- BBClist - maillist.psb.ugent.be

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 29 Aug '16

29 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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[Gtpb] GTPB Bioinformatics Training course announcement - QPB16 - Quantitative Proteomics using Bioinformatics
by Pedro L. Fernandes 28 Aug '16

28 Aug '16

The Gulbenkian Training Programme in Bioinformatics Applications for the bioinformatics training course QPB16 - Quantitative Proteomics using Bioinformatics with Mikhail Savitski (EMBL), Roman Zubarev (Karolinska) and Bo Zhang (Karolinska) IMPORTANT DATES for this Course Deadline for applications: Sep 24th 2016 Course dates: Oct 17th - Oct 19th 2016 http://gtpb.igc.gulbenkian.pt/bicourses/QPB16/ Course Description Recent years have seen rapid development in biological mass spectrometry and proteomics. In particular, the quantitative performance has taken a huge leap forward, both as a label-free (LF) approach and as multiplexed quantitative mass spectrometry. This development has enabled new technologies for unbiased characterization of drug molecules with protein targets, which is one of the major challenges in drug development. Here we will explain the basic principle of protein quantification by mass spectrometry. A pragmatic description of strengths and weaknesses of both label-free as well as the multiplexed methodology will be presented. A novel technology, thermal proteome profiling (TPP), will be explained that detects protein drug interactions in living cells. A practical session will take the students through the analysis and interpretation of quantitative mass spectrometry data stemming from the TPP experiment using an R package. In the LF part of the course, we will explain the basics of the identification software DeMix that performs deconvolution of the naturally multiplexed tandem mass spectra, thus significantly improving the identification aspects. An extension to quantification, DeMix Q, introduces the false discovery rate (FDR) for peptide identity transfer between the LC-MS runs, and greatly improves the quantification performance. Both DeMix and DeMix Q are realized based on Open MS package. The participants will learn how to use these programs and process their data. Note: this course is organised on the same week of PathProt, The International forum on Pathway Analysis in Proteomics, that meets annually at the IGC since 2008. Please contact me (pfern(a)igc.gulbenkian.pt) if you wish to submit an abstract. Website at http://gtpb.igc.gulbenkian.pt/PathProt 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 _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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Call for Participation: Computing a Tissue - 1st International Workshop on Modelling Multicellular Systems
by Sara Montagna 25 Aug '16

25 Aug '16

[Apologies for cross-postings. Please send to interested colleagues and students.] ********************************************************************************************************* CALL FOR PARTICIPATION COMPUTING A TISSUE 1st International Workshop on Modelling Multicellular Systems September 4, 2016 To be held in conjunction with the 15th European Conference on Computational Biology (ECCB 2016) The Hague, Netherlands; September 3-7, 2016 --- http://www.eccb2016.org<http://saso2012.univ-lyon1.fr/> ********************************************************************************************************* ---------------- Aims and Scope ---------------- Computational modeling and simulation are emerging as important tools to answer the age-old question in biology: How do cells form tissues? While modern microscopy and bio-image informatics are generating quantitative data on tissue formation at unprecedented rates, computational models are increasingly necessary to interpret these data, test biological hypotheses and ultimately provide a mechanistic understanding of the molecular and cellular mechanisms that drive the morpho-dynamics of multicellular systems. In recent years, computational models of multicellular systemshave been successfully applied in a wide range of fields including animal and plant morphogenesis, stem cell biology, regeneration, vascular development and tissue engineering. Despite notable differences in the application and validation of models, a common set of approaches has emerged to elucidate the logic of the biochemical and biomechanical interactions between cells. The workshop “Computing a tissue” present the state-of-the-art in computational modeling of multicellular systems. It highlights landmark studies of multicellular modeling across a range of biological fields, discusses the strengths and challenges of various modeling approaches and examines the current and upcoming computational methods and tools. All students and researchers interested in the computational modeling of multicellular systems are welcome. ------------------ Topics of Interest ------------------ * Applications of computational modeling to * animal and plant development * regeneration * organ physiology * skin homeostasis * tissue engineering * organoids * Innovative methods concerning * quantitative image analysis * image-based modeling * cell-based models * multi-scale modeling ------------------- Important Deadlines ------------------- Online registration: September 2, 2016 (extended) ---------------- Co - Organisers ---------------- Walter de Back, TU Dresden, Germany Roland Merks, CWI Amsterdam & Uni Leiden, the Netherlands Sara Montagna, Università di Bologna, Italy ————————— Speakers ————————— * Nadine Peyriéras<http://walter.deback.net/ECCB2016/speakers/#peyrieras> (CRNS, France) * Christophe Godin<http://walter.deback.net/ECCB2016/speakers/#godin> (INRIA, France) * Niels Grabe<http://walter.deback.net/ECCB2016/speakers/#grabe> (Uni Heidelberg, Germany) * Jörg Galle<http://walter.deback.net/ECCB2016/speakers/#galle> (Uni Leipzig, Germany) * Natalia Melnikova<http://walter.deback.net/ECCB2016/speakers/#melnikova> (ITMO Uni, Russia) * Stefan Hoehme<http://walter.deback.net/ECCB2016/speakers/#hoehme> (Uni Leipzig, Germany) * Mark Alber<http://walter.deback.net/ECCB2016/speakers/#alber> (Uni Notre Dame, USA) ————————— More Info at http://walter.deback.net/ECCB2016/ —————————

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Join the ECCB 2016 workshop What you need to know about data stewardship and future european research funding
by Celia van Gelder 24 Aug '16

24 Aug '16

*On Saturday 3 September 2016, Erik Schultes (DTL), Marco Roos (LUMC), Mark Thompson (LUMC), Mark Wilkinson (UPM), and Luiz Bonino (DTL, VU) will organise a workshop about FAIR Data stewardship. The workshop is part of the pre-programme of the 15th European Conference on Computational Biology (ECCB 2016 <http://www.eccb2016.org/>), 3-7 September in the Hague. * A broad community of stakeholders recently described a set of guiding principles to ensure that scientific data be Findable, Accessible, Interoperable, and Reusable (FAIR) <http://www.nature.com/articles/sdata201618>. This workshop will provide an introduction to FAIR Data Stewardship in the context of the European research initiatives <http://ec.europa.eu/research/openscience/index.cfm?pg=open-science-cloud>. The morning session will provide a brief introduction to the key issues and ample time for discussion. The afternoon session will be devoted to a practical introduction to data ‘FAIRification’ using real-life datasets. Depending on workshop attendance, the practical session may include hands-on coding activity guided by the workshop organizers. More information: http://www.eccb2016.org/programme/workshops/w6/ You can still register for this ECCB pre-meeting via: http://www.eccb2016.org/registration We look forward to seeing you September 3rd! -- 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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Join the ECCB 2016 workshop What you need to know about data stewardship and future european research funding
by Celia.vanGelder＠radboudumc.nl 24 Aug '16

24 Aug '16

On Saturday 3 September 2016, Erik Schultes (DTL), Marco Roos (LUMC), Mark Thompson (LUMC), Mark Wilkinson (UPM), and Luiz Bonino (DTL, VU) will organise a workshop about FAIR Data stewardship. The workshop is part of the pre-programme of the 15th European Conference on Computational Biology (ECCB 2016<http://www.eccb2016.org/>), 3-7 September in the Hague. A broad community of stakeholders recently described a set of guiding principles to ensure that scientific data be Findable, Accessible, Interoperable, and Reusable (FAIR)<http://www.nature.com/articles/sdata201618>. This workshop will provide an introduction to FAIR Data Stewardship in the context of the European research initiatives<http://ec.europa.eu/research/openscience/index.cfm?pg=open-science-cloud>. The morning session will provide a brief introduction to the key issues and ample time for discussion. The afternoon session will be devoted to a practical introduction to data ‘FAIRification’ using real-life datasets. Depending on workshop attendance, the practical session may include hands-on coding activity guided by the workshop organizers. More information: http://www.eccb2016.org/programme/workshops/w6/ You can still register for this ECCB pre-meeting via: http://www.eccb2016.org/registration We look forward to seeing you September 3rd! -- 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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