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

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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Job opening
by L.M. Kamminga 07 Oct '16

07 Oct '16

Dear all, I am looking for a computational biologist to study genetics and epigenetics of developmental biology to join my team. You can find the details about the job opening in the attachment. To apply go to: https://www.radboudumc.nl/werkenbij/Pages/Vacatures.aspx?vacid=39541&naam=Co mputational%20Biologist%20Genetics%20and%20Epigenetics%20of%20Developmental% 20Biology&afdeling=Department%20of%20Physiology&plaats=nijmegen Kind regards, Leonie Kamminga -- Leonie Kamminga, PhD Assistant Professor Molecular Biology RadboudUMC/RIMLS T +31(0)24 361 6850/3988 F +31(0)24 361 0520 http://rimls.aride.nl/people/k/kamminga/ MAIL RIMLS/RadboudUMC | 274 Dept. Molecular Biology | PO BOX 9101| 6500HB Nijmegen | The Netherlands VISITOR Molecular Biology 274 | Geert Grooteplein 26-28 | 6525GA Nijmegen | The Netherlands SHIPMENT RIMLS M850/3.079 Dept of Mol. Biol. 274 | Geert Grooteplein 30 | 6525GA Nijmegen | The Netherlands

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Schedule BIG N2N seminars 2016 - 2017
by Sophie Maebe 06 Oct '16

06 Oct '16

Dear All, Please find attached an overview of the BIG N2N seminars in 2016-2017. With kind regards, Sophie Sophie Maebe Administrative assistant Tel:+32 (0)9 331 38 08 Department of Plant Systems Biology VIB, Ghent University Technologiepark 927 9052 Ghent, Belgium http://www.psb.ugent.be

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BioSB Course Matlab (2nd edition), 28 October 2016, Wageningen
by Celia.vanGelder＠radboudumc.nl 04 Oct '16

04 Oct '16

BioSB Course Matlab, 28 October 2016, Wageningen Website: http://biosb.nl/education/course-portfolio-2/course-matlab/ . Coordinators: Hans Stigter (WUR), Celia van Gelder (BioSB, celia.van.gelder(a)biosb.nl<mailto:celia.van.gelder@biosb.nl>) Registration: http://biosb.nl/education/course-portfolio-2/course-matlab/enrollment-cours… Please note that if you are (or become) a member of BioSB this course is free of charge for PhD students and with reduced fee for other researchers! Goal The main goal of this course is to get acquainted with Matlab software for use within Systems Biology. After this introductory course you will have gained the basic knowledge to pursue further use via self-study of Matlab in order to apply more advanced programming techniques within Matlab in your own research. In summary, the sub-goals are: 1. To learn the philosophy behind Matlab and its syntax 2. To program simple Systems Biology models in Matlab (in ordinary differential equation format) and to solve these differential equations with Matlab Target audience Primarily targeting researchers from academia, but participants from the private sector are also welcome. The course focusses on the use of Matlab for building dynamic Systems Biology Models in terms of ordinary differential equations. Course Description This is a one-day introduction to the possibilities of Matlab as a programming environment for simulation and analysis of biological models. We will start with a simple introduction of the basics of Matlab (matrices, vectors, manipulation of matrices and presentation of data). Having obtained some basic programming knowledge (writing of simple scripts and functions in Matlab), we will move on to more advanced topics. These include programming and solving ordinary differential equation models (ODEs) and the concept of "vectorized thinking" while writing Matlab-code. Finally, calibration of parameters in ODE type of models using measured data will be discussed and examples will be given. The course also includes the basics of presenting your results (graphing) in various types of plots that can easily be drawn in Matlab. Participants will, of course, get hands-on experience with Matlab and write code themselves in a practical. Programme 09:45 Coffee/Tea 10:00 Welcome 10:05 Introduction Matlab Basics (functions, variables, matrices, etc) 10:45 Advanced Programming (vectorised thinking, solving dynamic ordinary differential equation models in Matlab, parameter estimation for ODE-models) 12:00 Afternoon: Solving basic and advanced problems in Matlab - hands-on experience on a PC. Exercises will be provided, but you can also bring your own problems that you have encountered in your own research. 12:30 Lunch 15:00 Coffee/tea 16:30 End BioSB Education Programme This course is part of the Education Programme of BioSB, the Netherlands Bioinformatics and Systems Biology Research School, which offers training and education in bioinformatics and systems biology. More information about BioSB can be found at www.biosb.nl<http://www.biosb.nl/> or via education(a)biosb.nl<mailto:education@biosb.nl>. 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<http://www.dtls.nl/>, www.biosb.nl<http://www.biosb.nl/> skype: celia.van.gelder Postal address: DTL PO Box 19245 3501 DE Utrecht 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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Registration open: BioSB course Comparative Genomics (3rd edition), 21-25 November 2016, Nijmegen
by Celia.vanGelder＠radboudumc.nl 04 Oct '16

04 Oct '16

BioSB Course Comparative Genomics: from evolution to function (3rd edition) - Registration open Date: November 21-25, 2016 Location: CMBI, Radboudumc, Nijmegen, the Netherlands Course coordinators: Berend Snel (UU), Martijn Huynen (Radboudumc), Jaap Heringa (VU), Celia van Gelder (BioSB) Course website: http://biosb.nl/education/course-portfolio/course-comparative-genomics/ Registration: http://biosb.nl/education/course-portfolio/enrollment-comparative-genomics-… More information: education(a)biosb.nl<mailto:education@biosb.nl> Course description Comparative genomics between species and between types of data facilitates the understanding of what these data really reflect about the underlying biological processes. Comparative genomics therewith relies on a solid understanding of basic elements of Bioinformatics like homology and orthology. Moreover it is important to know the assumptions and heuristics of bioinformatic methods for comparative genomics and hence we aim to let participants develop an understanding of why these methods sometimes fail (or misdetect) as a consequence of a variety of biological /evolutionary causes, and in which situations which method is most appropriate. The first two days of the course provide a basis for the course with the aim to move "beyond blast" in terms of the most sensitive homology searches, domain level analysis of protein evolution as well as more fine grained definitions of relatedness as can be obtained from the proper interpretation of gene trees (i.e. various levels of orthology). This foundation is used to discuss in the three following days in more detail three topics: (1) the study of functional and evolutionary consequence of (genome) duplications, (2) the evolution of interactions and complexes and (3) the prediction and evolution of genomic regulatory elements and of RNA structures Target audience The course is intended for PhD students and master students in bioinformatics or geneticists and experimental biologists with a strong interest in evolution of the eukaryotes. It is especially relevant to students who want to compare various types of genomics data between species. Participants are expected to have some hands on experience with tools like blast, constructing multiple sequence alignments and phylogenetic trees, and in addition to have some familiarity with concepts such as orthology, synteny and protein domains. Programme Monday November 21: Distant homology and protein domains (lecturer Jaap Heringa) Topics & Tools: Divergent and convergent evolution, (multiple) sequence alignment, psiblast, jackhmmer, hhsearch, pfam, homology and function, undetected orthology from failure to detect homology, paralogs and function specificity prediction Tuesday Nov 22: Comparative Interactomics (lecturers Jaap Heringa, Martijn Huynen/John van Dam) Topics & Tools: network alignment, phylogenetic profiles, biogrid, cytoscape, Bayesian data integration, neofunctionalization vs subfunctionalization Wednesday nov 23: Small scale orthology and large scale databases (lecturers Martijn Huynen, Berend Snel) Topics & Tools: tree reconciliation, relation between homology and orthology, ensembl compara, COGs, inparalogs vs outparalogs, fusion and fission Thursday nov 24 : Genome duplications (lecturer Berend Snel) Topics & Tools: yeast gene order browser, synteny, consequences of genome duplications, timing of duplications, ensembl biomart Friday nov 25: Finding functional elements in DNA and RNA sequences, Biased gene conversion (lecturer Martijn Huynen) Topics & Tools: phylogenetic footprinting, (phylogeny aware) gibbs sampling, RNA secondary structure prediction based on sequences and on experimental data, biased gene conversion & positive selection. BioSB Education Programme This course is part of the Education Programme of BioSB, the Netherlands Bioinformatics and Systems Biology research school, which offers training and education for in bioinformatics and systems biology. More information about BioSB can be found at www.biosb.nl<http://www.biosb.nl>. More information For more information about the course you can contact Celia van Gelder at education(a)biosb.nl<mailto:education@biosb.nl>. 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<mailto:celia.van.gelder@dtls.nl> websites: www.dtls.nl<http://www.dtls.nl/>, www.biosb.nl<http://www.biosb.nl/> skype: celia.van.gelder Postal address: DTL PO Box 19245 3501 DE Utrecht 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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Online Galaxy training material hackathon
by Frederik Coppens 04 Oct '16

04 Oct '16

Hi all I would like to bring this hackathon to your attention: https://www.elixir-europe.org/events/galaxy-training-material-hackathon <https://www.elixir-europe.org/events/galaxy-training-material-hackathon> It’s an online contribution fest organized by the Galaxy Training Network, October 6-7. This stems from an idea at GCC2016 to centralize Galaxy training material on github. Bjoern Gruening already collected a lot of material (checkout https://github.com/bgruening/training-material <https://github.com/bgruening/training-material>) and we’d like to further grow this resource and make it more uniform. You can (optionally) indicate your interest here: https://github.com/bgruening/training-material/issues/58 <https://github.com/bgruening/training-material/issues/58> You can find a list of topics here: https://github.com/bgruening/training-material/issues <https://github.com/bgruening/training-material/issues> Everybody’s welcome to join, you really don’t need programming skills to contribute. If the hackathon doesn’t fit your schedule (it’s a bit short notice, I realise), you can always contribute at a later point, as everything is available on github. cheers Frederik ================================================================== Frederik Coppens, Ph.D. Project Leader Applied Bioinformatics & Biostatistics IT manager Tel: 32 (0)9 3313812 Fax:32 (0)9 3313809 VIB DEPARTMENT OF PLANT SYSTEMS BIOLOGY, UGent Technologiepark 927, 9052 Gent, BELGIUM frcop(a)psb.ugent.be http://www.psb.ugent.be/abb ==================================================================

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Internship opportunities at EdgeLeap
by Thomas Kelder 03 Oct '16

03 Oct '16

Dear all, We at EdgeLeap http://www.edgeleap.com/ have multiple opportunities for internship projects for aspiring data scientists! Check out the attached description for details and please forward to your prospective bioinformatics students. Many thanks in advance! Best regards, The EdgeLeap team ------------ Thomas Kelder, PhD Chief Scientific Officer EdgeLeap B.V. Hooghiemstraplein 15 3514 AX Utrecht The Netherlands Phone: +31-6-41941301 Email: thomas(a)edgeleap.com www.edgeleap.com

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