October 2016 - BBClist - maillist.psb.ugent.be

PostDoc & PhD student positions at BIH (Berlin, Germany)
by Martin Kircher 04 Nov '16

04 Nov '16

Dear colleagues, I will start a computational research group at the Berlin Institute of Health (BIH) in Germany in March 2017. My research will be in the areas of sequence analysis, data mining and functional genomics. One focus will be non-coding sequence variation, specifically analysis of data from Massively Parallel Reporter Assays (MPRA) for promoter and enhancer variants as well computational approaches for identifying functionally relevant genetic changes. At this point, I am trying to fill one fully funded PostDoc position and one PhD student position. Starting date is March 1st, 2017 or later and the application deadline for the PostDoc position is Dec 1st, 2016. I hope you can help me distributing the attached job posts to interested students and researchers. Please do not hesitate to contact me with questions regarding these posts (mkircher(a)uw.edu) Thank you so much! Martin Kircher -- Dr Martin Kircher Senior Fellow Shendure lab University of Washington, Department of Genome Sciences Foege Building S-203B, Box 355065 3720 15th Ave NE, Seattle WA 98195-5065

2 1

[Gtpb] Introductory Bioinformatics IB16 . course announcement
by Pedro L. Fernandes 31 Oct '16

31 Oct '16

The Gulbenkian Training Programme in Bioinformatics Applications for the bioinformatics training course IB16S Introductory Bioinformatics (Second course in 2016) - our entry level course with a soft introduction to NGS data analysis with David P. Judge, Pedro Fernandes and Daniel Sobral IMPORTANT DATES for this Course Deadline for applications: November 30th 2016 Course date: December 12th - December 16th 2016 Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. Overview This is an entry level course aimed that those with a reasonable biological background but no significant experience with bioinformatics. The course is broadly based around a series of exercises in which a combination of simple analytical tools and reference to publicly available databases is applied to the investigation of a single human gene. The training manual for the course is comprised of detailed instructions for the tasks undertaken. Included are, questions (with answers) and discussion of and the interpretation of the results achieved. Participants are asked to imagine an interest in the disease aniridia. Course exercises then provide extremely detailed instruction leading participants to discover the gene primarily associated with this disease and all that is interesting about that gene and its protein products. This course will also provide a soft introduction to Next Generation Sequencing (NGS) data analysis. This part of the course aims at providing basic skills that are needed when one needs to process NGS data, such as evaluating data quality, trimming sequences, changing data formats, visualising data, etc. Then, participants will learn how to address a simple transcriptomics problem, stepwise, using open source bioinformatics tools. Objectives The operation of the various programs used in the exercises will be explained, but only to the extent that allows a user to select parameters intelligently and to interpret results. The course will provide participants with an awareness of a wide range of bioinformatics tools and sufficient experience to use those tools in basic investigations with a relatively high degree of user independence. In the training course design, this is intentionally built-in, to allow us to show a wide range of analytical techniques while providing enough experience to break the ice in all of them. Target Audience This course is intended for those wishing to investigate how they might begin to exploit the ever expanding abundance of computing and data resources for researchers seeking help in using them. Best, Pedro Fernandes -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt Upcoming courses: AAIRR16 - Analysis of Adaptive Immune Receptor Repertoires, Nov 2 AET16 - Applied Evolutionary Theory, Nov 7 IBSTAT16 - Introductory Biostatistics for Biologists, Nov 14 IB16S - Introductory Bioinformatics, Dec 12 _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

1 0

CORBEL: Data Visualisation for Biology
by Alexander Botzki 28 Oct '16

28 Oct '16

Data Visualisation for Biology: a practical workshop on design, techniques and tools 30th Jan - 3rd Feb 2017, EMBL-EBI Application deadline: Friday, 11th November 2016 http://www.ebi.ac.uk/training/events/2017/data-visualisation-biology-practi… As biological datasets increase in size and complexity, we are moving more and more from an hypothesis-driven research paradigm to a data-driven one. As a result, exploration of that data has become even more crucial than in the past. In this 5-day workshop, we will dive into the topic of biological data visualization and how it can be used to gain insight in and get a "feel" for a dataset, so that targeted analyses can be defined. We will start by covering theoretical questions like: What is data visualization? How do we perceive images? How can we visualise data in the best possible way? As the workshop continues, it will become more and more hands-on and interactive; a large part will be committed to creating visualisations using the P5 javascript library, based on biological data. In the workshop, we will focus on omics (e.g. genomics, transcriptomics) data rather than e.g. imaging data. This course is in association with CORBEL and KU Leuven Kind regards Vera -- Vera Matser PhD Training Liaison Officer, EMBL-EBI ORCID: 0000-0002-2010-6844 Tel: +44 (0)1223 49 4149 Skype: vera_matser e-mail: matser(a)ebi.ac.uk Twitter: @VeraMatser URL: www.ebi.ac.uk/training Find us in on-course®: www.on-course.eu European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Genome Campus Hinxton Cambridge CB10 1SD UK

1 0

[Second announcement] Python for Life Scientists, , Fall edition, November 10-11, Amsterdam
by Alvise Trevisan 25 Oct '16

25 Oct '16

Dear all, this week is the last chance to register at the Early Bird price for the course "Python for Life Scientists". Tailored to life scientists with little or no prior programming experience, the course is driven by real-life use cases. Participants will learn by doing, completing snippets of code that they will be able to reuse in their everyday tasks. Extensive use of IPython Notebooks (Jupyter) will encourage participants to annotate and document the code, building the basis for a sound and reproducible methodology for data analysis . The course will run on November 10-11, 2016 in Amsterdam. More information and the registration form are available at the web site: http://www.enpicom.com/training/python Feel free to spread this information to people that might be interested. Kind Regards, Alvise Trevisan -- Alvise Trevisan ENPICOM | Science Park 402 | 1098 XH Amsterdam | The Netherlands www.enpicom.com<http://www.enpicom.com/> +31 20 895 0964 +31 61 496 4730

1 0

Research Informatics, BASF
by Koen Bruynseels 21 Oct '16

21 Oct '16

Dear All, For the informatics-savvy ... We are looking for an expert in Research Informatics, for a position in CropDesign / BASF. Full description you can find in attach. Job content: ? As an integral member of various highly motivated and dynamic project teams in our global IT department you will work out computational solutions for research problems. ? You will collaborate with scientists and IT experts to improve and maintain the global research informatics platforms of BASF. ? Your responsibility will include requirements capturing, system conception and software implementation according to high quality standards. ? Besides you will also scout novel third party IT solutions to integrate them into the BASF IT landscape. Skills: * You have several years of experience in professional software development for scientific data analysis. * Your education in the areas of informatics, statistics or natural sciences provides a well-founded basis for understanding complex scientific problems. * You possess sound knowledge of IT concepts including relational databases, web applications, object oriented systems and service oriented architecture. * You have good knowledge and professional experience with programming languages (Java, R). * You have good analytical and communication skills, fluently speaking English (Dutch is a plus). Experience in interacting with scientists is of advantage. * You are a creative and motivated team player, open for changes and new challenges Dr. Koen Bruynseels Manager Systems Biology, R&D Digitization (GOM/BB) Phone: +32 92423-456 Mobile: +32 474 296 225 Fax: +32 92423-489 E-Mail: koen.bruynseels(a)cropdesign.com Postal Address: CropDesign N.V., GBP - BIO II, 9052 Gent (Zwijnaarde), Belgium CropDesign N.V. - A BASF Plant Science Company Registered address: CropDesign N.V. - Technologiepark 21 - 9052 Gent (Zwijnaarde) - Belgium - rpr gent: 0463 222 213 - General Telephone: 32-9-242 34 00 - Fax: 32-9-242 34 89 Confidentiality notice: The information contained in this e-mail is confidential and may be the subject of legal professional privilege. It is intended for the authorized use of the individual or entity addressed. If the receiver or reader of this message is not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is prohibited. If this email is received in error, please accept our apologies, delete all copies from your system, and notify us at info(a)cropdesign.com.

1 0

PhD position microbial bioinformatics - KU Leuven
by Karoline Faust 18 Oct '16

18 Oct '16

Dear all, I am looking for a highly motivated PhD candidate interested in developing novel network analysis techniques for microbial community sequencing data. For more information and application submission, please see: https://icts.kuleuven.be/apps/jobsite/vacatures/53933830 All the best, Karoline Karoline Faust --------------------------------------------------- Email: karoline.faust(a)kuleuven.be Web: http://tinyurl.com/MicrobialSysBio --------------------------------------------------- Room 7.A130, Rega Institute Laboratory of Molecular Bacteriology Department of Microbiology and Immunology KU Leuven, Campus Gasthuisberg Herestraat 49, postbus 1028 3000 Leuven Belgium ---------------------------------------------------

1 0

PhD vacancy 'Systems biology of metabolism for human health'
by Egon Willighagen 15 Oct '16

15 Oct '16

Hi all, I have a vacancy for a PhD position with the title "Systems biology of metabolism for human health". The full description can be found at AcademicTransfer: https://www.academictransfer.com/employer/UM/vacancy/36534/lang/en/ "Health research uses large scale (omics) methods to study the state of an individual, organs, and increasingly tissues and even single cells. These methods can measure gene expression, epigenetics, and protein abundances. While great steps forward are made in these fields, a further omics approach is upcoming. Metabolomics methods complement the aforementioned methods, by studying the abundances of small molecular compounds in bodily fluids, tissue samples, breath, etc. Combining data for low molecular compounds with data for gene products will provide an insight in how personal genetics leads to disease related metabolic phenotypes. Changes in metabolism are relevant for many diseases, such as metabolic diseases, hereditary diseases, and cancers, and is also relevant in the symbiotic interaction of the gut microbiome and the (human) body. [...]" I am looking for someone who can write software, has data analysis skills, and knows a good deal of chemistry and biology. Sharing with M.Sc. students is very much appreciated! With kind regards, Egon -- E.L. Willighagen Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ORCID: 0000-0001-7542-0286 ImpactStory: https://impactstory.org/u/egonwillighagen

1 0

Call for participation Lorentz workshop on “big data solutions for genomics in plant breeding”.
by Marcel Reinders - EWI 13 Oct '16

13 Oct '16

Call for participation Lorentz workshop on “big data solutions for genomics in plant breeding”. Currently, data is generated for thousands of accessions with each containing tens of millions of markers. Having many (e.g. over 1000) highdensity genotyped individuals available for per species will become reality for breeding companies within the coming years. Current de facto standard for storing variants are optimized for positional queries but do not allow for flexible and fast interrogation of the data on other features than position. Participants in this workshop will work together to investigate possible Big Data solutions (both in infrastructure as well as data accession schemes) and will explore pilot implementations. Interested? Please register at https://www.lorentzcenter.nl/lc/web/2016/851/info.php3?wsid=851&venue=Oort (registration is still possible!) This workshop is part of the NWO ICT With Industry Lorentz workshop: ------------------------------------------------------------------------------------------------------------------------------ Call for Participation The Steering Committee (Alexandru Iosup, Ana Oprescu, Arend Rensink, Claudia Hauff, Joaquin Vanschoren and Remco Veltkamp) of the workshop ICT with Industry 2016 invites you to participate in the Lorentz Center workshop ICT With Industry November 07 – 11, 2016 The workshop offers you one week to explore your research ideas on case studies submitted by ING, KLM/Thales, SNS bank and Virtual Laboratory Plant Breeding VLPB (Bejo Zaden, Bayer CropScience, Rijk Zwaan. You will be part of a team dedicated researchers from a various ICT-disciplines. The goal is to come to concrete ideas which can be used for e.g. scientific paper, funding proposal to be submitted to NWO, STW or Horizon 2020. Workshop Format The ICT with Industry workshop brings together scientists, in particular (junior) research staff and PhD’s, and professionals from industry and government, to face and resolve complex study cases. The workshop revolves around 5 concrete case studies, which are subject to an intense week of analyzing, discussing, modeling and accelerating solutions. The Lorentz Center stimulates an interactive atmosphere, encouraging collaborations between participants. This format typically generates extensive debates and enables significant progress to be made during the meeting. Lorentz Center Facilities The workshop is held at the Lorentz Center, located at the Faculty of Science campus of Leiden University, the Netherlands. The Lorentz Center provides each participant with office space and wireless internet access (LINUX and Windows). Thanks to the workshop sponsors, Lorentz Center also provides accommodations at the nearby hotel “Van der Valk Hotel Leiden” free of charge (based on shared rooms, or at a minimal charge in case you prefer a single room. In the last case please ask for this in the registration form), and bike rental. For further information, please refer to our website: http://www.lorentzcenter.nl<http://www.lorentzcenter.nl/>. Costs and Refunds Lorentz Center does not charge registration fees. In addition, all food and drinks during the workshop are free of charge. For PhD-students the workshop can be used as part of the school’s training program credits system, which means that participants can apply for credits by attending the workshop. At the end of the workshop NWO will issue a letter of attendance upon request. Although your personal participation would be very much appreciated, you are especially invited to bring the workshop to the attention of bright junior scientists in your environment, who may register in your stead. Their final approval to the workshop is at the discretion of the organizers. They will be informed on their admission in September 2016 at the latest. Female researchers are encouraged to participate in the workshop. If you or one of your group members decides to accept this invitation, we do expect participation for the entire week. Registration We hope that you are interested in participating in the workshop. If so, we kindly ask that you register asap via the workshop webpage: Lorentz Center: https://www.lorentzcenter.nl/lc/web/2016/851/info.php3?wsid=851&venue=Oort NWO: http://www.nwo.nl/over-nwo/organisatie/nwo-onderdelen/ew/bijeenkomsten/ict+… More information about the workshop: Lorentz Center: Martijn Fritsen fritsen(a)lorentzcenter.nl<mailto:fritsen@lorentzcenter.nl> or +31 71 527 55 42 NWO: Rosemarie van der Veen-Oei ictwithindustry(a)nwo.nl<mailto:ictwithindustry@nwo.nl> or +31 70 405 87 STW: Margriet Janz m.jansz(a)stw.nl<mailto:m.jansz@stw.nl> or +31 6 2907 28 12 ------------------------------------------------------------------------------------------------------------------------------

1 0

Python for Life Scientists, Fall edition 2016, November 10-11, Amsterdam
by Celia van Gelder 11 Oct '16

11 Oct '16

Dear all, I am writing to announce the Fall 2016 edition of the course "Python for Life Scientists" from ENPICOM. Tailored to life scientists with little or no prior programming experience, the course is driven by real-life use cases. Participants will learn by doing, completing snippets of code that they will be able to reuse in their everyday tasks. Extensive use of IPython Notebooks (Jupyter) will encourage participants to annotate and document the code, building the basis for a sound and reproducible methodology for data analysis . The course will run on November 10-11, 2016 in Amsterdam. More information and the registration form are available at the web site: http://www.enpicom.com/training/python Please notice that there is a reduction of the course fee for BioSB members. Feel free to spread this information to people that might be interested. Best Celia van Gelder -- Dr. Celia W.G. van Gelder Programme Manager Learning DTL/ELIXIR-NL Training Education Manager BioSB tel. +31613375327 e-mail: celia.van.gelder(a)dtls.nl websites: www.dtls.nl, www.biosb.nl skype: celia.van.gelder Postal address: DTL PO Box 19245 3501 DE Utrecht

1 0

PhD position "Graph Theory & Algorithms for Evolutionary Biology" at TU Delft, Netherlands
by Leo van Iersel 10 Oct '16

10 Oct '16

The optimisation group at Delft University of Technology in the Netherlands is seeking a PhD student on the project “Encoding, reconstructing and comparing complex evolutionary scenarios” financed by The Netherlands Organization for Scientific Research (NWO). This project aims at developing new graph theory, algorithms and software tools which can be used by biologists to reconstruct networks describing the evolutionary relationships between species. The standard, well-studied model for describing such relationships is the phylogenetic tree, which has leaves representing species and internal vertices representing divergence events. However, actual evolutionary histories are often complex webs of diverging and combining lineages, which can better be described by networks than by trees. Accurately reconstructing such networks is a challenging task. Therefore, this project involves the development of new (graph) theory, algorithms and software as well as working with biologists to apply the developed theory and software in practice. For more information, see https://www.academictransfer.com/employer/TUD/vacancy/36363/lang/en/

1 0