- BBClist - maillist.psb.ugent.be

[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

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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.

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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 ---------------------------------------------------

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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

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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 ------------------------------------------------------------------------------------------------------------------------------

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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

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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/

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winterschool in biological data visualization
by Jan Aerts 10 Oct '16

10 Oct '16

Hi all, We'd like to invite you to attend the winterschool in biological data visualization, which will be held at the European Bioinformatics Institute (Hinxton, UK) from January 30 till February 3, 2017. In this course, we will go into the need for (interactive) visualization in current-day data-rich biological science, including primers on e.g. cognition and perception. This will be followed by exercises to learn how to explore design space, and an introduction to coding in P5 (a javascript library for visualization). Ultimately, these newly-acquired skills will be applied in a project. For more information or to register, please check http://www.ebi.ac.uk/training/events/2017/data-visualisation-biology-practi… Kind regards, Jan Aerts --- Prof Jan Aerts Visual Data Analysis Lab (VDA-lab), ESAT/STADIUS KU Leuven http://www.esat.kuleuven.be/stadius/ http://vda-lab.be

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[Gtpb] GTPB Bioinformatics Training course announcement - IBSTATB16 - Introductory Biostatistics for Biologists
by Pedro L. Fernandes 10 Oct '16

10 Oct '16

The Gulbenkian Training Programme in Bioinformatics Applications for the bioinformatics training course IBSTATB16 Introductory Biostatistics for Biologists with Cristina Rocha and Fernanda Diamantino are now open. IMPORTANT DATES for this Course Deadline for applications: Nov 7th 2016 Course dates: Nov 14th - Nov 18th 2016 http://gtpb.igc.gulbenkian.pt/bicourses/IBSTATB16/ Course Description This is one of our "Foundations" type courses, providing a systematic and detailed review of fundamental concepts and techniques in Biostatistics. Participants can expect to go through a set of exercises that are based on biomedical problems. These exercises are preceded by short lectures that are simple to follow. The lectures are designed to provide the conceptual framework that is needed to release the training power of the exercises, not to flood the participants with formality, which will be kept to a minimum. We will make use of a highly interactive methodology, taking advantage of our well equipped Bioinformatics training room. With this approach, we expect to bring the participants to a high degree of usage independence in using the methods that we cover. Main topics: Descriptive Statistics; Probability; Statistical Inference; Design of Experiments. At the moment, GTPB has 5 training courses OPEN for applications. Best regards 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: 3DAROC16 - 3C-based data analysis and 3D reconstruction of chromatin folding, Oct 10 QPB16 - Quantitative Proteomics using Bioinformatics, Oct 17 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

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Introduction to ChIP-seq Data Analysis and Visualisation using Ensembl 22-23 Nov 2016 - Places available
by Bert Overduin 07 Oct '16

07 Oct '16

We still have a few places available on our workshop "Introduction to ChIP-seq Data Analysis and Visualisation using Ensembl" on 22-23 November 2016 in Edinburgh. For details, please see below. To apply, please go to: http://genomics.ed.ac.uk/services/introduction-chip-seq-data-analysis-and-v… With kind regards, Bert *Date:* Tuesday 22 - Wednesday 23 November 2016 *Venue:* The King's Buildings, The University of Edinburgh, Edinburgh, Scotland, UK *Application deadline:* Tuesday 25 October 2016 noon *Cancellation deadline:* Tuesday 15 November 2016 noon *Places:* 12 (selection of applicants) *Registration fee:* £310 (includes coffee/tea, and lunch) ChIP-seq (Chromatin ImmunoPrecipitation followed by Sequencing) is a popular high-throughput sequencing assay to identify binding sites of DNA-associated proteins and histone modifications. Determining how proteins interact with DNA and the epigenetic landscape is essential for elucidating the regulation of gene expression. The aim of this workshop is to familiarise the participants with the primary analysis of ChIP-seq data sets by providing a balanced set of lectures and practicals on analysis methodologies. Practicals include publicly available ChIP-seq datasets, processed using widely used and open-source software programs (e.g. FASTQC, BWA, samtools, bedtools, wiggletools, MACS2, MEME, TOMTOM, ngsplot) and visualised on the Ensembl genome browser. "Very well presented and the presenters were so knowledgeable and helpful." (July 2015) *Instructors* Dr. Myrto Kostadima (Ensembl Regulation Project Leader, European Bioinformatics Institute, Hinxton, Cambridge, UK) Dr. Ben Moore (Ensembl Outreach Officer, European Bioinformatics Institute, Hinxton, Cambridge, UK) * This workshop is made possible by the free of charge contribution of the Ensembl team * *Workshop format* The workshop consists of presentations, demos and hands-on tutorials. *Who should attend* Graduates, postgraduates, and PIs, who are using, or planning to use, ChIP-seq technology in their research and want to learn how to process and analyse ChIP-seq data. *Requirements* A general understanding of molecular biology and genomics, and elementary skills in computer usage are required. *Covered topics* High-throughput sequencing technology Considerations on experiment design for ChIP-seq Quality control of raw reads: FASTQC and fastx toolkit Read alignment to a reference genome: BWA File format conversion and processing: samtools and wiggletools Peak calling: MACS2 Motif analysis: MEME IDR analysis Genome browser visualisation and trackhub generation: Ensembl -- 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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