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

[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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