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[Gtpb] Proteomics Data Analysis Training Course
by Pedro L. Fernandes 06 Feb '17

06 Feb '17

Announcement / Reminder PDA17 Proteomics Data Analysis The GTPB is proud to announce that the above hands-on training course is open for applications Important dates IMPORTANT DATES for this Course Deadline for applications: Feb 25th 2017 (New) Course date: March 6th - March 10th 2017 Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. This course is delivered in a highly interactive fashion. A set of analysis techniques will be introduced. They allow for iterative refinements of the analysis of mass spectrometry data using public data resources and open source software. Participants will be invited to bring their own data for guided analysis using their news skills on the last day of the course. Hoping that this course meets your interests, Pedro Fernandes -- Pedro Fernandes Bioinformatics Training Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL 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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Reminder: BioSB 2017 Conference: Abstract submission deadline oral presentations: February 12!
by Femke Francissen 06 Feb '17

06 Feb '17

*BioSB 2017 conference - Reminder: abstract submission deadline oral presentations: February 12!* 4-5 April 2017 Congrescentrum De Werelt, Lunteren, NL Conference website: http://www.aanmelder.nl/biosb2017 *** BioSB 2017 Conference* ------------------------------------------------------------ BioSB 2017 <http://www.aanmelder.nl/biosb2017> is the 3rd edition of the Dutch Bioinformatics & Systems Biology conference. The conference discusses the latest developments in bioinformatics, systems and computational biology and interrelated disciplines, and their wide-ranging applications in life sciences & health, agriculture, food & nutrition. This year's conference will be co-organised by the BioSB research school <http://www.biosb.nl>, UMC Groningen <https://www.umcg.nl>, University of Groningen <http://www.rug.nl/> and ELIXIR-NL <http://www.dtls.nl/elixir-nl/elixir-nl-2/>. *** Reminder: Call for abstracts* ------------------------------------------------------------ Abstract submission for the BioSB 2017 conference is open. You can submit an abstract for the following topics/sessions: * Gene regulation * Genotype/phenotype & disease * Industrial applications & synthetic biology * Metabolomics * Modeling * Networks & data integration * NGS data analysis * Proteomics * Statistics * Systems medicine * ELIXIR-NL technology track * Metagenomics * Structural bioinformatics (NSBM) You can submit an abstract for a lecture in one of the sessions, a poster presentation or a poster/demo. Find out here how to submit your abstract <https://www.aanmelder.nl/biosb2017/wiki/218444/abstract%20submission> *** Key dates* ------------------------------------------------------------ * *12 February 2017 - abstract submission deadline oral presentations* * 3 March 2017 - Notification date oral presentations * 20 March 2017 - abstract submission deadline posters & demos *** Contact & more information* ------------------------------------------------------------ You can find the latest conference updates at the conference website <http://www.aanmelder.nl/biosb2017>. Regular updates will also be sent via the BioSB mailing list <http://biosb.nl/newsletter/>. If you have any questions concerning the conference, please contact Femke Francissen, via femke.francissen(a)biosb.nl * On Twitter we will use the hashtag: #BioSB17 * Follow us on Twitter via @BioSB_nl <https://twitter.com/biosb_nl?lang=en> * Like us on Facebook <https://www.facebook.com/BIOSB-122337454509903/?ref=hl> * Follow us on LinkedIn <https://www.linkedin.com/company/biosb-research-school>

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Bioionformatics vacancies at the Princess Maxima Center
by Patrick Kemmeren 03 Feb '17

03 Feb '17

Dear all, The Princess Máxima Center for Pediatric Oncology is a recently started, fastly growing research hospital for children with cancer. The institute houses an increasing number of research groups, which aim to develop cures for all children with cancer with minimal long-term side effects of existing treatment. Within the institute, we currently have two bioinformatics related vacancies at the Princess Máxima Center for Pediatric Oncology: http://prinsesmaximacentrum.nl/vacatures/bioinformatician-phd-or-similar-ex… http://prinsesmaximacentrum.nl/vacatures/scientist-bioinformatics-phd-or-ms… Please look at the website, or contact us in case you are interested! Regards, Patrick -- Patrick Kemmeren, PhD Principal Investigator T +31 (0)88 972 55 05 | M +31 (0)6 53 11 25 53 Princess Maxima Center * * *Princess Máxima Center for Pediatric Oncology* *Location Hubrecht institute*| Uppsalalaan 8 | 3584 CT Utrecht | T +31 (0)88 972 90 00 |***> Website* <http://prinsesmaximacentrum.com/>

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International Chemical Discovery & Design Course, 12-23 June 2017, Nijmegen, NL
by Barbara.vanKampen＠radboudumc.nl 30 Jan '17

30 Jan '17

International Chemical Discovery & Design Course, 12-23 June 2017, Nijmegen. Course website: http://www2.cmbi.ru.nl/groups/computational-discovery-and-design/icdd2017/ We would like to draw your attention to the 13th annual International Chemical Discovery & Design Course which will be held from 12-23 June 2017 at the Radboud University Nijmegen. This course covers the recent advances in discovery informatics, with a focus on the application to real life problems. The course, combining practicals and lectures, will introduce and discuss different scientific concepts as well as providing an opportunity to gain practical experience using industry standard software. You can expect lectures and practicals on the following topics: * Introduction to Computational Discovery & Design * Comparative Protein Modelling * Sequence Retrieval, Analysis and Alignment Techniques * Computational Medicinal Chemistry; Molecular Descriptors & Library Design * The Application of Computational Drug Design to Real Life Problems * Molecular Docking and Virtual Screening * Advanced 3D Database Searches and Scaffold Hopping * QSAR * Structure Based Drug Design Techniques The course is targeted to MSc students, PhD students and post-docs. A basic background in bioinformatics or computational chemistry is a prerequisite for attendance. Registration via email to Barbara van Kampen<mailto:barbara.vankampen@radboudumc.nl>. Please, provide information about your background and your motivation to participate in the course. The course is free. You should however pay for travelling and lodging expenses yourself. Best regards, Gijs Schaftenaar Barbara van Kampen --- Barbara van Kampen Operational manager CMBI [Radboudumckleine.png] CMBI 260 Radboud university medical center / RIMLS CMBI Office / Room 0.02 PO Box 9101 Geert-Grooteplein 26-28 6500 HB Nijmegen 6525 GA Nijmegen Phone: +31(0)24 36 19390 www.cmbi.ru.nl<http://www.cmbi.ru.nl/> The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629. 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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BioSB 2017 Conference (4-5 April) - Registration now open!
by Femke Francissen 25 Jan '17

25 Jan '17

*** BioSB 2017 Conference *** *April 4-5, Congrescentrum De Werelt, Lunteren, NL* *Conference website: http://www.aanmelder.nl/biosb2017 <http://www.aanmelder.nl/biosb2017>* *** Registration now open!* ------------------------------------------------------------ BioSB 2017 (http://www.aanmelder.nl/biosb2017) is the 3rd edition of the Dutch Bioinformatics & Systems Biology conference. BioSB 2017 discusses the latest developments in bioinformatics, systems and computational biology and interrelated disciplines, and their wide-ranging applications in life sciences & health, agriculture, food & nutrition. You can now register for the conference. Information about the registration fee can be found on the registration page. Register here <https://www.aanmelder.nl/biosb2017/wiki/218454/registration> *** Confirmed keynote speakers* ----------------------------------------------------------- Confirmed keynote speakers - Jens Nielsen, Systems and Synthetic Biology, Chalmers University of Technology, Sweden - Teresa (Terri) Attwood, School of Computer Science, University of Manchester - Boris Kholodenko, Deputy Director UCD Conway Institute, Ireland - Sten Linnarsson, Karolinska Institutet, Sweden - Ioannis Xenarios, Swiss Institute of Bioinformatics, Switzerland Read more <https://www.aanmelder.nl/biosb2017/wiki/218410/keynote%20speakers> *** Call for abstracts open* ------------------------------------------------------------ Abstract submission for the BioSB 2017 conference is open. You can submit an abstract for an oral presentation for the following topics/sessions: * Gene regulation * Genotype/phenotype & disease * Industrial applications & synthetic biology * Metabolomics * Modeling * Networks & data integration * NGS data analysis * Proteomics * Statistics * Systems medicine * ELIXIR-NL technology track * Metagenomics * Structural bioinformatics (NSBM) You can submit an abstract for a lecture in one of the sessions, a poster presentation or a poster/demo. *Abstract submission deadline for oral presentations is February 12! *Read more <https://www.aanmelder.nl/biosb2017/wiki/218444/abstract%20submission> *** Key dates* ------------------------------------------------------------ * *12 February 2017 - abstract submission deadline oral presentations* * 3 March 2017 - Notification date oral presentations * 20 March 2017 - abstract submission deadline for posters & demos *** BioSB PhD retreat 2017 - April 3rd * ------------------------------------------------------------ YoungCB (ISCB Regional Student Group Netherlands) is pleased to invite you to the BioSB PhD retreat 2017 in the afternoon of April 3rd, the day preceding the conference. We encourage all (PhD-) students and young researchers in the fields of computational biology, bioinformatics, systems biology and related fields to attend this annual retreat to discuss your research and build a network with fellow young peers in the Netherlands. The programme features: * Keynote: Amrapali Zaveri (Stanford University), Introduction to semantic web * Keynote: Erik Schultes (FAIR Data Scientific Project Leader DTL), FAIR Data for scientists * Workshop on How to use SPARQL Endpoints to query various biological data resources, by Dr. Amrapali Zaveri * PhD flash talks * Dinner & social event in the evening Read more <https://www.aanmelder.nl/biosb2017/wiki/218435/biosb%20phd%20retreat> *** Morning run* *--------------------------*---------------------------------- We are organising a morning run on April 5th at 7:00 AM in the morning. You can indicate if you would like to participate via the registration form. Don't forget to bring your running shoes! *** Sponsoring* ------------------------------------------------------------ BioSB 2017 is thé event for related industry to interact with bioinformatics and systems biology scientists, software developers and students from a broad selection of universities, UMC's and companies in the Netherlands. Last year's BioSB 2016 conference alone had more than 350 participants. We invite you to present your organisation or company to this diverse scientific public. We offer a number of attractive sponsorship packages, as well as exhibit space, but also custom made packages can be discussed. See: Sponsor opportunities <https://www.aanmelder.nl/biosb2017/wiki/218446/sponsoring> *** Contact & more information* ------------------------------------------------------------ You can find the latest conference updates at the conference website. Regular updates will also be sent via the BioSB mailing list. If you have any questions about the conference, please contact Femke Francissen, via femke.francissen(a)biosb.nl

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PhD Vacancy in Bio-informatics
by Jelle Matthijnssens 24 Jan '17

24 Jan '17

Dear, I would like to bring the following PhD vacancy at the KU Leuven to the attention of the members of the BBClist: https://icts.kuleuven.be/apps/jobsite/vacatures/54049520 Kind regards, Jelle --------------------------- Prof. Jelle Matthijnssens Change of affiliation: As of november 21st 2016, my new affiliation will be: Laboratory of Viral Metagenomics KU Leuven | REGA Institute | Laboratory of Viral Metagenomics | Herestraat 49, box 1040 | B-3000 Leuven | Belgium https://rega.kuleuven.be/cev/viralmetagenomics/ tel. +32 16 321161 fax. +32 16 330026 jelle.matthijnssens(a)kuleuven.be (NOTE: jelle.matthijnssens(a)uz.kuleuven.ac.be and jelle.matthijnssens(a)uzleuven.be will be inactivated in the near future)<mailto:Jelle.matthijnssens@uz.kuleuven.ac.be>

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New Edinburgh Genomics workshop: Introduction to Linux and Workflows for Biologists 24-28 April 2017
by Bert Overduin 18 Jan '17

18 Jan '17

Dear all, I am happy announce a new workshop offered by Edinburgh Genomics, i.e. a 5-day INTRODUCTION TO LINUX AND WORKFLOWS FOR BIOLOGISTS. This workshop will be taught by Martin Jones, who also teaches our Python workshops. This would be a great workshop for anyone who want to learn more than the bare minimum when it comes to the command-line. More information about the workshop can be found below. If you have any questions regarding this workshop, please feel free to mail Martin (martin(a)pythonforbiologists.com) or me (bert.overduin(a)ed.ac.uk) With kind regards, Bert Overduin ********** INTRODUCTION TO LINUX AND WORKFLOWS FOR BIOLOGISTS DATE: Monday 24 – Friday 28 April 2017 VENUE: The King's Buildings, The University of Edinburgh, Edinburgh, Scotland, UK REGISTRATION DEADLINE: Monday 10 April 2017 noon CANCELLATION DEADLINE: Monday 17 April 2017 noon PLACES: 20 (first come, first served) REGISTRATION FEE: £525 (includes coffee/tea, but no lunch) TO REGISTER: http://genomics.ed.ac.uk/services/introduction-linux-and- workflows-biologists Most high-throughput bioinformatics work these days takes place on the Linux command line. The programs which do the majority of the computational heavy lifting — genome assemblers, read mappers, and annotation tools — are designed to work best when used with a command-line interface. Because the command line can be an intimidating environment, many biologists learn the bare minimum needed to get their analysis tools working. This means that they miss out on the power of Linux to customise their environment and automate many parts of the bioinformatics workflow. This course will introduce the Linux command line environment from scratch and teach students how to make the most of its tools to achieve a high level of productivity when working with biological data. INSTRUCTORS Dr. Martin Jones (Founder, Python for Biologists) Dr. Bert Overduin (Training and Outreach Bioinformatician, Edinburgh Genomics) WORKSHOP FORMAT The workshop is delivered over nine half-day sessions (see the detailed curriculum below). Each session consists of roughly a one hour lecture followed by two hours of practical exercises, with breaks at the organiser’s discretion. There will also be plenty of time for students to discuss their own problems and data. WHO SHOULD ATTEND This workshop is aimed at researchers and technical workers with a background in biology who want to learn to use the Linux operating system and the command line environment. REQUIREMENTS Students should have enough biological background to appreciate the examples and exercise problems, and have at least some interest in working with DNA sequence data. No previous computer skills are necessary, as we will introduce Linux starting with the very basics. Students need to bring a laptop with a Linux virtual machine installed (we will distribute instructions for downloading and installing the virtual machine before the course starts). SESSION CONTENT 1. The design of Linux In the first session we briefly cover the design of Linux: how is it different from Windows/OSX and how is it best used? We’ll then jump straight onto the command line and learn about the layout of the Linux filesystem and how to navigate it. We’ll describe Linux’s file permission system (which often trips up beginners), how paths work, and how we actually run programs on the command line. We’ll learn a few tricks for using the command line more efficiently, and how to deal with programs that are misbehaving. We’ll finish this session by looking at the built in help system and how to read and interpret manual pages. 2. System management We’ll first look at a few command line tools for monitoring the status of the system and keeping track of what’s happening to processor power, memory, and disk space. We’ll go over the process of installing new software from the built in repositories (which is easy) and from source code downloads (which is trickier). We’ll also introduce some tools for benchmarking software (measuring the time/memory requirements of processing large datasets). 3. Manipulating tabular data Many data types we want to work with in bioinformatics are stored as tabular plain text files, and here we learn all about manipulating tabular data on the command line. We’ll start with simple things like extracting columns, filtering and sorting, searching for text before moving on to more complex tasks like searching for duplicated values, summarizing large files, and combining simple tools into long commands. 4. Constructing pipelines In this session we will look at the various tools Linux has for constructing pipelines out of individual commands. Aliases, shell redirection, pipes, and shell scripting will all be introduced here. We’ll also look at a couple of specific tools to help with running tools on multiple processors, and for monitoring the progress of long running tasks. 5. EMBOSS EMBOSS is a suite of bioinformatics command-line tools explicitly designed to work in the Linux paradigm. We’ll get an overview of the different sequence data formats that we might expect to work with, and put what we learned about shell scripting to biological use by building a pipeline to compare codon usage across two collections of DNA sequences. 6. Using a Linux server Often in bioinformatics we’ll be working on a Linux server rather than our own computer— typically because we need access to more computing power, or to specialized tools and datasets. In this session we’ll learn how to connect to a Linux server and how to manage sessions. We’ll also consider the various ways of moving data to and from a server from your own computer, and finish with a discussion of the considerations we have to make when working on a shared computer. 7. Combining methods In the next two sessions — i.e. one full day — we’ll put everything we have learned together and implement a workflow for next-gen sequence analysis. In this first session we’ll carry out quality control on some paired-end Illumina data and map these reads to a reference genome. We’ll then look at various approaches to automating this pipeline, allowing us to quickly do the same for a second dataset. 8. Combining methods The second part of the next-gen workflow is to call variants to identify SNPs between our two samples and the reference genome. We’ll look at the VCF file format and figure out how to filter SNPs for read coverage and quality. By counting the number of SNPs between each sample and the reference we will try to figure out something about the biology of the two samples. We’ll attempt to automate this analysis in various ways so that we could easily repeat the pipeline for additional samples. 9. Customisation Part of the Linux design is that everything can be customised. This can be intimidating at first but, given that bioinformatics work is often fairly repetitive, can be used to good effect. Here we’ll learn about environment variables, custom prompts, soft links, and ssh configuration — a collection of tools with modest capabilities, but which together can make life on the command line much more pleasant. In this last session there will also be time to continue working on the next-gen sequencing pipeline. The last afternoon is reserved for finishing off the next-gen workflow exercise, working on your own datasets, or leaving early for travel. -- Bert Overduin, PhD TRAINING AND OUTREACH BIOINFORMATICIAN Bert.Overduin(a)ed.ac.uk orcid.org/0000-0002-5281-8838 EDINBURGH GENOMICS The University of Edinburgh Ashworth Laboratories The King's Buildings Charlotte Auerbach Road Edinburgh EH9 3FL Scotland, United Kingdom tel. +44(0)1316507403 http://genomics.ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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FW: Invitation to an exceptional lecture by Prof. Eric Lander - February 7 at 11:00
by Alexander Botzki 17 Jan '17

17 Jan '17

________________________________ From: Nathalie Krack [mailto:nathalie.krack@uclouvain.be] Subject: Invitation to an exceptional lecture by Prof. Eric Lander - February 7 at 11:00 Dear Colleagues, I would like to invite you to an exceptional lecture by Professor Eric Lander, who will narrate "The 35-year journey of genomic medicine". The lecture will take place on Tuesday, February 7 at 11:00, in the Maisin auditorium on the UCL Health Sciences campus in Brussels. It will be followed by a reception. Eric Lander is the president and founding director of the Broad Institute of MIT and Harvard. Geneticist, molecular biologist and mathematician, he was the principal leader of the international Human Genome Project. He developed and applied methods for discovering the molecular basis of rare genetic diseases, common diseases and cancer. He did pioneering work on genetic variation, population history, evolutionary forces, regulatory elements, long non-coding RNAs, three-dimensional folding of the human genome, and developed methods to systematically identify the genes essential for biological processes. Eric Lander will be awarded the title of doctor honoris causa of the UCL on February 6. He will be visiting our campus as part of this event. More information is available on the registration page<https://www.deduveinstitute.be/about/news-events/eric-lander-visits-our-cam…>. For security reasons, registration before January 27 is mandatory. I sincerely hope that you will not miss this unique opportunity to hear and meet an outstanding figure of modern biomedical sciences. With best wishes, Sophie Lucas Academic Sponsor of Eric Lander for the DHC2017 ceremony PLEASE FORWARD THIS INFORMATION WITHIN YOUR FACULTY/INSTITUTE/SOCIETY _______________________________ Pr Sophie Lucas de Duve Institute - UCLouvain av Hippocrate, 74 1200 Brussels - Belgium Mail: sophie.lucas(a)uclouvain.be<mailto:sophie.lucas@uclouvain.be> Tel: +32 2 764 74 74 Web: https://www.deduveinstitute.be/fr/tregs-and-tgfb [cid:5A3D2571-D274-485B-9205-B411ED61CB80]

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PhD student Applied Cancer Bioinformatics
by Dorsman, JC 17 Jan '17

17 Jan '17

Dear all, In Amsterdam, The Netherlands, we have a vacancy for a PhD student Applied Cancer Bioinformatics. Due to the multidisciplinary environment, you are expected to develop proficiencies that are equally relevant to academia and industry. Already published papers of the previous student : https://www.ncbi.nlm.nih.gov/pubmed/?term=Kooi+I Furthermore: https://www.werkenbijvumc.nl/vacatures/phd-student-applied-cancer-bioinform… When you have additional questions, do not hesitate to ask. Sincerely, Josephine Dorsman. Dr. Josephine Dorsman, PI Oncogenetic labs Department of Clinical Genetics Cancer Center Amsterdam De Boelelaan 1118 1081 HV Amsterdam The Netherlands Office 2-28 Tel. 31-020-4448424 Email: JC.Dorsman(a)vumc.nl

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Metabolomics meeting: NMC meeting on the 'Gut Mircobiome', January 27, Leiden
by Femke Francissen 17 Jan '17

17 Jan '17

*** NMC Meeting 2017: the Gut Micobiome *** *Date:* Friday January 27, 2017, *Venue:* Gorlaeus Lab, Leiden University *Register:* https://www.eventbrite.co.uk/e/nmc-meeting-2017-gut-microbiome-tickets-3029… The Netherlands Metabolomics Centre <http://www.metabolomicscentre.nl/> is organizing their annual meeting on January 27, 2017 at the Leiden University. The meeting will focus on the 'Gut Microbiome'. *Confirmed speakers:* - Jakob Stokholm (University of Copenhagen) - Nelus Schoeman (Leiden University) - Dina Vojinovic (Erasmus MC) - Ilja Arts (Maastricht Centre for Systems Biology) - Bjørn Koch (Leiden University) - Michael van Vliet (Leiden University) - Yingjuan Fu (Groningen University) - Bart Keijser (TNO) *The full programme is online*, see: http://www.metabolomicscentre.nl/node/1369 The meeting is open for anyone with an interest in the subject. *Registration:* - Participation is free charge for people working at NMC partner organisations (Universiteit Leiden, Universiteit van Amsterdam, TNO, PRI/RIKILT, UMC Utrecht, Radboudumc, Unilever, DSM, Janssen Pharmaceutica, MS-Omics). - For other participants we will ask a fee of 100 Euro. Register now! <https://www.eventbrite.co.uk/e/nmc-meeting-2017-gut-microbiome-tickets-3029…>

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