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

position BioExpert project: using knowledge base in systems biology
by AHC van Kampen 03 Aug '10

03 Aug '10

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Postdoc position in systems biology
by Marijn Vandevoorde 02 Aug '10

02 Aug '10

The Division of Bioinformatics and Systems Biology at the VIB Department of Plant Systems Biology, Ghent University invites applications for an Expert Scientist position in the field of Computational Systems Biology. We seek highly-motivated individuals with an interest in developing novel algorithms and software tools for the integration of high-throughput genomic data and the inference and modelling of regulatory networks. The ideal candidate should hold a doctoral degree in a relevant field (physics, computer science, applied mathematics, engineering or life sciences), with several years of postdoctoral experience, and have a proven record of its application for the life sciences. Major duties include: * Responsible for the functioning of a small group of researchers (PhD students and postdocs). * Develop new and innovative (breakthrough) projects in line with the strategic plan of the Department and VIB. * Provide scientists in the Department and VIB with transfer of in-depth knowledge. * Transfer science into publications in high impact journals. * Detect potential technology transfer possibilities. The position will initially be available for 2 years (starting September 1st, 2010), with the possibility of a 3 year extension depending on positive evaluation. For further information please consult our homepage (bioinformatics.psb.ugent.be) or contact the Scientific Director Prof. Dr. Yves Van de Peer (yves.vandepeer(a)psb.vib-ugent.be) Applications including a motivation letter, CV, list of publications, names and contact information of three references and a research proposal (2-3 pages) should be sent to Prof. Dr. Yves Van de Peer before August 31st 2010.

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Position as computational biologist / bioinformatics developer
by Marijn Vandevoorde 02 Aug '10

02 Aug '10

The Bioinformatics & Systems Biology group (http://bioinformatics.psb.ugent.be/) at the VIB Department of Plant Systems Biology studies the structure, function and evolution of biological networks in multiple organisms. As part of its research, the team continuously develops, in collaboration with other Flemish universities, novel software tools for the integration of large-scale data sets and the inference of regulatory networks. In a next phase, VIB wishes to increase and optimize the use of those tools for a variety of large-scale data projects. Such projects will be in collaboration with research groups within VIB as well as with external academic and industrial partners. Therefore, VIB attracts a Computational Biologist/Bioinformatics Developer As a member of VIB's a new bioinformatics project framed in the computational systems biology research group, you will be responsible for the commercialization of our software tools and, in close collaboration with the research scientists, for the development of software usability improvements. Responsibilities include: · Providing consultancy services for software testing and validation: definition of suitable test data sets, NDA, running software and analyzing output together with the company's bioinformatics team. · Developing and implementing software improvements and extensions, especially with regards to usability improvement (user interface, output visualization, etc.) and integration of multiple tools (often written in different programming environments). · Writing project applications (e.g. IWT) for proof-of-concept studies. · Participating in meetings with bio, pharmaceutical, agbio and food companies to present our in-house systems biology software tools. Profile: · PhD in computational or biological sciences, with experience or strong interest in computational systems biology. · Fluent in English. · Excellent communication skills. · Strong interest in technology transfer and research commercialization. · Fluent in multiple programming languages (Java, Matlab, Perl, etc.). · Work experience in industry is a plus. Contact: · If you have the necessary skills and would like to be considered, please send your resume by email to Barbara Leyman (Barbara.Leyman(a)vib.be) Applications will be accepted until the position is filled. -- Marijn Vandevoorde Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM marijn.vandevoorde(a)psb.vib-ugent.be http://www.psb.vib-ugent.be ==================================================================

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Position as system administrator / bioinformatician
by Marijn Vandevoorde 02 Aug '10

02 Aug '10

The Bioinformatics & Systems Biology group (http://bioinformatics.psb.ugent.be/) at the VIB Department of Plant Systems Biology studies the structure, function and evolution of biological networks in multiple organisms. As part of its research, the team continuously develops, in collaboration with other Flemish universities, novel software tools for the integration of large-scale data sets and the inference of regulatory networks. In a next phase, VIB wishes to increase and optimize the use of those tools for a variety of large-scale data projects. Such projects will be in collaboration with research groups within VIB as well as with external academic and industrial partners. Therefore, VIB attracts a System Administrator/Bioinformatician As a member of VIB's a new bioinformatics project framed in the computational systems biology research group, you will be responsible for the evolution and support of our software tools and, in close collaboration with the other project team members (computational biologist and bioinformatics developers), for the development of software usability improvements. Responsibilities include: · Develop an appropriate platform to use software in a separate smooth running environment capable of handling the analysis needs in isolation from the main VIB system. Such platform includes the optimization of software access, security, storage, flexibility of location. The platform supports the development of production systems, workflow and web portals. · Develop and deploy VMware based approach to the platform to allow systems to be moved and implemented in a hardware independent manner. · Implementation and support of system and user requirements tracking tools including “bug tracking” and improvement monitoring. · System Admin would also support the needs of both Computational Biologists on a daily basis Profile: · Bachelor in Informatics or Master in Industrial Sciences. · Fluent in English. · Excellent communication skills. · A strong history of Bioinformatics support/development or a supporting role in such an environment · Fluent in multiple programming languages (Java, Matlab, Perl, PHP, etc.) and excellent knowledge of Linux servers. Contact: · If you have the necessary skills and would like to be considered, please send your resume by email to Barbara Leyman (Barbara.Leyman(a)vib.be) Applications will be accepted until the position is filled. -- Marijn Vandevoorde Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM marijn.vandevoorde(a)psb.vib-ugent.be http://www.psb.vib-ugent.be ==================================================================

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Academic position in statistical methods for high throughput genomics experiments
by Marijn Vandevoorde 02 Aug '10

02 Aug '10

A full-time position with a starting rank as Professor in the rank of Lecturer in Ghent University’s Faculty of Bioscience Engineering, department of Applied Mathematics, Biometrics and Process Control will be available via the Tenure Track system with effect from 1 February 2011. The position will be part of the Multidisciplinary Research Partnership (MRP) “Bloinformatics: from nucleotides to networks”. A short description of the MRP follows. For bioinformatics and systems biology to be truly successful, computer scientists, physicists, mathematicians, statisticians, engineers, and molecular biologists need to join forces. Bioinformatics is a very interdisciplinary field of research and scientists with different backgrounds will need to work closely together to (1) deal with the ever-growing avalanche of data, (2) serve an ever-demanding community of molecular experimental biologists, bioengineers, and medical doctors, and (3) to address the bigger questions in biology through integrated systems biology approaches. The MRP team has the objective 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 modelling biological networks), and 4) apply these tools and approaches to Sustainable Agriculture and Successful Aging. This ambitious project joins the expertise of fourteen excellent research teams from five different faculties (Science, Bioengineering, Engineering, Pharmaceutical Sciences and Medicine The position will be granted in the following academic field: Statistical methods for high throughput genomics experiments, particularly next generation sequencing studies using multiple platforms (Illumina, Roche 454, SOLiD, Complete Genomics, others). The position involves developing, applying and integrating statistical and computational pipelines for designing, analyzing and visualizing high throughput genomic experiments. The position also involves assisting with the design and data analyses of experiments that are conducted at the NXTGNT sequencing facility of Ghent University. This is initially a five-year temporary appointment in a Tenure Track system focussing primarily on research, with a teaching load limited to max. 60 teaching hours per semester. Teaching activities will be primarily related to statistics education. If the university board evaluates the performance of the appointed staff member positively, the position will lead to a permanent position as Senior Lecturer, 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 - Have carried out outstanding scientific research in the field of study concerned, that is proven by research output of a high level in peer-reviewed international publications (journals and/or books); - Have strong didactic, communicative and organisational skills; - Have experience in heading up research projects and/or coaching PhD students; - Have acquired international academic experience; The governing language at Ghent University is Dutch. However, persons who do not speak Dutch as a native language are welcome to apply and are expected to acquire a working knowledge of the language. Applications must be sent in duplicate by registered post 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 short description will be made available. The deadline is 7 September 2010. The date of posting is accepted as the date of receipt. Further information concerning these vacancies can be requested from the Faculty of Bioscience Engineering (Yves.VanDePeer(a)UGent.be) The required application form for this position can be requested from Ghent University, F.A.O. Department of Personeel and Organisation, Sint-Pietersnieuwstraat 25, 9000 Ghent, or requested via telephone on. +32 (0)9 264 31 29 or +32 (0)9 264 31 30. The required application for is also available on the internet http://www.ugent.be/nl/werken/aanwerving/formulieren/zap/formulier.doc/view -- Marijn Vandevoorde Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM marijn.vandevoorde(a)psb.vib-ugent.be http://www.psb.vib-ugent.be ================================================================== -- Marijn Vandevoorde Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM marijn.vandevoorde(a)psb.vib-ugent.be http://www.psb.vib-ugent.be ================================================================== "Have you tried turning it off and on again?" --Roy Trenneman

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Academic position in computational biology
by Marijn Vandevoorde 02 Aug '10

02 Aug '10

A full-time position with a starting rank as Professor in the rank of Lecturer in Ghent University’s Faculty of Science, Department of Plant Biotechnology and Genetics, Department of Plant Biotechnology and Genetics, will be available via the Tenure Track system with effect from 1 February 2011. The position will be part of the Multidisciplinary Research Partnership on Bioinformatics, an interdisciplinary field that brings together the expertise of scientists with different backgrounds to solve problems in (molecular) biology through computational means. A short description can be found on: http://www.ugent.be/nl/onderzoek/beleid/projectplanVANDEPEER.pdf The position will be granted in the academic field of Bioinformatics more specific in the field of Computational Biology. This new Academic Staff member will be granted the privilege of focusing primarily on research with only a limited teaching responsibility for a period of five years. Subsequently, the time devoted to education, research and service to society may be altered by the university management. A full time position in the rank of Lecturer leads to a temporary 5-year tenure track appointment. Subsequently, this period will result in a permanent position as Senior Lecturer if the candidate’s performance is evaluated positively by the university board. A position in the rank of Lecturer includes: - a full-time tenure track position; - a 5-year contract which, subject to a positive evaluation, will become a permanent position; - terms of employment equivalent to all autonomous academic staff of Ghent University. Profile: the candidate should: - hold a PhD degree with doctoral thesis or a degree recognized as equivalent, and have at least two years of post-doctoral research experience by February 1st, 2011; - have carried out excellent research in their field of study, proven by, among other things, recent outstanding publications in national and international peer reviewed journals and/or books; - have experience in supervising research and/or coaching Ph.D. students; - international mobility is recommended, e.g. through research stays at institutes other than the university where the highest degree was obtained; - possess the necessary didactic, organisational and communication skills; - the ideal candidate has research experience in the field data mining and machine learning, systems biology, and/or computational biology; The governing language at Ghent University is Dutch. However, persons who do not speak Dutch as a native language are welcome to apply and are expected to acquire a working knowledge of the language. Applications must be sent in duplicate by registered post 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 short description will be made available. The deadline is 7 September 2010. The date of posting is accepted as the date of receipt. Further information concerning these vacancies can be requested by contacting Prof. Anna Depicker (Anna.Depicker(a)UGent.be; + 32 (0)9 33 13 940), chair or by contacting Prof. Yves Van de peer, (Yves.VandePeer(a)UGent.be; + 32 (0)9 33 13 807). The required application form for this position can be requested from Ghent University, F.A.O. Department of Personnel and Organisation, Sint-Pietersnieuwstraat 25, 9000 Ghent, or requested via telephone on. +32 (0)9 264 31 29 or +32 (0)9 264 31 30. The required application form is also available on the internet, http://www.ugent.be/nl/werken/aanwerving/formulieren/zap/formulier.doc/view -- Marijn Vandevoorde Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM marijn.vandevoorde(a)psb.vib-ugent.be http://www.psb.vib-ugent.be ==================================================================

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Academic position in high performance computing in systems biology
by Marijn Vandevoorde 02 Aug '10

02 Aug '10

A full-time position with a starting rank as Professor in the rank of Lecturer in Ghent University’s Faculty of Engineering, Department of Information Technology will be available via the Tenure Track system with effect from 1 October 2011. The position will be part of the Multidisciplinary Research Partnership on Bioinformatics, an interdisciplinary field that brings together the expertise of scientists with different backgrounds to solve problems in (molecular) biology through computational means. The position will be granted in the following academic field: High Performance Computing in Systems Biology. This is initially a five-year temporary appointment in a Tenure Track system focussing primarily on research, with a teaching load limited to max. 60 teaching hours per semester. If the university board evaluates the performance of the appointed staff member positively, the position will lead to a permanent position as Senior Lecturer, at which point the teaching load may be revised. Profile: the candidate should: - meet the degree requirements (PhD in Engineering 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 October 2004, but not later than 1 October 2009. - have carried out outstanding scientific research in the field of study concerned, that is proven by research output of a high level in peer-reviewed international publications (journals and/or books). - have strong didactic, communicative and organisational skills. - have experience in heading up research projects and/or coaching PhD students. - have acquired international academic experience. The governing language at Ghent University is Dutch. However, persons who do not speak Dutch as a native language are welcome to apply and are expected to acquire a working knowledge of the language. Applications must be sent in duplicate by registered post 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 short description will be made available. The deadline is 17 January 2011. The date of posting is accepted as the date of receipt. Further information concerning these vacancies can be requested from the Faculty of Engineering, Department of Information Technology, Prof. Daniël De Zutter (Daniel.DeZutter(a)UGent.be) The required application form for this position can be requested from Ghent University, F.A.O. Department of Personnel and Organisation, Sint-Pietersnieuwstraat 25, 9000 Ghent, or requested via telephone on. +32 (0)9 264 31 29 or +32 (0)9 264 31 30. The required application form is also available on the internet: http://www.ugent.be/nl/werken/aanwerving/formulieren/zap/formulier.doc/view. -- Marijn Vandevoorde Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM marijn.vandevoorde(a)psb.vib-ugent.be http://www.psb.vib-ugent.be ==================================================================

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PRIB (submission deadline 9 August): short papers and poster submission
by Elena Marchiori 02 Aug '10

02 Aug '10

- Apologies for multiple postings - Please distribute within your lab - Dear Colleague, We are inviting submissions for short papers and poster abstracts at PRIB 2010. The deadline has been extended to ** 9 August **. Kind regards, The PRIB 2010 Organizing Committee ---- *** PRIB 2010: Call for short papers and poster abstracts *** http://www.prib2010.org/ The Pattern Recognition in Bioinformatics conference aims to bring together top researchers, practitioners and students from around the world to discuss the applications of pattern recognition methods in the field of bioinformatics to tackle problems in the life sciences. Prospective authors are invited to submit papers in the research areas of interest to the conference. These include: •Bio-sequence analysis •Gene and protein expression analysis •Protein structure and interaction prediction •Motifs and signal detection •Metabolic modelling and analysis •Systems and synthetic biology •Pathway and network analysis •Immuno- and chemo-informatics •Evolution and phylogeny •Biological databases, integration and visualisation •Bio-imaging Pattern recognition techniques of interest include, but not limited to: •Static, syntactic and structural pattern recognition •Data mining, Data based modelling •Neural networks, Fuzzy systems •Evolutionary computation and swarm intelligence •Hidden Markov models, Graphical models We are inviting submissions of short papers (up to 6 pages in LNCS formats) and poster abstracts (up to 1 page) in all the areas of relevance to the conference. Accepted short papers will be published in the PRIB 2010 supplementary proceedings. Authors of both short papers and abstracts will be expected to present their work in the form of a poster at the conference. To submit short papers select the "Short Paper" category in the EasyChair submission system. Important Dates •Short Paper Submission: 9 August 2010 •Author Notification: 15 August 2010 •Early Bird Registration: 20 August 2010

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Academic position in comparative genomics
by Marijn Vandevoorde 02 Aug '10

02 Aug '10

A full-time position with a starting rank as Professor in the rank of Lecturer in Ghent University’s Faculty of Science, Department of Plant Biotechnology and Genetics, Department of Plant Biotechnology and Genetics, will be available via the Tenure Track system with effect from 1 February 2011. The position will be part of the Multidisciplinary Research Partnership on Bioinformatics, an interdisciplinary field that brings together the expertise of scientists with different backgrounds to solve problems in (molecular) biology through computational means. A short description can be found on: http://www.ugent.be/nl/onderzoek/beleid/projectplanVANDEPEER.pdf The position will be granted in the academic field of Bioinformatics more specific in the field of Comparative Genomics. This is initially a five-year temporary appointment in a tenure track system focusing primarily on research, with a teaching load limited to max. 60 teaching hours per semester. If the university board evaluates the performance of the appointed staff member positively, the position will lead to a permanent position as Senior Lecturer, at which point the teaching load may be revised. A position in the rank of Lecturer includes: - a full-time tenure track position; - a 5-year contract which, subject to a positive evaluation, will become a permanent position; - terms of employment equivalent to all autonomous academic staff of Ghent University. Profile: the candidate should: - Meet the degree requirements (PhD based on a doctoral thesis or an equivalent degree), 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; - have carried out outstanding scientific research in the field of study concerned, that is proven by research output of a high level in peer-reviewed international publications (journals and/or books); - have experience in heading up research projects and/or coaching PhD students; - international mobility is recommended, e.g. through research stays at institutes other than the university where the highest degree was obtained; - have strong didactic, communicative and organizational skills; - the ideal candidate has a strong background in comparative and integrative genomics and tool development. The governing language at Ghent University is Dutch. However, persons who do not speak Dutch as a native language are welcome to apply and are expected to acquire a working knowledge of the language. Applications must be sent in duplicate by registered post 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 short description will be made available. The deadline is 7 September 2010. The date of posting is accepted as the date of receipt. Further information concerning these vacancies can be requested by contacting Prof. Anna Depicker (Anna.Depicker(a)UGent.be; + 32 (0)9 33 13 940), chair or by contacting Prof. Yves Van de peer, (Yves.VandePeer(a)UGent.be; + 32 (0)9 33 13 807). The required application form for this position can be requested from Ghent University, F.A.O. Department of Personnel and Organisation, Sint-Pietersnieuwstraat 25, 9000 Ghent, or requested via telephone on. +32 (0)9 264 31 29 or +32 (0)9 264 31 30. The required application form is also available on the internet: http://www.ugent.be/nl/werken/aanwerving/formulieren/zap/formulier.doc/view. -- Marijn Vandevoorde Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM marijn.vandevoorde(a)psb.vib-ugent.be http://www.psb.vib-ugent.be ==================================================================

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positions for PhD students
by laurence lins 02 Aug '10

02 Aug '10

Please find hereby two positions for PhD students at ULg-Gembloux ABT. -- Dr Laurence Lins Maître de recherches FNRS Centre de Biophysique Moléculaire Numérique Université de Liège-Gembloux Agro Bio Tech Passage des Déportés,2-5030 Gembloux-Belgium Tél : (00-32) (0)-81-622534 Fax : (00-32) (0)-81-622522 Email : l.lins@ulg.ac.be/lins.l@fsagx.ac.be

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