- BBClist - maillist.psb.ugent.be

Job Opening: Bioinformatician at OpenAnalytics (Belgium)
by tobias.verbeke＠openanalytics.eu 24 Jul '12

24 Jul '12

OpenAnalytics is an international company providing data analysis services and products across geographies and industrial sectors. We are currently looking to expand our team of bioinformaticians with a candidate who fits the following profile: Bioinformatician: MSc / PhD in Computational Biology, Bioinformatics or Computer Science A detailed description can be found at http://www.openanalytics.eu/jobs Kind regards, Tobias Verbeke -- Tobias Verbeke Manager OpenAnalytics BVBA Kortestraat 30A 2220 Heist-op-den-Berg Belgium E tobias.verbeke at openanalytics.eu M +32 499 36 33 15 http://www.openanalytics.eu

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NGS workshop Ghent
by Michiel Van Bel 23 Jul '12

23 Jul '12

Dear, The Bioinformatics and Systems Biology division of the Department of Plant Systems Biology (VIB -- Ghent University) is organizing a scientific event from the 25th of November 2012 until the 5th of December 2012 about *Generation and Analysis of Next Generation Sequence (NGS) data*. This two-week workshop is sponsored by the *European Science Foundation (ESF)*, and will discuss recent advances and future perspectives in next generation sequence analysis, together with the necessary applications on the data of user submitted projects. The workshop is open to participants from across Europe, and is *fully reimbursed* (see http://bioinformatics.psb.ugent.be/ngs_workshop/workshop/registration) through the ESF. Applicants will need to fill in a one page motivation letter which will allow us to identify individuals with suitable bioinformatics experience. The deadline to submit an application is August 15. Please visit http://bioinformatics.psb.ugent.be/ngs_workshop/ for more information. kind regards, The organizing commitee PS: Can this information also be spread to interested European colleagues not subscribed to the BBC-list? -- ================================================================== Michiel Van Bel PhD student 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 mibel(a)psb.vib-ugent.be http://www.psb.vib-ugent.be http://bioinformatics.psb.ugent.be ==================================================================

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Position Available: Bioinformatics & Integrative Genomics Specialist, VIB & KU Leuven
by Stein Aerts 19 Jul '12

19 Jul '12

Bioinformatics & Integrative Genomics Specialist - Manager Bioinformatics Consulting Core The VIB Center for the Biology of Disease at the University of Leuven is a vibrant and international research centre where key issues relevant to major human health challenges are tackled. Within this Center, we are seeking a highly motivated and experienced Bioinformatics & Integrative Genomics Specialist. You will collaborate with the 14 research groups within the Center and provide essential input on computational biology aspects of their research projects. In this job you will be confronted with exciting research questions in cancer and neurodegeneration; and with a broad spectrum of computational challenges and omics data sets. You will be embedded in the Laboratory of Computational Biology at the University of Leuven (Stein Aerts Lab: http://med.kuleuven.be/bioinformatics) and you will be part of an active bioinformatics community in Leuven, allowing daily interactions with colleague bioinformaticians. Your main activity will be to provide support for large-scale data analysis, and to setup and manage a Bioinformatics consulting core within the Center through which: you will collaborate with wet-lab scientists on a variety of research problems. You will deal with the data analysis part of the research project. The focus of the service will be mainly on genome bioinformatics: microarrays, RNA-Seq, ChIP-Seq, exome/genome re-sequencing, gene regulation, network biology, pathway analysis, gene prioritization, data integration, text-mining, etc. you will gradually manage a team of 1-3 Bioinformatics experts you will interact with the core facility of the VIB-BITS (http://www.bits.vib.be/) with the Genomics Core facility at the University Hospital (allowing close interaction with the next-generation sequencing instruments Illumina HiSEQ2000, Illumina MiSEQ, Roche 454, PacBio), and with other consulting units and research groups, for example for advanced biostatistics or proteomics data analysis. you will make hardware (e.g., local linux servers, high performance computing, cloud), software (e.g., a local Galaxy instance), and analysis pipelines (e.g., scripts, workflows) available to scientists; train and guide scientists to analyze their own datasets; and organize training courses and seminars. you will take your own initiatives to continuously optimize the bioinformatics flux through the Center, through the VIB and through the Group of Biomedical Sciences, for example to organize a weekly "data clinic" where small user problems can be solved. Qualifications: Master's degree in Life sciences or computational field PhD degree is strongly preferred At least five years bioinformatics experience Proven track record of high-impact publications in the field of computational biology, analysis of high-throughput data sets, data integration Solid experience with Linux, programming (e.g. Java), and database management (sql and no-sql). Solid experience with bioinformatics programming and statistics for bioinformatics, including scripting (e.g., Python), R (incl. Bioconductor), Galaxy, UCSC Genome Browser, Ensembl API, etc. Thorough understanding of molecular and developmental biology, and of disease biology (preferably cancer and/or neurological disorders). Experience with the analysis of next-generation sequence data is a plus: whole exome re-sequencing, whole-genome re-sequencing, SNP/indel calling, CNV, Structural variation; RNA-Seq, ChIP-Seq Experience with pathway analysis and cis-regulatory sequence analysis is a plus. Knowledge of machine learning and data mining is a plus. Links: The Center for the Biology of Disease The Laboratory of Computational Biology Center for Human Genetics University of Leuven Highly motivated candidates can apply by sending a motivation letter, names and contact information for three references, publication list, and CV to stein.aerts(a)med.kuleuven.be.

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Integrative Bioinformatics 2011: 2nd call for abstracts
by Jack Leunissen 16 Jul '12

16 Jul '12

Dear colleague, The 2011 International Symposium on Integrative Bioinformatics (IB2011) will take place on March 21-23, 2011 in Wageningen (the Netherlands). This seventh meeting on Integrative Bioinformatics will be of interest to bioinformaticians, computer scientists and all working in, or interested in the developing area of integrative bioinformatics. There will be opportunities to present and discuss methods, theoretical approaches, and their practical applications. We invite you to register for the conference, and to send in an abstract for a presentation at the conference. Accepted abstracts will be invited for a presentation at the conference, and will also be invited to send in a full manuscript, to be published (after peer reviewing) in the IB2011 Special Issue of the Journal of Integrative Bioinformatics. The deadline for sending in an extended abstract is January 15th; submissions should not exceed 4 pages. Authors will be informed of acceptance before February 1st. There are also opportunities for presenting posters and software demonstrations at the Symposium. The deadline for sending in abstracts for posters or a software demo is February 15th, 2011. The best poster will receive an award sponsored by IMBio e.v. The conference website is open for registration and abstract submission, and can be found at www.bioinformatics.nl/ib2011/ and www.imbio.de/ib2011/. We hope to meet you in March in Wageningen. On behalf of the organizing committee, Jack Leunissen Wageningen UR IB2011 is organized by Wageningen University, the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, and IMBio e.V. == Disclaimer: We have tried our best to remove duplicate e-mail addresses from our mailing list to reduce the amount of clutter in your mailbox. It may nevertheless still happen that you receive this mail via different channels. We apologize if you receive this mail more than once.

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[Gtpb] SBTM12 - Bioinformatics Training Course anouncement
by Pedro Fernandes 13 Jul '12

13 Jul '12

ANNOUNCEMENT SBTM12 - SEQUENCE-BASED TYPING METHODS for MICROORGANISMS with Keith Jolley, Nick Loman, João Carriço, Mario Ramirez, Nuno Faria and Teresa Conceição IMPORTANT DATES for SBTM12 Deadline for applications: September 10th 2012 Notification of acceptance dates: EARLY: September 3rd 2012 (on special request, see Application) NORMAL: September 12th 2012 Course date: September 25th - September 28th 2012 Course Description Overview Technological advances in DNA sequencing have led to the adoption of sequence-based typing methods as the standard techniques for bacterial identification at strain level, specially due to their portability and reproducibility. The widespread use of remotely accessible databases offering different typing data and the development of diverse data analysis techniques show the impact of Bioinformatics in this field, and the need for understanding how to operate with the databases and algorithms. Recently, the capability of sequencing whole bacterial genomes in a few days using Next Generation Sequencing (NGS) methodologies, opened a new door for the development of more sophisticated strain identification tools. Objectives This training course is directed for the data analysis of sequence based typing methods, from the raw-data to the identification of a strain type by several typing methodologies, and the use of analysis algorithms to create groups of related strains. It will span from Single Locus Sequence Typing methods, such as spa typing or emm typing, to the now established MultiLocus Sequence Typing (MLST) and Multilocus Variable Number of Tandem Repeats Analysis (MLVA) methodologies. The course will also cover methods that apply to whole genome sequence data, and show how NGS data can be analyzed and made sense of, in this context. The course will be essentially hands-on. Short presentations will be interweaved by tutored assited exercises. The participants are expected to gradually gain user independence by acquiring new analytical skils in using software and online databases for specific typing methods. Special attention will be given to methods that can use NGS datasets. Target Audience This course is aimed to anyone working in molecular epidemiology, that wants to develop or consolidate skills in the use and analysis of sequence-based typing methods. The course will be illustrated with examples from different bacterial species, but the concepts are applicable to any species and to other sequence-based typing methods, not explicitly referred to in the course. Course Pre-requisites Basic understanding of molecular biology, namely in microbial typing methodologies and elementary computer interaction skills are expected. Futher details, including application instructions available at http://gtpb.igc.gulbenkian.pt/bicourses/SBTM12 thank you for your interest Pedro Fernandes -- Pedro Fernandes GTPB Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt ----- End forwarded message ----- _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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vacancies for bioinformatics PhD students
by Kris Laukens 12 Jul '12

12 Jul '12

Dear colleagues, In the Biomedical Informatics research Center Antwerpen (biomina) we are looking for two doctoral students in bioinformatics. - Doctoral grant in the area of Integrative Bioinformatics of epigenome, transcriptome and proteome data (Department of Mathematics and Computer Science, Faculty of Sciences). http://www.ua.ac.be/main.aspx?c=.DEPTPERSONEEL&n=108899&ct=108899&e=301323 - Doctoral grant in the area of Medical Genetics & Next Generation Sequencing Bioinformatics (Antwerp Center of Medical Genetics) http://www.ua.ac.be/main.aspx?c=.DEPTPERSONEEL&n=104282&ct=104282&e=301591 Feel free to forward this announcement to potential candidates. Best regards, Kris Laukens -- Advanced Database Research and Modelling (ADReM) University of Antwerp Middelheimlaan 1, G.219, B-2020 Antwerpen, Belgium T +32 (0)3 265 33 10 E kris.laukens(a)ua.ac.be W adrem.ua.ac.be Biomedical Informatics research center Antwerpen (biomina) Wilrijkstraat 10, B-2650 Edegem, Belgium T +32 (0)3 821 59 47 W www.biomina.be

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Register now: ECCB12 Workshop Bioinformatics Training for Life Scientists: Showcases and Challenges from tutors’ perspectives
by Celia van Gelder 12 Jul '12

12 Jul '12

*Workshop Bioinformatics Training for Life Scientists: Showcases and Challenges from tutors? perspectives * 9 September, 2012, Basel Switzerland (Satellite event of the European Conference on Computational Biology ECCB'12) *Early registration deadline: 1 August, 2012. * This workshop represents a platform where those involved in bioinformatics training to life scientists can meet, confront and share experiences, as well as discuss future directions and collaboration in joint efforts.Topics will include: - Current state of the art and challenges in bioinformatics training for life scientists in the world. - Specific challenges for those delivering bioinformatics training ? organizers and teachers - and how we can address these. - Successful showcases of teaching bioinformatics to life science researchers. - Exchange views on the future of Bioinformatics Training, going global: building and strengthening networks of trainers, possible collaborations, international developments, and getting recognition for training efforts. *Target Audience* - Experienced and beginner trainers - Researchers involved in training *Advantages in attending* Get inspiration for your own training Be acquainted with training methods that are effectively used by expert trainers Have the opportunity to connect to the network of trainers & organizers (BTN) Be recognized by and become part of the training community Program and registration at: http://www.eccb12.org/WS4 *Organisers * Patricia Palagi (SIB Swiss Institute of Bioinformatics) Vicky Schneider (European Bioinformatics Institute, EBI) Allegra Via (Dept of Physics, Sapienza University of Rome) Celia van Gelder (Netherlands Bioinformatics Centre, NBIC)

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TPNC 2012: call for posters
by GRLMC 11 Jul '12

11 Jul '12

The 1st International Conference on the Theory and Practice of Natural Computing (TPNC 2012) invites authors to submit poster presentations. TPNC 2012 will be held in Tarragona (Spain) on 2-4 October, 2012. See http://grammars.grlmc.com/tpnc2012/ Poster presentations are intended to enhance informal interactions with the conference participants, at the same time permitting in-depth discussion. TOPICS We encourage authors to submit presentations that discuss novel work in progress on: - nature-inspired models of computation, - synthesis of nature by means of computation, - nature-inspired materials, - information processing in nature, - applications of natural computing. Posters do not need to present final research results. Work that is being developed and may lead to new interesting ideas is welcome. KEY DATES Submission deadline: August 26, 2012 Notification of poster acceptance or rejection: September 2, 2012 SUBMISSION Please submit an abstract through: https://www.easychair.org/conferences/?conf=tpnc2012 The abstract should contain the title, author(s) and detailed affiliation, and should not exceed 500 words. PRESENTATION Posters will be allocated 10 minutes each in the programme for oral presentation. Moreover, they will remain hanging during the whole conference for discussion. PUBLICATION Posters will not be published in the LNCS proceedings volume of TPNC 2012. However, there will be a specific section in the LNCS proceedings volume of TPNC 2013 reserved for those accepted papers that derive from 2012 posters. REGISTRATION Authors of accepted posters have to register to the conference. Their registration fare, however, will be very reduced: 135 Euro (one third of the early fare for PhD students).

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bioinformatics postdoc and programmer positions at UMC Groningen
by M.A.Swertz 11 Jul '12

11 Jul '12

Dear bioinformatics colleage, I am happy to announce we have a postdoc and a programmer Boinformatics position available: These positions are at the Genomics Coordination Center (GCC), a bioinformatics research group of the University of Groningen and the University Medical Center Groningen, headed by Dr. Morris A. Swertz (m.a.swertz(a)rug.nl) You will design, develop and document research portals that help geneticists, epidemiologists and clinicians to integrate across biobanks and visualize data from DNA to disease. You will be part of an international team of ten bio-informaticians working closely in daily SCRUMs to unravel this data and publish in the context of national and EU biobank consortia including BBMRI-NL, NBIC, EU-BioMedBridges, LifeLines, Top Institute Food & Nutritions, CTMM and EU-BioSHaRE To read the full story and apply: http://www.academictransfer.com/employer/UMCG/vacancy/14767/lang/en/ Feel free to forward :-) Cheers, Morris

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SSMBio 2012: final announcement
by GRLMC 09 Jul '12

09 Jul '12

*To be removed from our mailing list, please respond to this message with UNSUBSCRIBE in the subject* ********************************************************************* 2012 INTERNATIONAL SUMMER SCHOOL IN METHODS IN BIOINFORMATICS SSMBio 2012 Tarragona, Spain August 27-31, 2012 Organized by: Research Group on Mathematical Linguistics (GRLMC) Rovira i Virgili University http://grammars.grlmc.com/ssmbio2012/ ********************************************************************* AIM: SSMBio 2012 offers a broad and intensive series of lectures at different levels on bioinformatics. The students choose their preferred courses according to their interests and background. Instructors are top names in their respective fields. The School intends to help students initiate and foster their research career. The previous event in this series was WSMBio 2012: http://grammars.grlmc.com/wsmbio2012/ ADDRESSED TO: Graduate (and advanced undergraduate) students from around the world. Most appropriate degrees include: Computer Science, Biology and Medicine. Other students (for instance, from Engineering or Mathematics) are welcome too. The School is appropriate also for people more advanced in their career who want to keep themselves updated on developments in the field. There is no overlap in the class schedule. COURSES AND PROFESSORS: - Rita Casadio (U Bologna), Human Protein Variants: Structural and Functional Annotation [advanced, 8 hours] - David Gilbert (Brunel U, London), Multiscale Modelling for Systems Biology [intermediate/advanced, 6 hours] - Minoru Kanehisa (Kyoto U), Translational Bioinformatics: From Genomes to Diseases and Drugs [introductory/intermediate, 4 hours] - Bin Ma (U Waterloo), Mass Spectrometry Data Analysis for Proteomics [introductory/intermediate, 6 hours] - Luay Nakhleh (Rice U), Gene Tree Reconciliations: Incomplete Lineage Sorting, Duplication/Loss, and Reticulation [introductory/intermediate, 4 hours] - Gajendra P.S. Raghava (Institute of Microbial Technology, Chandigarh), Bioinformatics Approach for Designing Therapeutic Peptides, particularly Subunit Vaccines [intermediate/advanced, 8 hours] - Joachim Selbig (University of Potsdam & Max Planck Institute of Molecular Plant Physiology), Integrative 'Omics' Data and Network Analysis [intermediate/advanced, 6 hours] - Wing-Kin Sung (National U Singapore), Extracting Information from Next Generation Sequencing Data [introductory/intermediate, 6 hours] - Michael Zhang (U Texas Dallas), From Computational -Omics to Systems Biology [intermediate, 6 hours] REGISTRATION: It has to be done on line at http://grammars.grlmc.com/ssmbio2012/Registration.php FEES: They are variable, depending on the number of courses each student takes. The rule is: 1 hour = - 10 euros (for payments until June 2, 2012), - 15 euros (for payments after June 2, 2012). PAYMENT PROCEDURE: The fees must be paid to the School's bank account: Uno-e Bank banks address: Julian Camarillo 4 C, 28037 Madrid, Spain IBAN: ES3902270001820201823142 BIC/SWIFT: UNOEESM1 account holder: C. Martin GRLMC account holders address: Av. Catalunya 35, 43002 Tarragona, Spain Please mention SSMBio 2012 and your name in the subject. A receipt will be provided on site. Remarks: - Bank transfers should not involve any expense for the School. - People claiming early registration will be requested to prove that the bank transfer order was carried out by the deadline. - Students may be refunded only in the case when a course gets cancelled due to the unavailability of the instructor. People registering on site at the beginning of the School must pay in cash. For the sake of local organization, however, it is much recommended to do it earlier. ACCOMMODATION: Information about accommodation is available on the website of the School. CERTIFICATE: Students will be delivered a certificate stating the courses attended, their contents, and their duration. IMPORTANT DATES: Announcement of the programme: April 21, 2012 Starting of the registration: April 21, 2012 Early registration deadline: June 2, 2012 Starting of the School: August 27, 2012 End of the School: August 31, 2012 QUESTIONS AND FURTHER INFORMATION: Lilica Voicu: florentinalilica.voicu(a)urv.cat WEBSITE: http://grammars.grlmc.com/ssmbio2012/ POSTAL ADDRESS: SSMBio 2012 Research Group on Mathematical Linguistics (GRLMC) Rovira i Virgili University Av. Catalunya, 35 43002 Tarragona, Spain Phone: +34-977-559543 Fax: +34-977-558386 ACKNOWLEDGEMENTS: Diputació de Tarragona Universitat Rovira i Virgili

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