March 2013 - BBClist - maillist.psb.ugent.be

Computational Cancer Biology Positions
by Lodewyk Wessels 12 Jul '13

12 Jul '13

COMPREHENSIVE COMPUTATIONAL MODELING FOR COMBINATION TREATMENT DESIGN PROJECT OUTLINE All cancers arise due to alterations in their genomes. Although insight into the genetic lesions in tumors by genome sequencing does already assist in selecting some drug regimens, it rarely results in disease eradication due to the emergence of drug-resistance. More sophisticated combination therapies in which several oncogenic pathways are targeted simultaneously could alleviate this problem. However, at present we are unable to extract and interpret the necessary information from tumors to predict which drug regimen will be most adequate. In this project we will collaborate with Welcome Trust Sanger Center and employ the 1000 cancer cell line data set to tackle this problem. This data set comprises large-scale molecular characterization and cancer drug screening of all cell lines for 400 anti-cancer drugs. The molecular data currently consists of gene expression, copy number (SNP-6), and whole exome sequencing data and is being expanded. The successful candidate will work closely with scientists at the Welcome Trust Sanger Center and the Netherlands Cancer Institute and employ computational approaches to mine this rich, valuable pre-clinical resource. Potential results include 1) new molecular biomarkers to identify sensitive populations 2) repositioning of existing drugs in other tumor types and 3) potential drug combinations aimed at overcoming resistance mechanisms. Hypotheses emerging from these analyses will be validated in model systems and where possible in clinical settings. CANDIDATE REQUIREMENTS – EDUCATION AND EXPERIENCE We are seeking highly motivated Postdoc or PhD candidates with a degree in bioinformatics, computer science, mathematics or physics and with a strong cancer biology interest. Preferably applicants should have a documented experience in analyzing high-throughput genomic data. The candidate needs to be proficient in common bioinformatics scripting and programming languages. Fluency in spoken and written English is a strong requirement. LOCATION The project involves groups at the Netherlands Cancer Institute, Amsterdam (Rene Bernards, Molecular Carcinogenesis, and Lodewyk Wessels, Computational Biology) and the Welcome Trust Sanger Institute (Mathew Garnet and Ultan McDermott, Cancer Genome Project). This position will be embedded in the Computational Biology Group lead by Lodewyk Wessels. CONTACT DETAILS Please contact Lodewyk Wessels, tel. +31 20 512 7987 or e-mail: l.wessels(a)nki.nl. When applying, please ensure you include a CV, list of publications and the names and addresses of at least two persons that can be approached as references. Also see bioinformatics.nki.nl for further information. CLOSING DATE 3 February 2013

1 1

NBIC PhD course on Managing Life Science Information: registration is open!
by Celia van Gelder 01 May '13

01 May '13

*NBIC PhD Course on Managing Life Science Information (2nd edition) *Course coordinators: Marco Roos, Scott Marshall _Date:_ 17-21 October 2011 (one week of tutorials) and a final workshop on Friday 28 October 2011 to discuss project results _Location:_ Science Park, Amsterdam _Registration:_ http://www.nbic.nl/education/nbic-phd-school/enrolment/ _Website: _http://www.nbic.nl/education/nbic-phd-school/course-schedule/managing-life-science-information/ Did you ever suspect that the data that you need is somewhere but neither discoverable nor accessible? Have you ever produced valuable data that nobody can use anymore, including yourself? Have you ever wondered how to create a federation of distributed data sources? If you do not want your data to end up in a data graveyard, and for many other information management issues, we have organised a course for you. In this course we will teach you methods to make data shareable and self-describing. You will learn how: 1. the 'Linked Data' principle works and how it can be applied for 'meaningful' data integration 2. to expose your local data (including relational databases) for use in other systems. 3. Web Services can be used to analyse data from anywhere. 4. text mining can be applied to link resources such as biobanks. 5. human knowledge can be made computable and associated with data. 6. to make your data publishable artifacts for which you can get scientific credit. 7. to use tools such as MolGenis <http://www.molgenis.org/>, Taverna <http://www.taverna.org.uk/>, SPARQL <http://www.w3.org/TR/sparql11-query/>, D2RQ <http://www4.wiwiss.fu-berlin.de/bizer/d2rq/>, SWObjects <http://tinyurl.com/swobjects-swat4ls>, NCBO's BioPortal <http://bioportal.bioontology.org/>, Anni <http://www.biosemantics.org/index.php?page=anni-2-0>, LarKC <http://larkc.org/>(Large Knowledge Collider). 8. to collaboratively solve an information management problem _Program_ (tentative) Monday: Introduction by leading Semantic Web expert Prof. Dr. Frank van Harmelen; Hands-on with RDF and SPARQL (Scott Marshall) Tuesday: XML, RDF, Minimal information models, and exposing data from local databases (Scott Marshall); hands-on with MolGenis (Erik Roos) Wednesday: Data integration with Web Services (Katy Wolstencroft); hands-on with Taverna (Katherine Wolstencroft) Thursday: Knowledge management and nano-publication (Andrew Gibson); hands-on federated queries with SWObjects (Scott Marshall) Friday: Text mining for linking biobanks and hands-on with Anni (Marco Roos, Kristina Hettne); Hands-on with LarKC (Spyros Kotoulas); DRINKS!!! -- 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

2 2

Bio-statistics course using R/Bioconductor for beginners
by Hebels D (TGX) 28 Mar '13

28 Mar '13

Dear all, >From May 14-16 the European Bioinformatics Institute (EBI) in Cambridge is organizing a microarray data analysis course using R/Bioconductor aimed at researchers and scientists. This course will provide participants with a basic understanding of the R syntax and ability to manipulate R objects and as such no prior knowledge of R or Bioconductor is assumed. After this course students should feel comfortable with the R/Bioconductor environment and be in a position to continue their own explorations of the functionality of R and start using R for their basic biostatistics needs. In addition the course will focus on performing quality control analysis and data exploration methods on your microarray data. More information can be found here: http://www.dixa-fp7.eu/dixa-training/dixa-training-agenda/dixa-microarray-t… If you know other people who might benefit from this course, feel free to forward this email to them or hand out the attached flyer. Regards, Dennie [cid:image002.jpg@01CE2A2C.0CBAA810] Dr. Dennie Hebels Post-doctoral fellow Department of Toxicogenomics (TGX) d.hebels(a)maastrichtuniversity.nl<mailto:d.hebels@maastrichtuniversity.nl> www.maastrichtuniversity.nl<http://www.maastrichtuniversity.nl/> / www.toxicogenomics-um.nl<http://www.toxicogenomics-um.nl/> Universiteitssingel 50, Room F4.112 P.O. Box 616, 6229 ER Maastricht, The Netherlands T +31 (0)43 3882127 F +31 (0)43 3884146

1 0

NBIC 2013 Conference: registration deadline April 1
by Barbara van Kampen 25 Mar '13

25 Mar '13

Dear all, The registration deadline for the NBIC 2013 conference is *April 1, 2013 *At this event also the NSBM Spring meeting will take place. Program and registration form can be found at: http://www.aanmelder.nl/nbic2013/* * with kind regards, Barbara van Kampen -- Barbara van Kampen CMBI 260 Radboud University Nijmegen-Medical Centre / NCMLS CMBI Office / Room 0.02 PO Box 9101 Geert-Grooteplein 26-28 6500 HB Nijmegen 6525 GA Nijmegen Phone: +31(0)24 36 19390 Fax: +31 (0)24 36 19395 www.cmbi.ru.nl

1 0

Tiscornia Park and LMC
by adamsas5＠msu.edu 23 Mar '13

23 Mar '13

Hello everyone, Did some birding at Tiscornia Park. Had well over 200 WW Scoters, some gorgeous male Long-tailed Ducks, some Horned Grebe (some in breeding plumage), red-throated and common loon, and Glaucous Gull along with the regular smattering of Scaups and Mergansers. I also did a quick stop at LMC. Mostly Canada Geese, but there were some redheads, a hooded merg, and my FOY green-winged Teal. Happy Birding! Ashely Adams

1 0

Eighth Summer School on Advanced Statistics and Data Mining (Madrid, June 24th - July 5th, 2013)
by Rubén Armañanzas 20 Mar '13

20 Mar '13

Dear colleagues, The Technical University of Madrid (UPM) will once more organize the summer school on 'Advanced Statistics and Data Mining' in Madrid between June 24th and July 5th. This year's programme comprises 12 courses divided into 2 weeks. Attendees may register in each course independently. Early registration is now *OPEN*. Extended information on course programmes, price, venue, accommodation and transport is available at the school's website: http://www.dia.fi.upm.es/ASDM <http://www.dia.fi.upm.es/ASDM> Please, send this information to your colleagues, students, and whoever may find it interesting. Best regards, Pedro Larrañaga, Concha Bielza and Pedro L. López-Cruz. -- The coordinators of the school. *** List of courses and brief description *** * Week 1 (June 24th - June 28th, 2013) * 1st session: 9:30 - 12:30 Course 1: Bayesian networks (15 h) Basics of Bayesian networks. Inference in Bayesian networks. Learning Bayesian networks from data. Real applications. Course 2: Statistical inference (15 h) Introduction. Some basic statistical test. Multiple testing. Introduction to bootstrap methods. Introduction to Robust Statistics. 2nd session: 13:30 - 16:30 Course 3: Supervised pattern recognition (15 h) Introduction. Assessing the performance of supervised classification algorithms. Preprocessing. Classification techniques. Combining multiple classifiers. Comparing supervised classification algorithms. Course 4: Multivariate data analysis (15 h) Introduction. Data examination. Principal component analysis. Factor Analysis. Multidimensional scaling. Correspondence analysis. Tensor analysis. Multivariate Analysis of Variance. Canonical Correlation Analysis. Latent Class Analysis. 3rd session: 17:00 - 20:00 Course 5: Neural networks (15 h) Introduction. Perceptrons. Training algorithms. Accelerating convergence. Useful tricks for MLPs. Deep networks. Practical data modelling with neural networks. Course 6: Feature Subset Selection (15 h) Introduction. Filter approaches. Wrapper methods. Embedded methods. Drawbacks and future strands. Practical session. * Week 2 (July 1st - July 5th, 2013) * 1st session: 9:30 - 12:30 Course 7: Time series analysis (15 h) Introduction. Probability models to time series. Regression and Fourier analysis. Forecasting and Data mining. Course 8: Hidden Markov Models (15 h) Introduction. Discrete Hidden Markov Models. Basic algorithms for Hidden Markov Models. Semicontinuous Hidden Markov Models. Continuous Hidden Markov Models. Unit selection and clustering. Speaker and Environment Adaptation for HMMs. Other applications of HMMs. 2nd session: 13:30 - 16:30 Course 9: Bayesian classifiers (15 h) Discrete predictors. Gaussian Bayesian networks-based classifiers. Other Bayesian classifiers. Bayesian classifiers for: positive and unlabeled data, semi-supervised learning, data streams, temporal data. Course 10: Unsupervised pattern recognition (15 h) Introduction. Prototype-based clustering. Density-based clustering. Graph-based clustering. Cluster evaluation. Miscellanea. 3rd session: 17:00 - 20:00 Course 11: Support vector machines, regularization and convex optimization (15 h) Introduction. SVM models. SVM learning algorithms. Convex non differentiable optimization. Course 12: Hot topics in intelligent data analysis (15 h) Multi-label and multi-dimensional classification. Multi-dimensional classification and multi-output regression. Advanced Clustering. Partially supervised classification with uncertain class labels. Directional statistics. Spatial point processes.

1 0

Fwd: Registration open: Black Forest Summer School on Bioinformatics for Molecular Biologists
by Klaas Vandepoele 20 Mar '13

20 Mar '13

Dear, please find attached the flyer for the summer school. The homepage can be accessed at http://plantco.de/BFSS2013/ - I would be grateful if you could distribute this information to potentially interested institutions and persons. Thanks and kind regards, Stefan Rensing -- Stefan A. Rensing, PhD Prof., Department of Cell Biology Faculty of Biology, University of Marburg Karl-von-Frisch-Str. 8, D-35043 Marburg http://plantco.de/ stefan.rensing(a)biologie.uni-marburg.de "Everything is backwards now, like out there is the true world, and in here is the dream."

1 0

Vacancy senior scientist bioinformatics at Galapagos
by Véronique Deiteren 15 Mar '13

15 Mar '13

Please find the vacancy at Galapagos for a Senior Scientist bioinformatician. Galapagos is a mid-size, clinical stage biotechnology company active in discovery and development of small molecule and antibody therapies, many of which are based on proprietary disease-modifying drug targets in disease areas for which there is a need for safe and effective medicines. Galapagos funds its research through alliance payments from its pharma partners, cash generated by its profitable service operations, licensing agreements, and its cash reserves. GLPG0634, its most advanced program in Phase II, is partnered with AbbVie for up to $1.35 billion in milestones and double-digit royalties. Together with service operations BioFocus, Argenta and Fidelta, Galapagos' research activities across Europe are successful thanks to our highly motivated staff of more than 800 employees, a unique technology base, and a strong financial position. For our site in Mechelen, we are looking for a Senior Scientist Bioinformatics (m/f) full time MEC 115 Job description As member of the Information Sciences group you will provide day to day bioinformatics support to research teams using dedicated bioinformatics software, in support of the various target and drug discovery projects at Galapagos. You will carry out target annotations: collecting, analyzing, storing and reporting assay, DNA and protein sequence, pathway, toxicity, druggability and related data, You will support project teams in experiment design and in complex analysis of large data sets (eg. microarray data analysis). You will collect bioinformatics-related end-user requirements and propose solutions. You will adapt or co-develop new bioinformatics applications and/or contribute to the implementation of third-party software. You will support the research teams in optimally using these tools. You will closely collaborate with multidisciplinary disease biology and drug discovery teams, the Discovery Informatics group and possible outsourcing partners. Required skills and Experience: · PhD in bioinformatics/biology/chemistry or equivalent through experience, with demonstrated track record in bioinformatics. 5 years of working experience, some of it in industry. · Good Bioinformatics skills (multiple sequence alignment, expression data analysis, pathway analysis, clustering, data and text mining, proteomics, etc.) · Good understanding of statistics and experimental design. Good knowledge of R or equivalent environment is a plus. · Good scientific computing skills: programming expertise (e.g., in C#, Java, Perl or Python), database query experience (e.g., SQL) and a working knowledge of Linux are desirable. The aptitude and zeal to acquire any of these skills are essential. At Galapagos we aim to recruit the best people, who stand out among their peers, with integrity and excellent interpersonal and organizational skills. Our employees are the strength behind Galapagos, a highly motivated team, eager to maintain Galapagos' leading position and achieve breakthroughs in pharmaceutical research. Do you have the qualifications for this job opening, and are you up to the challenge of joining our entrepreneurial team? If so, please send your application (preferably by e-mail) to: Galapagos NV - Human Resources Generaal De Wittelaan L11 A3 B-2800 Mechelen, Belgium E-mail: jobs_be(a)glpg.com<mailto:jobs_be@glpg.com> -- This e-mail and its attachment(s) (if any) may contain confidential and/or proprietary information and is intended for its addressee(s) only. Any unauthorized use of the information contained herein (including, but not limited to, alteration, reproduction, communication, distribution or any other form of dissemination) is strictly prohibited. If you are not the intended addressee, please notify the originator promptly and delete this e-mail and its attachment(s) (if any) subsequently. Neither Galapagos nor any of its affiliates shall be liable for direct, special, indirect or consequential damages arising from alteration of the contents of this message (by a third party) or as a result of a virus being passed on.

1 0

PhD position in Amsterdam: Computational biomechanics of extracellular matrix materials and cell-matrix interactions during blood vessel growth
by Roeland Merks 15 Mar '13

15 Mar '13

Centrum Wiskunde & Informatica (CWI) is the Dutch national research institute for mathematics and computer science and linked to the Netherlands Organisation for Scientific Research(NWO). The mission of CWI is to conduct pioneering research in mathematics and computer science, generating new knowledge in these fields and conveying it to trade, industry, and society at large. CWI is located at Science Park Amsterdam. It is an internationally oriented institute, with 160 scientists from approximately 27 countries. The facilities are first-rate and include excellent IT support, career planning, training, and courses. The Life Sciences research group has a vacancy for a talented PhD student, on the subject of: Computational biomechanics of extracellular matrix materials and cell-matrix interactions during blood vessel growth. The opening is a research position within the field of applied mathematics or computational science. Research group: The work will be embedded in the Biomodeling and Biosystems Analysis group at the CWI in Amsterdam. The group carries out biomodeling research with experimental collaborators working, and focuses on modelling pattern formation and morphogenesis in multicellular organisms. Job description: The outgrowth of new blood vessels from pre-existing vessels, called angiogenesis, is a crucial step in wound healing and tumor growth. Cell-based simulation models help to analyze how cells assemble into blood vessels and other tissue structures. Present cell-based numerical techniques, including the cellular Potts model, lack an accurate description of the biochemistry and biomechanics of one of the main controlling factors of angiogenesis and tumor progression: the extracellular matrix (ECM). The ECM is a diverse class of jelly or hard materials providing structural support to the tissue. The ECM also acts as a medium for cell-cell communication. As part of an NWO-funded Vidi-project on angiogenesis, your task will be to develop and apply state-of-the-art and efficient numerical methods for simulating the biomechanics of the ECM. These partial-differential equation and/or agent-based simulations will interface naturally with pre-existing, stochastic models of endothelial cell behavior. You will also integrate the codes into an existing, internationally developed open-source cell-based modeling framework, called CompuCell3D, and will perform numerical simulation experiments. You will interact closely with a PhD-student in applied computational biology and with experimental biologists at the Institute for Cardiovascular Research of the VU University Medical Center in Amsterdam. Requirements: Candidates are required to have a Master’s degree in applied mathematics, computational physics, theoretical biology, computer science or a related discipline, and able to communicate with scientists in biology and mathematics. Preferable qualifications for candidates include proven research talent, excellent programming skills in C++ or willingness and ability to learn, an excellent command of English, and good academic writing and presentation skills. Terms and conditions" The terms of employment are in accordance with the Dutch Collective Labour Agreement for Research Centres ("CAO-onderzoeksinstellingen"). The gross monthly salary, for a PhD student on a full time basis, is €2,057 during the first year and increases to €2,636 over the four year period. Employees are also entitled to a holiday allowance of 8% of the gross annual salary and a year-end bonus of 8,33%. CWI offers attractive working conditions, including flexible scheduling and help with housing for expat employees. Application: Applications can be sent before 8 April 2013 to apply(a)cwi.nl. All applications should include a detailed resume, motivation letter, list of your MSc courses and grades, copy of your Master’s thesis and preferably a list of publications. For more information about the vacancy, please contact dr. Roeland Merks, email Roeland.Merks(a)cwi.nl, telephone +31(0)20 592 4117. For more information about CWI, please visit www.cwi.nl. More information about the group can be found on http://biomodel.project.cwi.nl. Or watch our video “A Fundamental Difference” about working at CWI: https://www.cwi.nl/general/a-fundamental-difference.

1 0

2013 Galaxy Community Conference (GCC2013), 30 June - 2 July, Oslo
by Dave Clements 12 Mar '13

12 Mar '13

Hello all, We are pleased to announce that early registration<http://wiki.galaxyproject.org/Events/GCC2013/Register> and paper and poster abstract submission<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts> are now open for the 2013 Galaxy Community Conference (GCC2013)<http://wiki.galaxyproject.org/Events/GCC2013> . GCC2013 will be held 30 June through July 2 in Oslo Norway, at the University of Oslo <http://uio.no/>. GCC2013 <http://wiki.galaxyproject.org/Events/GCC2013> is an opportunity to participate in two full days of presentations, discussions, poster sessions, keynotes, lightning talks and breakouts, *all about high-throughput biology and the tools that support it*. The conference also includes a Training Day<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> for the second year in a row, this year with more in-depth topic coverage, more concurrent sessions, and more topics. If you are a biologist or bioinformatician performing or enabling high-throughput biological research, then please consider attending. GCC2013 is aimed at: - Bioinformatics tool developers and data providers - Workflow developers and power bioinformatics users - Sequencing and Bioinformatics core staff - Data archival and analysis reproducibility specialists *Early registration <http://wiki.galaxyproject.org/Events/GCC2013/Register>* *saves up to 75% off regular registration costs,* and is very affordable, with combined registration (Training Day<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> + main meeting) starting at ~ €95 for post-docs and students. Registering early also assures you a spot in the Training Day workshops you want to attend. Once a Training Day session becomes full, it will be closed to new registrations. Early registration closes 24 May. *Abstract submission<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts> * for oral presentations closes 12 April, and for posters on 3 May. Please consider presenting your work. If you are working with big biological data, then the people at this meeting want to hear about your work. Thanks, and hope to see you in Oslo! The GCC2013 Organizing Committee<http://wiki.galaxyproject.org/Events/GCC2013/Organizers> PS: And please help get the word out<http://wiki.galaxyproject.org/Events/GCC2013/Promotion> ! -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

1 0