected to acquire a working knowledge of the language. Applications must be sent in duplicate by registered mail to the Vice-Chancellor of Ghent University, Vice-Chancellor?s Office, Sint-Pietersnieuwstraat 25, 9000 Ghent, using the necessary application form, together with proof of suitability (e.g., copies of the applicant?s diplomas). After preselection, candidates will be asked to submit a research project plan which fits into the research objectives of the Multidisciplinary Research Partnership. A description will be made available. The deadline for submission is April 29, 2011. The date of posting is accepted as the date of receipt. Further information concerning this vacancy is available on http://www.ugent.be/nl/actueel/vacatures/zap/BC20110214-bof01 and/or can be requested by contacting Stijn Vansteelandt (stijn.vansteelandt(a)ugent.be) or Els Goetghebeur (els.goetghebeur(a)ugent.be) The required application form for this position is available on the internet, http://www.ugent.be/nl/werken/aanwerving/formulieren/zap/formulier.doc/view or can be requested from Ghent University, F.A.O. Department of Personnel and Organisation, Sint-Pietersnieuwstraat 25, 9000 Ghent, or via telephone on. +32-9-264 31 29 or +32-9-264 31 30.

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ECAL 2011, Deadline extension, April 13
by Tom Lenaerts 04 Apr '11

04 Apr '11

[Apologies if you receive multiple copies of this announcement.] [Please kindly help forward it to potentially interested attendees.] ============================================== !!! BY POPULAR DEMAND, DEADLINE EXTENSION THROUGH APRIL 13 !!! ============================================== *** PROCEEDINGS WITH MIT PRESS - BEST PAPERS INVITED TO ALIFE JOURNAL ============================================== *** 6 KEYNOTE eSPEAKERS - PIONEERS' PANEL - ART EXHIBIT & SHOW - 14 WORKSHOPS ============================================== *** REGISTRATION NOW OPEN ============================================== CALL FOR PAPERS: ECAL 2011 << Back to the origins of Alife >> ECAL 2011, European Conference on Artificial Life, an international conference on the simulation and synthesis of living systems 8-12 August 2011, Paris, France www.ecal11.org ============================================== Artificial Life is an interdisciplinary undertaking that investigates the fundamental properties of living systems through the simulation and synthesis of biological entities and processes. It also attempts to design and build artificial systems that display properties of organisms, or societies of organisms, out of abiotic or virtual parts. ECAL, the European Conference on Artificial Life, is a biennial event that alternates with the US-based Alife conference series. --------------------- Welcome to ECAL 2011! Back then, in the early 1990's, the first two ECAL conferences in Paris and Brussels were mainly centered on theoretical biology and the physics of complex systems. Today, we feel that Alife can look back on these origins and take more inspiration from new developments at the intersection between computer science and theoretical biology ó thus it is our wish to refocus the conference on *complex biological systems*. Closing a loop, this ECAL will mark the 20th anniversary of the 1st ECAL and will be framed as a tribute to the late Francisco Varela, co-organizer in 1991 with two of this year's committee members (Paul Bourgine, CREA, and Hugues Bersini, IRIDIA). We look forward to seeing you in Paris. ** You are invited to submit papers (full and abstract) to this exciting event! ** 6 KEYNOTE SPEAKERS (Confirmed) --------------------- * Eric Wieschaus, Princeton University, 1995 Nobel Prize in Physiology * Jacques Demongeot, Université Joseph Fourier, Grenoble * David Harel, Weizmann Institute of Science * James D. Murray, Universities of Washington and Oxford * Jordan Pollack, Brandeis University * Ricard Solé, Universitat Pompeu Fabra, Barcelona A PANEL DISCUSSION WITH ALIFE PIONNEERS (Tentative list) --------------------- * Mark Bedau, Reed College and Portland State University, Oregon * Rodney Brooks, Massachusetts Institute of Technology, Cambridge * J. Doyne Farmer, Santa Fe Institute, New Mexico * Stuart Kauffman, University of Vermont, Burlington * Pier Luigi Luisi, Roma Tre University, Italy * Norman Packard, European Center for Living Technology, Venice * Steen Rasmussen, University of Southern Denmark, Odense * Luc Steels, Vrije Universiteit Brussel & Sony Labs ART EXHIBIT AND PERFORMANCE (Confirmed, possibly more) --------------------- * Louis Bec, Zoosystematician ( http://www.v2.nl/archive/people/louis-bec ) * Francois Chapet, Jazz Player / Researcher, Sony Labs ( http://www.csl.sony.fr/~pachet/ ) 14 WORKSHOPS & TUTORIALS (Confirmed) --------------------- * AAALE - Alife Approaches to Artificial Language Evolution * ACCS - Artificial Chemical Computing Systems * BioChemIT - 1st COBRA Workshop on Biological and Chemical Information Technologies * Closure - Metabolic closure: From (M,R) systems and autopoiesis to self-referential equations * CoSMoS - 4th Workshop on Complex Systems Modelling and Simulation * CS-Sports - Complex Systems in Sports * iBioMath - First International Workshop on Integral Biomathics * INCUP - Novel Computing Substrates: Information Coding Perspective * MASmms - Workshop on Multi-Agent Systems in Biology at meso or macroscopic scales * MEW - 3rd Morphogenetic Engineering Workshop * RUTSAC - Research Using The Stringmol Artificial Chemistry * SIM-A - System Immunology Models of Autopoesis * SynBioCCC - Workshop on the Design, Simulation, Construction and Testing of Synthetic Gene Regulatory Networks for Computation, Control and Communications * WAAT - Workshop on Artificial Autonomy: 20 years of practice of autonomous systems IMPORTANT DATES --------------------- o Start of early registration rates: March 15, 2011 o !!! NEW PAPER & ABSTRACT SUBMISSION: April 13, 2011 !!! o Paper & abstract notification: May 20, 2011 o Camera-ready versions: June 10, 2011 o Start of standard registration rates: June 10, 2011 o Start of late registration rates: July 31, 2011 o Conference: August 8-12, 2011 THEMES --------------------- "A new body of disciplines": Over the past two decades, biological knowledge has grown at an unprecedented rate, giving rise to new disciplines such as systems biology ó- testimony of the striking progress of modeling and quantitative methods across the field. During the same period, highly speculative ideas have matured, and entire conferences and journals are now devoted to them. Synthesizing artificial cells, simulating large-scale biological networks, storing and making intelligent use of an exponentially growing amount of data (e.g., microarrays), exploiting biological substrates for computation and control, and deploying bio-inspired engineering are all cutting-edge topics today. "Life itself": ECAL 2011 will leverage the remarkable development of biological modeling and extend the topics of Artificial Life to the fundamental properties of living organisms: their multiscale pattern-forming morphodynamics, their autopoiesis, robustness, capacity to self-repair, cognitive capacities, and co-adaptation at all levels, including ecological ones. ECAL 2011 will bring together a large interdisciplinary community of biologists, computer scientists, physicists, and mathematicians. It will invite them to reflect on how traditional boundaries between disciplines have become blurred, and to revisit in depth what constitutes ìlifeî. Papers are welcome in all areas of Artificial Life, including, but not limited to: - (Chemical) Self-Assembly & Complexity - Artificial Chemistries - Biological & Chemical Information Processing and Production - Biosemiotics - Complex Networks - Emergent Engineering - Evolutionary & Learning Dynamics - Minimal (Bottom up) Synthetic Cells - Minimal Cognition & Physical Intelligence - Mixed Living (Technology) Systems - Modular Robotics - Morphogenesis, Generative & Developmental Systems - Multilevel Ecologies - Organizations & Collective Intelligence - Origins of Life - Philosophy of Artificial Life & Living Technology - Protocellular Energetics & Metabolic Networks - Robotic Energy Autonomy - Robotic Self-Assembly - Socio-Technical Systems - Swarm Intelligence - Systems Biology - Theoretical & Computational Frameworks - Top-Down Artificial Cells Authors are encouraged to explain how their work sheds light on the fundamental properties of living systems and makes progress on the important open questions identified during previous meetings. PAPER/ABSTRACT FORMAT --------------------- Detailed information concerning the formatting guidelines, templates, online submission process, and proceedings can be found athttp://www.ecal11.org/submission There are two options for submission: either *full paper* or *abstract*. Note that the format is exactly the same for both options. The only difference resides in the number of pages and type of contents: 1. Full papers have an *8-page* maximum length and should report on new, unpublished work 2. Abstracts are limited to a *2-page* length and should discuss work previously published in a journal. It is therefore essential that a reference to the previous article is clearly cited in the abstract. All submissions will be subject to peer review, and all accepted submissions will be allocated either an oral presentation slot or a poster slot with no distinction being made between the two submission options (full paper or abstract). PUBLICATION --------------------- Every accepted full-paper and abstract, which was submitted to the main conference (not the satellite workshops), will be published by MIT Press in a single online open-access proceedings volume. The top 10 accepted publications will have the opportunity to publish a revised and expanded version of their conference paper in the Artificial Life journal. LOCATION & REGISTRATION ----------------------- The conference will be held at the CitÈ Internationale Universitaire de Paris (CIUP), located on a wooded park at the southern edge of the French capital. See more information at http://www.ecal11.org/venue ** Registration information is posted at http://www.ecal11.org/registration ** ORGANIZATION --------------------- * RenÈ Doursat (chair) Complex Systems Institute/CREA, Ecole Polytechnique & CNRS, Paris * Hugues Bersini IRIDIA, UniversitÈ Libre de Bruxelles * Paul Bourgine Complex Systems Institute/CREA, Ecole Polytechnique & CNRS, Paris * Tom Lenaerts (program chair) Department of Computer Science, Université Libre de Bruxelles and Vrije Universiteit Brussel * Mario Giacobini (program co-chair) Molecular Biotechnology Center, University of Torino * Marco Dorigo IRIDIA, Université Libre de Bruxelles PROGRAM COMMITTEE --------------------- * Hussein Abbass * Bart De Boer * Daniel Lobo * Hiroki Sayama * Andy Adamatzky * Ralf Der * Fernando Lobo * Matthias Scheutz * Chris Adami * Gianni Di Caro * Robert Lowe * Thomas Schmickl * Andreas Albrecht * Cecilia Di Chio * Penousal Machado * Marc Schoenauer * Fernando Almeida E Costa * Ezequiel A. Di Paolo * Steven Maere * Luis Seabra Lopes * Lee Altenberg * Peter Dittrich * Davide Marocco * Roberto Serra * Paul Andrews * Marco Dorigo * John McCaskill * Cosma Shalizi * Takaya Arita * Alan Dorin * Chris Mcewan * Linda Smith * Wolfgang Banzhaf * Rene Doursat * Barry Mcmullin * Ricard Sole * Xabier E. Barandiaran * Marc Ebner * Jose Mendes * Antoine Spicher * Andrea Baronchelli * Arantza Etxeberria * Olivier Michel * Peter Stadler * Zoltan Barta * Nazim Fates * Martin Middendorf * Susan Stepney * Jacob Beal * Christoph Flamm * Eduardo Miranda * Charles Taylor * Mark Bedau * Luca Gambardella * Colin Molter * Tim Taylor * Randall Beer * Carlos Gershenson * Luís Moniz Pereira * Gianluca Tempesti * Tony Belpaeme * Mario Giacobini * Sara Montagna * Christof Teuscher * Peter Bentley * Takashi Gomi * Jason Moore * Jon Timmis * Hugues Bersini * Roderich Gross * Federico Moran * Peter Todd * Luc Berthouze * Thilo Gross * Chrystopher L. Nehaniv * Marco Tomassini * Mauro Birattari * Pauline C Haddow * Jason Noble * Arne Traulsen * Joris Bleys * Emma Hart * Stefano Nolfi * Elio Tuci * Josh Bongard * Inman Harvey * Ann Nowe * Gunnar Tufte * Paul Bourgine * Paulien Hogeweg * Charles Ofria * Ali Emre Turgut * Seth Bullock * Phil Husbands * Alexandra Penn * Karl Tuyls * Stefano Cagnoni * Fumiya Iida * Andrew Philippides * Jon Umerez * Alexandre Campo * Yaochu Jin * Raphaël Plasson * Sven Van Segbroeck * Philippe Capdepuy * Colin Johnson * Daniel Polani * Patricia A. Vargas * Ciro Cattuto * Istvan Karsai * Vitorino Ramos * Mirko Viroli * Anders Christensen * Jozef Kelemen * Charles Richter * Paul Vogt * Dominique Chu * Serge Kernbach * Marylyn Ritchie * Richard Watson * Netta Cohen * Daeeun Kim * Luis M. Rocha * Alan Winfield * Luis Correia * Kalevi Kull * Miguel Rocha * Rachel Wood * Ernesto Costa * Renaud Lambiotte * Pierre Rouze * Andrew Wuensche * Tamas Czaran * Doron Lancet * Kepa Ruiz-Mirazo * Larry Yaeger * Christian Darabos * Tom Lenaerts * Erol Sahin * Klauspeter Zauner * Joachim De Beule * Pedro U. Lima * Francisco C. Santos * Tom Ziemke CONTACT --------------------- For further information about the conference program and travel arrangements, please see the website, http://www.ecal11.org. For questions about the submission, reviewing process and other issues, email to: contact(a)ecal11.org.

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