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Environmental Metagenomics Symposium, 19 September 2014, Wageningen, the Netherlands
by Celia.vanGelder＠radboudumc.nl 22 Aug '14

22 Aug '14

Dear colleague, Metagenomics has quickly become one of the most important discovery tools in microbial ecology. Metagenomics is a powerful tool to study the organisms in microbial communities, that has numerous applications in many areas of biomedical science. By bypassing the need for laboratory culturing, this technology can unlock the massive uncultured microbial diversity, enabling the microbial component of specific environments to be surveyed, discover new organisms, and explore the dynamic ecology of microbial populations under changing conditions. The high throughput nature of metagenomics means that huge datasets are generated, and in order to extract biological information from these data, advanced bioinformatics and statistical tools are indispensable. On 19 September 2014, we are organizing an Environmental Metagenomics Symposium which will bring together renowned scientists in microbial ecology and bioinformatics, who will present their recent explorations of the microbiota of different environments. Moreover, we will welcome the presentations of several students of the metagenomics course held in the week leading up to this symposium. Together, this will be an exciting opportunity to see the latest advances in environmental metagenomics from young talents as well as established leaders in the field. The symposium is open for everyone interested in environmental metagenomics. Symposium website: http://nioo.knaw.nl/en/metagenomics-symposium Symposium fee: Attending the symposium is free of charge, but you have to register via the symposium website A pdf with the programme of both course and symposium is attached to this mail. The organization of course and symposium has been made possible with the generous support of AllBio.<http://www.allbioinformatics.eu/doku.php> Best regards, Bas Dutilh (Utrecht University & Radboudumc) Eiko Kuramae (NIOO-KNAW) Celia van Gelder (Radboudumc) Dr. Celia W.G. van Gelder Projectleader Education NBIC/BioSB Coordinator Education CMBI Programme Manager Learning DTL tel. +31-(0)24-3666120 e-mail: Celia.vanGelder(a)radboudumc.nl<mailto:C.vanGelder@umcn.nl> websites: www.nbic.nl<http://www.nbic.nl/>, www.biosb.nl, www.cmbi.ru.nl<http://www.cmbi.ru.nl/>, www.dtls.nl Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre PO Box 9101 6500 HB Nijmegen The Netherlands Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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FW: bioinformatics vacancies at Scientific Institute of Public Health
by Katrijn Vannerum 21 Aug '14

21 Aug '14

These vacancies reached me through the N2N (Nucleotides2Networks) network (www.nucleotides2networks.be<http://www.nucleotides2networks.be>). Enclosed the two bioinformatician profils we are recruiting in our Intitute. If you can diffuse it,… - The permanent position (statutaire) - The PhD 4 years Thanks Nancy [cid:image002.jpg@01CFBC50.BE044470]Dr Ir Nancy ROOSENS, Ph.D Head o f Division Platform Biotechnologie en Moleculaire Biologie / Plateforme Biotechnologie et Biologie Moléculaire Operationele Directie Expertise, Dienstverlening en Klantenrelaties Direction Opérationnelle Expertise, Prestations de service et relations clients Rue Juliette Wytsmanstraat 14 | 1050 Brussels T 02 642 52 58 | F 02 642 52 92 nancy.roosens(a)wiv-isp.be<mailto:nancy.roosens@wiv-isp.be> Wetenschappelijk Instituut Volksgezondheid Institut Scientifique de Santé Publique Scientific Institute of Public Health www.wiv-isp.be<http://www.wiv-isp.be> ________________________________ Checked as being free of known viruses. Scientific Institute of Public Health, Brussels, Belgium Wetenschappelijk Instituut Volksgezondheid, Brussel, België Institut scientifique de Santé Publique, Bruxelles, Belgique Visit our website: http://www.wiv-isp.be ________________________________ DISCLAIMER<http://www.iph.fgov.be/disclaimer.asp> : Please see https://www.wiv-isp.be/Pages/EmailDisclaimer.aspx ________________________________

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[Gtpb] ABSTAT14 Advanced Biostatistics training course - announcement
by Pedro Fernandes 19 Aug '14

19 Aug '14

REMINDER The Gulbenkian Training Programme in Bioinformatics is happy to announce that the ABSTAT14 - "Advanced Biostatistics for Bioinformatics Tool Users using R" training course is open for applications IMPORTANT DATES for this Course Deadline for applications: September 5th 2014 <========= Latest acceptance notification: September 6th 2014 <========= Course date: September 15th - 18th 2014 Attendance fee: Euro 320.00 Course description This course is a standalone advanced Biostatistics course that can be taken as a continuation of the Introductory Biostatistics for Bioinformatics (IBSTAT) course that precedes it in GTPB. It is targeted for Biostatistical techniques often employed in analytical tools for high throughput data and multivariate data. Participants can expect to attend a thorough set of lectures that will reveal the conceptual frameworks that are needed to understand the methods. Extensive hands-on practice will be the main vehicle for providing the skills and user independence. To keep things in context, the course is exclusively based on biological examples, worked with Bioinformatics tools. Care has been taken not to use any proprietary data or software, so that the hands-on experience can carry on after the course, providing maximum user independence. We will be using custom-built R scripts and packages that are available from the CRAN and Bioconductor repositories. Methodology This intensive course will introduce a relatively high number of concepts and methods. To keep it highly practical, we will spend most of the time in hands-on sessions. - We will focus on each method using examples taken from real world Bioinformatics practice. - We will then dissect the method, identifying the concepts and exploring their interrelationships. - The applicability and limitations of each method will be emphasized. - The use of the method will be illustrated using appropriate Bioinformatics tools and biological data resources. ------------------------------------------------------------ Due to the summer period, there will be little time to deal with the applications, so the sooner you apply the better and we will do our best to make the acceptance process run smoothly. Early acceptance decisions will be the rule, not the exceptions, though you can help in justifying why you need to know about it in advance (please use the appropriate space in the Application Form). More details, including APPLICATION instructions can be found under the URL: http://gtpb.igc.gulbenkian.pt/bicourses/ABSTAT14/ Thank you for your interest P. Fernandes GTPB Coordinator -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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Internship call for Schneider lab
by ISCBSC announcement 11 Aug '14

11 Aug '14

Dear all, The ISCB Student Council is pleased to announce a 6-month internship position with the Schneider group at Bioinformatics Core, Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg. The internship is expected to start in October and it is available to Masters and PhD students in computational biology or related areas from developing nations. More information can be found in the attachment. Please forward this email to all who might be interested. Best regards, Susanne Hermans ISCBSC outreach committee

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ECCB 2014 Tutorial : Analysis of Cis-Regulatory Motifs from High-Throughput
by Jacques van Helden 08 Aug '14

08 Aug '14

There are still some places available for this tutorial: ECCB Tutorial T01 Analysis of Cis-Regulatory Motifs from High-Throughput Sequence Sets Date: Saturday Sept 6, 2014 Place: Forum building of the Faculty of Medicine of Strasbourg Time: 9am – 5.30pm (registration starts from 8am) Contact e-mail: mthomas(a)biologie.ens.fr More details: http://www.eccb14.org/program/tutorials/cis-r How to register: http://www.eccb14.org/registration Registration includes lunch & coffee breaks on the day of the workshop and the tutorial material (.pdf and/or print). ECCB Tutorial rates: 110 € (academic) or 60 € (student) ---------- Short description ---------- This tutorial aims at introducing the theoretical principles and giving practical skills to use specialized software tools to extract motifs from full-scaled NGS datasets (typically covering tens of Mb). --------- Teachers ---------- - Jacques van Helden, Aix-Marseille Université (France) - Morgane Thomas-Chollier, Ecole Normale Supérieure (France) - Carl Herrmann, University Heidelberg (Germany). - Alejandra Medina-Rivera, SickKids Research Institute, Toronto (Canada) ---------- Description ---------- Next Generation Sequencing led to the development of novel methods (ChIP-seq, FAIRE-seq, clip-seq, ) to acquire massive data about diverse signals involved in genome regulation and function (cis-regulation, chromatin conformation, RNA maturation, recombination, replication, ...). Extracting relevant information from the raw data requires not only specialized software tools, but also a good understanding of their principles and parameters. In this tutorial we will demonstrate how to analyze ChIP-seq data using the Regulatory Sequence Analysis Tools (RSAT, http://www.rsat.eu/) via their different ways of access: web-interface, command-line, and web-services. This tutorial aims at introducing the theoretical principles and giving practical skills to use specialized software tools to extract motifs from full-scaled NGS datasets (typically covering tens of Mb). ---------- Contents ---------- The tutorial will be organized in 2 half days: 1) Analysis of cis-regulatory elements with the Regulatory Sequence Analysis Tools (RSAT): methods and website utilization (http://www.rsat.eu/) 2) Using RSAT in command-line and via web services (SOAP/WSDL). Topics: - Motif discovery in NGS peak sets. - Impact of the background models. - Comparison between motifs. - Motif enrichment in peak sequences. - Evaluating the quality of motifs extracted from NGS peaks. - Building control sets to estimate the rates of false positives. ---------- Topics not covered ---------- Other steps for the analysis of ChIP-seq data (e.g. read mapping, peak calling, functional enrichment of peaks, other tools for pattern discovery and matching). ---------- Target audience ---------- The course is addressed to bioinformaticians and biologists. The afternoon will require being familiar with the Unix shell (Linux) and basic programming skills (Perl or Python) to implement clients for web services. ---------- In practice ---------- * Participants will need to bring their own laptop. * All command-line programs will be run on the IFB cloud platform (https://cloud.france-bioinformatique.fr/) managed by Christophe Blanchet (IBCP, Lyon, France). Each participant will be given a (free) account to access this cloud and thereby a fully functional virtual machine with RSAT. * Wireless internet will be available at the conference venue. * An indicative reading list will be available a few weeks before the tutorial. * The hands-on will be organized in a cookbook mode: we will distribute protocols explaining the steps to solve selected test cases. * For the practicals, we ensure that there is no need to transfer data from the conference room to the servers. ----------------------------------------------------------------

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[Gtpb] Fwd: ABSTAT14 Advanced Biostatistics training course - reminder
by Pedro Fernandes 06 Aug '14

06 Aug '14

The Gulbenkian Training Programme in Bioinformatics is happy to announce that the ABSTAT14 - "Advanced Biostatistics for Bioinformatics Tool Users using R" training course is open for applications IMPORTANT DATES for this Course Deadline for applications: September 5th 2014 <========= Latest acceptance notification: September 6th 2014 <========= Course date: September 15th - 18th 2014 Attendance fee: Euro 320.00 Course description This course is a standalone advanced Biostatistics course that can be taken as a continuation of the Introductory Biostatistics for Bioinformatics (IBSTAT) course that precedes it in GTPB. It is targeted for Biostatistical techniques often employed in analytical tools for high throughput data and multivariate data. Participants can expect to attend a thorough set of lectures that will reveal the conceptual frameworks that are needed to understand the methods. Extensive hands-on practice will be the main vehicle for providing the skills and user independence. To keep things in context, the course is exclusively based on biological examples, worked with Bioinformatics tools. Care has been taken not to use any proprietary data or software, so that the hands-on experience can carry on after the course, providing maximum user independence. We will be using custom-built R scripts and packages that are available from the CRAN and Bioconductor repositories. Methodology This intensive course will introduce a relatively high number of concepts and methods. To keep it highly practical, we will spend most of the time in hands-on sessions. - We will focus on each method using examples taken from real world Bioinformatics practice. - We will then dissect the method, identifying the concepts and exploring their interrelationships. - The applicability and limitations of each method will be emphasized. - The use of the method will be illustrated using appropriate Bioinformatics tools and biological data resources. ------------------------------------------------------------ Due to the summer period, there will be little time to deal with the applications, so the sooner you apply the better and we will do our best to make the acceptance process run smoothly. Early acceptance decisions will be the rule, not the exceptions, though you can help in justifying why you need to know about it in advance (please use the appropriate space in the Application Form). More details, including APPLICATION instructions can be found under the URL: http://gtpb.igc.gulbenkian.pt/bicourses/ABSTAT14/ Thank you for your interest P. Fernandes GTPB Coordinator -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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[Gtpb] ABSTAT14 Advanced Biostatistics training course - announcement
by Pedro Fernandes 01 Aug '14

01 Aug '14

The Gulbenkian Training Programme in Bioinformatics is happy to announce that the ABSTAT14 - "Advanced Biostatistics for Bioinformatics Tool Users using R" training course is open for applications IMPORTANT DATES for this Course Deadline for applications: September 5th 2014 <========= Latest acceptance notification: September 6th 2014 <========= Course date: September 15th - 18th 2014 Attendance fee: Euro 320.00 Course description This course is a standalone advanced Biostatistics course that can be taken as a continuation of the Introductory Biostatistics for Bioinformatics (IBSTAT) course that precedes it in GTPB. It is targeted for Biostatistical techniques often employed in analytical tools for high throughput data and multivariate data. Participants can expect to attend a thorough set of lectures that will reveal the conceptual frameworks that are needed to understand the methods. Extensive hands-on practice will be the main vehicle for providing the skills and user independence. To keep things in context, the course is exclusively based on biological examples, worked with Bioinformatics tools. Care has been taken not to use any proprietary data or software, so that the hands-on experience can carry on after the course, providing maximum user independence. We will be using custom-built R scripts and packages that are available from the CRAN and Bioconductor repositories. Methodology This intensive course will introduce a relatively high number of concepts and methods. To keep it highly practical, we will spend most of the time in hands-on sessions. - We will focus on each method using examples taken from real world Bioinformatics practice. - We will then dissect the method, identifying the concepts and exploring their interrelationships. - The applicability and limitations of each method will be emphasized. - The use of the method will be illustrated using appropriate Bioinformatics tools and biological data resources. ------------------------------------------------------------ Due to the summer period, there will be little time to deal with the applications, so the sooner you apply the better and we will do our best to make the acceptance process run smoothly. Early acceptance decisions will be the rule, not the exceptions, though you can help in justifying why you need to know about it in advance (please use the appropriate space in the Application Form). More details, including APPLICATION instructions can be found under the URL: http://gtpb.igc.gulbenkian.pt/bicourses/ABSTAT14/ Thank you for your interest P. Fernandes GTPB Coordinator -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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FW: vacature bioinformatician
by Katrijn Vannerum 29 Jul '14

29 Jul '14

There is a bioinformatician position at Bayer CropScience in Ghent. Project manager N2N (From Nucleotides to Networks) Multidisciplinary Research Partnership Bioinformatics and Systems Biology Ghent University http://www.nucleotides2networks.be/ twitter: @N2N_UGent Katrijn.Vannerum(a)UGent.be<mailto:Katrijn.Vannerum@UGent.be> Technologiepark 927 9052 Gent, Belgium +32 (0)9 331 36 85 [cid:image001.png@01CFAB15.B5757370]

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Bioinformatics Research Position @ CRP-Santé, Luxembourg
by Francisco Azuaje 29 Jul '14

29 Jul '14

Research Engineer Position in Bioinformatics As part of an international research cooperation project, infused-project.eu, we are seeking a highly motivated research engineer with demonstrable capacity to develop new software for biological research. Essential skills and experience: The successful candidate will meet all of the following requirements: 1. BSc or equivalent degree in computing, bioinformatics or closely related area. 2. MSc in bioinformatics, systems biology or related area. 3. Demonstrable experience developing Web-based, data-driven applications. 4. Good communication skills in English. Desirable skills and experience: Candidates possessing these skills and experience will be given priority: 1. Experience in database development. 2. Solid understanding of data mining and visualization. 3. Experience in coding applications for multi-source data integration. What we offer: Apart from remuneration, the successful candidate will have different career advancement opportunities, including: 1. Working in a truly inter-disciplinary team-oriented research environment. 2. Developing experience in translational bioinformatics. 3. Improvement of scientific communication skills. 4. Potential co-authorship of publications. Where and when: The successful applicant will be affiliated with the NORLUX Neuro-Oncology Laboratory of CRP-Santé in Luxembourg (www.crp-sante.lu<http://www.crp-sante.lu>). This full-time position may begin as early as 1 October 2014, and will have a total duration of 12 months. If you wish to apply for this position, email your CV (no longer than 2 pages), screenshots of GUIs previously developed (no longer than 2 pages), and a 1-page cover letter. Applications must be submitted via: http://www.crp-sante.lu/Jobs2/Jobs-opportunities/Selection (Department of Oncology, REF: ME/REngineer/SN/LRNO) All documents must be provided in a single PDF file. Applications not complying with this format, or not meeting all the essential selection criteria will not be considered. Deadline for receiving applications: 1 September 2014. _________________________________ Francisco Azuaje, PhD Senior Researcher NORLUX Neuro-Oncology Laboratory Centre de Recherche Public de la Santé (CRP-Santé) 1A-B, rue Thomas Edison, L-1445 Strassen Luxembourg Tel: +352 26970-875 Fax: +352 26970-396 Email: francisco.azuaje(a)crp-sante.lu<mailto:francisco.azuaje@crp-sante.lu> Website: http://www.crp-sante.lu Join us on Facebook and follow our activities on Twitter: http://www.facebook.com/crpsante http://twitter.com/crpsante http://www.norlux.lu This message (including any attachments) is intended for the addressee only and may contain confidential and/or privileged information and/or information protected by intellectual property rights. If you have received this message by mistake, please notify the sender by return e-mail and delete this message from your system. You should not use, alter, copy or distribute this message or disclose its contents to anyone. E-mail transmission can not be guaranteed to be secure or error free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. CRP-Santé shall not be responsible nor liable for the proper and complete transmission of the information contained in this communication nor for any delay in its receipt or damage to your system.

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9th Benelux Bioinformatics Conference (BBC 2014) - call for abstracts
by Joanna SMULA-OSTASZEWSKA 28 Jul '14

28 Jul '14

Dear Colleagues, Luxembourg Centre for System Biomedicine of University of Luxembourg (LCSB) and Centre de Recherché Public de la Santé (CRP-Santé) organize the 9th edition of the Benelux Bioinformatics Conference (BBC 2014). The conference is affiliated by International Society for Computational Biology (ISCB)<http://www.iscb.org/>. The event entitled "Bioinformatics: Integrating data, teams and disciplines" will take place in Novotel-Kirchberg in Luxembourg, on December 8th-9th. Conference coordinators invite you to submit your abstracts through the registration/submission system<http://lcsb.ldorganisation.lu/v2/produits.php?langue=english&cle_menus=1240…>. Conference topics cover all fields of bioinformatics, including: * Biotechnologies * Computational biology * Research on biological networks * Structural bioinformatics * The analysis of the high-throughput sequencing data * Micro-array expression data, etc. Detailed information may be found on the conference website http://www.bbc2014.lu/ We anticipate that the BBC 2014 will once again greatly foster the collaboration and research activities between scientists in the Benelux area. Please feel free to distribute this announcement to your interested colleagues and do not hesitate to contact us in case of further questions. Regards, Joanna Smula-Ostaszewska Dr.Eng. Joanna Smula-Ostaszewska Scientific assistant Université du Luxembourg Luxembourg Centre for Systems Biomedicine (LCSB) Campus Belval; 7, Avenue des Hauts-Fourneaux; L-4362 Esch-Belval; Luxembourg T: +352 46 66 44 6373 http://lcsb.uni.lu<http://lcsb.uni.lu/> --- This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.

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