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[Gtpb] ANNOUNCEMENT: GTPB Bioinformatics Training course AAIRR16 - Analysis of Adaptive Immune Receptor Repertoires
by Pedro L. Fernandes 05 Sep '16

05 Sep '16

The Gulbenkian Training Programme in Bioinformatics Applications for the bioinformatics training course AAIRR16 - Analysis of Adaptive Immune Receptor Repertoires With Simon Frost (U. Cambridge) are open. Please refer to the course website http://gtpb.igc.gulbenkian.pt/bicourses/AAIRR16 for details. IMPORTANT DATES for this Course Deadline for applications: Oct 12th 2016 Course dates: Nov 2nd - Nov 4th 2016 Course Description This course will cover the analysis of B and T cell repertoires (adaptive immune receptor repertoires, or AIRR) from high-throughput sequencing data using bioinformatics workflows. Topics include germline allele assignment, identification of clones, and visualisation/analysis of clonal frequencies. The course will also cover emerging standards (VDJML, Change-O) in the analysis and reporting of Adaptive-immune Receptor Repertoire (AIRR) data. In addition to an introduction to software used, such as IgBLAST, pRESTO, Change-O, etc., the course will also provide an introduction to the use of Jupyter notebooks for conducting exploratory analyses and the Common Workflow Language to automate analyses. To get a flavour of the techniques and software that will be used in the course. IgBLAST pRESTO Change-O Discussion site: B-T.CR Best regards Pedro Fernandes -- Pedro Fernandes GTPB Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt Upcoming courses: PM16 - Precision Medicine, Sep 27 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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[Gtpb] REMINDER: GTPB Bioinformatics Training course announcement/reminder - Precision Medicine - PM16
by Pedro L. Fernandes 05 Sep '16

05 Sep '16

Deadline for Applications - September 12th 2016 The Gulbenkian Training Programme in Bioinformatics Applications for the bioinformatics training course PM16 - Precision Medicine with Fatima Al-Shahrour, Javier Perales and Elena Piñero are open. Please refer to the course website http://gtpb.igc.gulbenkian.pt/bicourses/PM16 for details. Course Description The implementation of cancer genomics into the clinic is becoming a reality. Personalized medicine or Precision medicine as other authors refers, uses molecular data of a specific patient to guide clinical decisions such as prevention, diagnosis and treatment. This will revolutionize healthcare and will play a dominant role in the future of cancer therapy. Bioinformatics analyses are essential to identify patients who will benefit from treatment based on their molecular profile, and to tailor chemotherapeutic regimens accordingly. The aim of the course is to present a complete computational pipeline for the analysis and interpretation of Next-Generation Sequencing (NGS) data such as exome sequencing or targeted panels that are commonly used in the clinic. We will address the implementation of large-scale genomic sequencing in clinical practice and the recently developed computational strategies for the analysis of NGS data with a particular emphasis on the interpretation of the results, selection of biomarkers of drug response and afford opportunities to match therapies with the characteristics of the individual patient's tumour. Exercises and case studies focused on cancer will be used to illustrate the principles of how genetics influence led to refining diagnoses and personalized treatment of cancer disease. Best regards Pedro Fernandes -- Pedro Fernandes GTPB Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt Upcoming courses: PM16 - Precision Medicine, Sep 27 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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Announcement META-scan workshop: MRS and Systembiology 3-oct-2016 Utrecht NL - Registration deadline 19-sept-2016
by Jeneson, JAL (med) 02 Sep '16

02 Sep '16

Are you a Magnetic Resonance user? or a computational modeler? Then we have just the workshop for you! On Monday October 3rd 2016, we will bring together MR users, computational modelers and physicians to exchange methods and ideas on how these disciplines may be bundled to advance Systems Medicine efforts to combat complex human diseases such as cancer and metabolic disease including diabetes. This one-day workshop will feature a morning session with introductory lectures by experts from the field of Systems Medicine, followed by an afternoon session with break-out groups on specific organ/disease topics to stimulate discussion and future collaboration between in vivo MR experimentalists and computational modelers. A panel discussion followed by drinks will close the day. A more detailed program of the workshop can be found at the end of this email. Registration for this one-day workshop at UMC Utrecht is free. Just send an email that you will attend the workshop to: mrsandsystembiology(a)gmail.com<mailto:mrsandsystembiology@gmail.com> before Monday September 19th. Please specify your background (experimentalist versus modeler) as well as your preference for a particular break-out group in the afternoon session (choose from [1] cancer; [2] heart; [3] liver; [4] musculoskeletal). Please send out this invitation to your co-workers who might be interested to join! We look forward to seeing you in Utrecht on October 3rd! The organizers. - Jannie Wijnen, Jeanine Prompers and Jeroen Jeneson Program Workshop on Magnetic Resonance and Systems Medicine Monday October 3 2016 UMC Utrecht, Auditorium Q1 Program 9:30 - 10:00 Coffee and tea 10:00 - 10:05 Welcome and opening - Dennis Klomp Morning lectures: 10:05 - 10:30 "Complex Human Disease and Systems Medicine" - Hanneke van Laarhoven, MD/PhD, Clinical Oncology, AMC 10:30 - 11:15 "Systems Medicine - what is it? what does it bring to medical research and care?" - Barbara Bakker, PhD, Professor of Systems Medicine, Dept of Pediatrics, UMCG 11:15 - 12:00 "Systems Medicine and in vivo MRS - Examples from Cardiovascular Physiology and Medicine" - Dan Beard, PhD, Carl J. Wiggers Collegiate Professor of Cardiovascular Physiology and Professor of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA 12:00 - 12:25 "Systems Medicine and in vivo MRS: practice - in vivo MRS" - Ot Bakermans, Ir PhD, Postdoctoral Fellow, Dept of Radiology, AMC 12:25 - 12:30 Announcements afternoon program 12:30 - 13.30 Lunch Afternoon break-out sessions: 13:30 - 15:00 Oncology Moderated by Hanneke van Laarhoven and Natal van Riel (van Peperzeel room) Cardio Moderated by Tim Leiner and Dan Beard (Puylaart room) Musculoskeletal Moderated by Daniel Saris and Jeroen Jeneson (Klinkhamer room) Liver Moderated by Aart Nederveen and Barbara Bakker (Q01.305) 15:00 - 15:15 Coffee and tea 15:15 - 15:45 Wrap up of break-out sessions (van Peperzeel room) 15:45 Drinks ________________________________ De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.

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SECOND CALL - ISCB Belgium RSG and IB2 Bioinformatics STUDENT DAY
by Cuypers Bart 31 Aug '16

31 Aug '16

[cid:image008.png@01D1D2CF.7D3D07F0] SPECIAL BIOINFORMATICS EVENT ISCB Belgium RSG and IB2 Bioinformatics STUDENT DAY Friday, the 7th of October 2016 ULB-VUB La Plaine Campus, Brussels REGISTRATION (deadline 1st of October) Registration is free. Please register before the 1st of October with the following link : https://goo.gl/forms/qnJo31wynmyiiZ233 ABSTRACT CALL (deadline 16th of September) Twelve PhDs-Postdoc abstracts will be selected for oral presentations. Please send your abstract to this address ib2rgs(a)gmail.com<mailto:ib2rgs@gmail.com> For the Full program and abstract call information, please see the attached pdf Keynote speakers Prof. Richard REDON INSERM, Nantes, France Deciphering the genetic architecture of complex disorders: one experience on the Brugada syndrome 11.30 am – 12.30 pm Prof. Antonio RAUSELL IMAGINE, Paris, France Bioinformatics and functional genomics of human immune diseases: from genome analysis to single-cell transcriptomics 2 - 3 pm Prof. Jacques BECKMANN SWISS BIOINFORMATICS INSTITUTE, Lausanne, Switzerland Evidence-based precision medicine in the context of big data 5 - 6 pm On Behalf of RSG Belgium and IB2, Guillaume, Andrea and Bart

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BioSB course RNA-seq data analysis course (6th edition), 26-28 September 2016
by Celia van Gelder 30 Aug '16

30 Aug '16

BioSB RNA- seq data analysis course (6th edition) Date: 26-28 September, 2016 Location: Leiden, the Netherlands Course coordinators: Peter-Bram 't Hoen (LUMC), Jan Oosting (LUMC), Celia van Gelder (BioSB, <mailto:education@biosb.nl> education(a)biosb.nl ) Course website: <http://biosb.nl/education/course-portfolio/rna-seq/> http://biosb.nl/education/course-portfolio/rna-seq/ . Registration: <http://biosb.nl/education/course-portfolio/rna-seq/enrollment-rnaseq-2016/> http://biosb.nl/education/course-portfolio/rna-seq/enrollment-rnaseq-2016/ More information: <mailto:education@biosb.nl> education(a)biosb.nl Course description BioSB and partner LUMC are organizing a 3-day course on RNA-seq. This is an expert course for people with experience in NGS and a follow-up course on the general NGS data analysis course (coordinator Jeroen Laros, LUMC). The course will consist of seminars and hands-on command line, Galaxy and R practicals and will focus on data preprocessing, quality control, alignment, visualization and statistics for differential transcript expression. Examples will be taken from human and mouse studies. The course does not cover prokaryotic RNA profiling nor plant- and metagenomics aspects. Course topics RNA-seq experimental approaches Alignment and de novo assembly Statistics for differential gene expression eQTL analysis and allele specific expression Variant calling and RNA editing Small RNA profiling Software for RNA-seq data analysis Programme The programme can be found here: <http://biosb.nl/wp-content/uploads/2016/07/RNAseq_program_2016_v4.pdf> http://biosb.nl/wp-content/uploads/2016/07/RNAseq_program_2016_v4.pdf Target audience Participants for the RNA-seq course should preferably have participated in the general NGS course or otherwise have demonstrated hands-on experience with NGS data analysis. The course is aimed at PhD students and post-docs, but scientific programmers and data analysts with a background in biology and bioinformatics may also attend. The practicals are mostly in R. We require that participants have at least basic knowledge of R and experience in running R scripts. Registrations will be handled on a first-come-first-served basis but experience and motivation will be reviewed. Seats have been reserved for participants in the FP7-funded projects <http://rd-connect.eu/> RD-Connect, <http://www.rd-neuromics.eu/> Neuromics, <http://www.eurenomics.eu/> Eurenomics and <https://www.bbmri.nl/> BBMRI-NL. BioSB Course Programme This course is part of the <http://biosb.nl/education/course-portfolio-2/> Course Portfolio 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 <http://www.biosb.nl> www.biosb.nl. More information For more information about the course you can contact Celia van Gelder at <mailto:education@biosb.nl> education(a)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: <http://www.dtls.nl/> www.dtls.nl, <http://www.biosb.nl/> www.biosb.nl skype: celia.van.gelder Postal address: DTL PO Box 19245 3501 DE Utrecht

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Fwd: Symposium on computational protein and drug design
by Daniele Parisi 30 Aug '16

30 Aug '16

-------- Original Message -------- Subject: Symposium on computational protein and drug design Date: 2016-08-30 15:48 From: Daniele Parisi <dparisi(a)esat.kuleuven.be> To: stadius(a)esat.kuleuven.be, BIG(a)ls.kuleuven.be Dear all, you are cordially invited to attend the Symposium on computational protein and drug design, in honour of the Professor Marc De Maeyer retirement (Chemistry department). It will take place on the 23th September at Thermotechnisch Instituut, Aula van de Tweede Hoofdwet (TI 01.02) 14h, followed (17h) by a free reception. Everything is free, but registration required here https://www.chem.kuleuven.be/emeritaat/ I hope to see you there, Kind regards Daniele Pari PhD student Member of PhD Leuven society and RSG Belgium KULeuven, ESAT-STADIUS, Bioinformatics group of Yves Moreau Leuven, Belgium -- Daniele Parisi PhD student Member of PhD Leuven society and RSG Belgium KULeuven, ESAT-STADIUS, Bioinformatics group of Yves Moreau Leuven, Belgium

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job opening Utrecht University: PhD student Genome Evolution of Basal Cellular Processes
by Berend Snel 29 Aug '16

29 Aug '16

PhD student Genome Evolution of Basal Cellular Processes (1.0 FTE, 4 years) Utrecht University We are looking for a PhD student as part of the recently awarded NWO VICI proposal “coevolution and convergence: understanding and exploiting genomic diversity of core cellular processes". An integral part of this project is the use of comparative genomics to study traces of coevolution and recurrent evolution in large genome data sets. This PhD project will encompass development of tools and databases that will allow the detection of these patterns in the rapidly increasing but also noisy data set of completely sequenced eukaryotic genomes. Profile We are looking for a motivated PhD student with a keen interest in evolution, bioinformatics and cell biology. The candidate has a Msc degree in bioinformatics, biology, biochemistry, computer science or a related field. Ideally the candidate has hands on research experience on ortholog inference methods and phylogenetic reconstruction. For more information and/or to apply see: http://www.peoplexs.com/Peoplexs22/CandidatesPortalNoLogin/Vacancy.cfm?Port… yours sincerely, Berend Snel

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Benelearn 2016: final call for participation
by Yvan Saeys 29 Aug '16

29 Aug '16

FINAL CALL FOR PARTICIPATION: BENELEARN 2016 September 12-13, 2016. Kortrijk, Belgium http://www.kuleuven-kulak.be/benelearn/ Benelearn is the annual machine learning conference of Belgium and The Netherlands. It serves as a forum for researchers to exchange ideas, present recent work, and foster collaboration in the broad field of Machine Learning and its applications. The 25th edition is co-organised by KU Leuven, UGent and the Flemish Supercomputer Centre, in cooperation with the Dutch Research School for Information and Knowledge Systems (SIKS), at the Katholieke Universiteit Leuven, Campus Kortrijk (KULAK). PROGRAM: This anniversary edition of Benelearn is organised on two days, where the first day focuses on large scale data analysis. The program consists of 8 invited talks, 8 selected talks, 16 short talks and around 50 posters. In order to stimulate discussion among PhD students / postdocs and the invited speakers, we will have a meet-the-speaker session. Furthermore, the conference dinner and lunch breaks will provide ample opportunity for networking. Finally, a job board will be available for the participants where perhaps you will find your next job in industry or academia! The full program is available at the conference website:http://www.kuleuven-kulak.be/benelearn/. List of invited speakers: Jeff Ullman (Stanford University): A Complexity Theory for MapReduce Algorithms Isaac Triguero (UGent / University of Nottingham): Big Data Learning in Practice Hugo Ceulemans (Janssen R&D): Predicting the activity of chemical compounds across 1001 biological assays at industrial scale Kristian Kersting (TU Dortmund): To be announced Greg Tsoumakas (Aristotle University of Thessaloniki): Multi-Target prediction: Challenges and applications Emilia Barakova (Technische Universiteit Eindhoven): Learning robots for autism therapy Christian Blum (University of the Basque Country): Combining metaheuristics with ILP solvers: Construct, Merge, Solve & Adapt Luc De Raedt (KU Leuven): On the history and future of machine learning: a personal interpretation and perspective REGISTRATION: Registration can be done through the conference website:http://www.kuleuven-kulak.be/benelearn/. Registration is possible up to and including Sunday 4 September. -- ====================================================================== Prof. dr. Yvan Saeys VIB Group Leader Data mining and modeling for biomedicine Inflammation Research Center, a VIB-UGent Department UGent Department of Internal Medicine, Respiratory Medicine (GE01) Technologiepark 927 , B-9052 Zwijnaarde , Belgium Tel : +32(0)9 331 37 40 Fax : +32(0)9 221 76 73 Mailto: yvan.saeys(a)ugent.be http://www.dambi.ugent.be ======================================================================

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Join the Bioinformatics for Young inTernational researchers Expo
by Cirillo Elisa (BIGCAT) 29 Aug '16

29 Aug '16

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[Gtpb] Fwd: GTPB Bioinformatics Training course announcement - AAIRR16 - Analysis of Adaptive Immune Receptor Repertoires
by Pedro L. Fernandes 28 Aug '16

28 Aug '16

The Gulbenkian Training Programme in Bioinformatics Applications for the bioinformatics training course AAIRR16 Analysis of Adaptive Immune Receptor Repertoires with Simon Frost (U. Cambridge) are now open. IMPORTANT DATES for this Course Deadline for applications: Oct 12th 2016 Course dates: Nov 2nd - Nov 4th 2016 http://gtpb.igc.gulbenkian.pt/bicourses/AAIRR16/ Course Description This course will cover the analysis of B and T cell repertoires (adaptive immune receptor repertoires, or AIRR) from high-throughput sequencing data using bioinformatics workflows. Topics include germline allele assignment, identification of clones, and visualisation/analysis of clonal frequencies. The course will also cover emerging standards (VDJML, Change-O) in the analysis and reporting of Adaptive-immune Receptor Repertoire (AIRR) data. In addition to an introduction to software used, such as IgBLAST, pRESTO, Change-O, etc., the course will also provide an introduction to the use of Jupyter notebooks for conducting exploratory analyses and the Common Workflow Language to automate analyses. To get a flavour of the techniques and software that will be used in the course. IgBLAST pRESTO Change-O Discussion site: B-T.CR Target audience The course was designed for experimentalist and students who want to explore adaptive immune repertoires using NGS data. Individuals that are working - or looking forward to work - in the area of T cell or B cell receptor analysis will benefit from attending this training course. At the moment, GTPB has 5 training courses OPEN for applications. Best regards Pedro Fernandes -- Pedro Fernandes GTPB Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt Upcoming courses: PM16 - Precision Medicine, Sep 27 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 ----- End forwarded message ----- _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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