- BBClist - maillist.psb.ugent.be

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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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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