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[Gtpb] GTPB Bioinformatics Training Course Announcement
by Pedro Fernandes 15 Jun '15

15 Jun '15

ANNOUNCEMENT / REMINDER Dear Research Applications are open for PGDH15 Population Genetics and Demographic History: model-based approaches with Mark Beaumont, Lounes Chikhi, Willy Rodriguez and Barbara Parreira IMPORTANT DATES for this Course Deadline for applications: June 28th 2015 Latest notification of acceptance: July 1st 2015 Course date: July 6th - July 9th 2015 Details are available at: http://gtpb.igc.gulbenkian.pt/bicourses/PGDH15/ Course description Genetic data are increasingly used by ecologists and evolutionary biologists in general. It has thus become important for many biologists with different levels of experience to produce and analyse genetic (and genomic) data. In this course we will take a practical approach to the analysis of genetic data, but we will also provide some of the theoretical background required to understand the outputs of the software used. This course will be organised so as to mix lectures where important notions are introduced with practicals where freely available software will be used. While this will not be the focus of the course, we will also introduce and discuss genealogical (coalescent-based) simulation methods and those based on forward-in-time simulations. Altogether this will allow to discuss the potentialities and limitations of the tools available to the community. In this four-day course we will introduce the main concepts that underlie many of the models that are frequently used in population genetics. We will focus on the importance of demographic history (e.g. effective sizes and migration patterns) in shaping genetic data. We will go through the basic notions that are central to population genetics, insisting particularly on the statistics used to measure genetic diversity and population differentiation. The course will also cover a short introduction to coalescent theory, Bayesian inference in population genetics and data simulation, as they are connected to what makes landscape genetics today on the basis of multilocus data. We will also introduce two methods that have been recently developed to analyse genomic data. The PSMC of Li and Durbin reconstructs the demographic history of a species or population with the genome of a single individual. The Rehh package is an R implementation of the Extended Haplotype Homozygosity (EHH) test for selective sweeps and looks for signals of selection based on the analysis of genomic regions. Most theory will be put into practice in practical sessions, analyzing real and/or simulated datasets. In these sessions, we will look at measures of genetic diversity and differentiation and use methods to detect population structure as implemented in the program STRUCTURE and discuss related programs such as FastSTRUCTURE. We will learn how to perform coalescent simulations of genetic data (using SPAms and ms). Some exercises will make use of R scripts (R being a freely available statistical program). Basic R knowledge is a pre-requisite but we will provide a short introduction to R. The R statistical package is a very powerful tool to analyse data outputs from many population genetics software, and can also be used to simulate genetic data under simple demographic scenarios. Thanks for your interest, Pedro -- Pedro Fernandes GTPB Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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job opening Bayer CropScience
by David De Vleesschauwer 15 Jun '15

15 Jun '15

Dear, We currently have a job opening at Bayer CropScience for a junior researcher skilled in programming (see attachment). Would it be possible to post this job ad on the BBClist website? Thank you very much. Best Regards / Vriendelijke Groeten / Cordialement / Freundliche Grüße David De Vleesschauwer, Phd Postdoctoral fellow - Lysine Nimbus [cid:image001.gif@01D06D24.C63CD4B0] Bayer CropScience NV- INNOVATION CENTER Trait Discovery Tel: +32 9 243 0734 Fax: +32 9 383 6731 E-mail: david.devleesschauwer(a)bayer.com<mailto:david.devleesschauwer@bayer.com> Web: http://www.bayercropscience.com<http://www.bayercropscience.com/> BTW en ondernemingsnummer: BE 0412 639 087 RPR Brussel ________________________________________________________________________ The information contained in this e-mail is for the exclusive use of the intended recipient(s) and may be confidential, proprietary, and/or legally privileged. Inadvertent disclosure of this message does not constitute a waiver of any privilege. If you receive this message in error, please do not directly or indirectly use, print, copy, forward, or disclose any part of this message. Please also delete this e-mail and all copies and notify the sender. Thank you. For alternate languages please go to http://bayerdisclaimer.bayerweb.com ________________________________________________________________________

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Data Visualization for Biology: a practical workshop on design, techniques and tools 23-27 November 2015
by Alexander Botzki | VIB | 12 Jun '15

12 Jun '15

Web Version<http://trainingvib.cmail2.com/t/r-e-atdelt-dlhhdihde-r/> | Update preferences<http://trainingvib.updatemyprofile.com/r-atdelt-67B0562B-dlhhdihde-y> | Unsubscribe<http://trainingvib.cmail2.com/t/r-u-atdelt-dlhhdihde-j/> [Forward icon]<http://trainingvib.forwardtomyfriend.com/r-dlhhdihde-67B0562B-atdelt-l-t> Forward<http://trainingvib.forwardtomyfriend.com/r-dlhhdihde-67B0562B-atdelt-l-i> Data Visualization for Biology: a practical workshop on design, techniques and tools We would like to invite you to 'Data Visualization for Biology: a practical workshop on design, techniques and tools' - a workshop jointly organized by KU Leuven ESAT/STADIUS, EMBL-EBI and VIB, taking place in Leuven from 23 to 27 November 2015. As biological datasets increase in size and complexity, we are moving more and more from an hypothesis-driven research paradigm to a data-driven one. As a result, exploration of that data has become even more crucial than in the past. In this 5-day workshop, we will dive into the topic of biological data visualization and how it can be used to gain insight in and get a "feel" for a dataset, so that targeted analyses can be defined. We will start by covering theoretical questions like: What is data visualization? How do we perceive images? How can we visualise data in the best possible way? As the workshop continues, it will become more and more hands-on and interactive; a large part will be committed to creating visualisations using the D3 javascript library, including 2-day projects creating interactive visualisations based on data brought by the students themselves. Confirmed speakers and instructors: · Jan Aerts (KU Leuven ESAT/STADIUS, Belgium) · Eamonn Maguire (University of Oxford, UK) · Francis Rowland (EMBL-EBI, UK) · Marc Streit (Johannes Kepler University Linz, Austria) · Herwig Van Marck (VIB BioInformatics Training and Service facility, Belgium) Have a look at the training website<http://trainingvib.cmail2.com/t/r-l-atdelt-dlhhdihde-x/> and sign up to join us from 23 to 27 November 2015 in Leuven (KU Leuven ESAT/STADIUS). Please get in touch, if you need further information. Best regards, Alexander VIB BITS, on behalf of the organizers

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bioinformatics openings @ IMGT
by Sofia KOSSIDA 05 Jun '15

05 Jun '15

Bioinformatics / Immunnoinformatics positions @ IMGT®, the international ImMunoGeneTics information system® http://www.imgt.org, in Montpellier, France IMGT®, the international ImMunoGeneTics information system® http://www.imgt.org, is the global reference in immunogenetics and immunoinformatics, created in 1989 by Marie-Paule Lefranc (Université de Montpellier<http://www.umontpellier.fr/> and CNRS<http://www.cnrs.fr>). IMGT® is a high-quality integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) of human and other vertebrate species, and in the immunoglobulin superfamily (IgSF), MH superfamily (MhSF) and related proteins of the immune system (RPI) of vertebrates and invertebrates. IMGT® provides a common access to sequence, genome and structure Immunogenetics data, based on the concepts of IMGT-ONTOLOGY and on the IMGT Scientific chart rules. IMGT® works in close collaboration with EBI<http://www.ebi.ac.uk/> (Europe), DDBJ<http://arsa.ddbj.nig.ac.jp/top-e.html> (Japan) and NCBI<http://www.ncbi.nlm.nih.gov/gene> (USA). IMGT® consists of sequence databases, genome database, structure database, and monoclonal antibodies database, Web resources and interactive tools. IMGT® is located within IGH, http://www.igh.cnrs.fr , in Montpellier, France and close to the University of Montpellier. The successful applicants will join a multidisciplinary team, working with biologists, chemists, engineers and bioinformatics scientists, independently and as team players. We are looking to recruit: 1. A computer scientist with proven programming capability. Good knowledge of Java is required. Knowledge of R is a plus. 2. A biocurator with knowledge of molecular biology and usage of bioinformatics tools. Knowledge of immunology is a plus. 3. A bioinformatician with programming capability and usage of bioinformatics tools. Good team player and oral communication skills are required for all the positions. A Master's degree is a plus but not required. An initial contract of 2 years with possible extension of 1 plus 1 year, 4 years in total maximum is offered for all the positions. The positions remain open up until they are filled. For more information please contact: sofia.kossida(a)igh.cnrs.fr<mailto:sofia.kossida@igh.cnrs.fr> or marie-paule.lefranc(a)igh.cnrs.fr<mailto:marie-paule.lefranc@igh.cnrs.fr>

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Sharing Human Molecular Profiling Data: 12 June - 9:30-12:30 - VU
by Sanne Abeln 04 Jun '15

04 Jun '15

We would like to invite you to our workshop on Sharing Human Molecular Profiling Data. The workshop will be held at the Vrije Universiteit in Amsterdam, on 12 June 2015 between 9:30 and 12:30. This morning programme of the ELIXIR: EGA - TraIT kick-off workshop is open to all. Please send an email to Jochem Bijlard (j.bijlard(a)vu.nl) to register for the meeting. Location: VU University, De Boelelaan 1105, 1081 HV Amsterdam Room: WN-C147 Morning Programme 9:30 - 12:30 09:30 - 09:40 Sanne Abeln Opening 09:40 - 9:55 Jan-Willem Boiten General introduction to CTMM-TraIT 10:00 - 10:15 Sanne Abeln Introduction to molecular profiling data within TraIT 10:20 - 10:35 Wim van der Linden TranSMART 10:40 - 11:00 Justin Paschall Introduction to EGA (and ELIXIR) Coffee break 11:20 - 11:35 Youri Hoogstrate Galaxy workflows in TraIT 11:40 - 12:00 Marco Roos / Barend Mons (TBC) FAIR Data principles 12:05 - 12:30 James Malone Applying ontologies to biomedical data https://docs.google.com/document/d/1I5kvQzhqJi4eB0qH_K06kCh-w7Cz1W2ZMFMpT0v… Kind regards, Sanne Abeln -- Sanne Abeln Assistant Professor Bioinformatics - VU University Amsterdam s.abeln(a)vu.nl +31 20 59 87816 www.few.vu.nl/~abeln

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BioJS Conference 3-4 July, Norwich, UK - preceding Galaxy Communit
by Frederik Coppens 04 Jun '15

04 Jun '15

On behalf of Manuel Corpas: BioJS CONFERENCE 3-4 JULY, NORWICH, UK http://conf.biojs.net/ <http://conf.biojs.net/> Are you - a researcher interested in interactive visualisation of massive biological datasets on the web? - a developer interested in data visualisation? - interested to understand current industry-based end user needs? Would you like to meet recognised leaders in the field of visualisation in bioinformatics, including representatives from a variety of SMEs, big pharma and for profit organisations? It is our pleasure to invite you to join us for the 1st Annual BioJS Conference (BioJS.conf) <http://conf.biojs.net/> and hackathon on 3-4 July 2015, hosted at The Genome Analysis Centre (TGAC), Norwich, UK. As part of the conference we will have an industry-led session organised by the Repositive.io <http://repositive.io/> SME. The aim of this session is to understand the needs, wants, and limitations of front-end interfaces applied to industry-based end users. Current confirmed speakers include: Suzi Lewis (Berkeley) Henning Hermjakob (EBI) Ian Mulvany (eLife) Michiel Helvensteijn (Leiden) Jessie Kennedy (Napier University, Edinburgh) Registration open NOW! <http://conf.biojs.net/#register> Please help us spread the word! The BioJS.conf Organising Committee <http://conf.biojs.net/#organisers> ================================================================== Frederik Coppens, Ph.D. Project Leader Applied Bioinformatics & Biostatistics Tel: 32 (0)9 3313692 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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[Gtpb] IBSTATB15 Biostatistics for Biologists
by Pedro Fernandes 02 Jun '15

02 Jun '15

Dear GTPB This is too short notice, I know and apologise. However it is still a great opportunity to learn or relearn statistics with lots of practicals using R. IMPORTANT DATES for this Course Deadline for applications: June 12th 2015 Course dates: June 15th - June 19th 2015 http://gtpb.igc.gulbenkian.pt/bicourses/IBSTATB15/ 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. See the Detailed Program." Regds Pedro -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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BioSB Course Quantitative and Predictive Modelling, 22-26 June 2015, Wageningen
by Celia.vanGelder＠radboudumc.nl 02 Jun '15

02 Jun '15

BioSB Course Quantitative and Predictive Modelling Date: 22-26 June, 2015 Location: Wageningen Course Coordinators: Jaap Molenaar (WUR), Natal van Riel (TUE) Website: http://biosb.nl/education/course-portfolio-2/course-quantitative-and-predic… Registration: http://biosb.nl/education/course-portfolio-2/course-quantitative-and-predic…. Note: This course is a BioSB Core Course<http://biosb.nl/education/course-portfolio-2/> and as such this course is free of charge for all PhDs who are member of BioSB, and with a reduced fee for researchers (non-PhD) who are member of BioSB. You can find more information about the BioSB Membership here<http://biosb.nl/about/members/biosb-membership-information/>. On June 22-26 2015, BioSB organises the first edition of the course Quantitative and Predictive Modelling. The main theme of the Quantitative and Predictive Modelling course is how to describe the dynamic behaviour of biological systems and integrate experimental data. Concepts of modelling are introduced via a great variety of examples taken from diverse practices. The emphasis is on providing an overview of modelling approaches rather than an in-depth treatment of a few techniques. After classification of biological systems (metabolic, regulatory, signalling, population, multi-scale, statistical models), the concepts of top-down versus bottom-up modelling will be introduced, with emphasis on bottom-up approaches. Parameter estimation is an important modelling tool and will receive adequate attention. In the course Matlab will be used as software tool for the practicals. Participants not familiar with Matlab will get a short introduction. This course is primarily targeted at academic researchers such as PhD students and Postdocs in Life Sciences, Bioinformatics, Systems Biology or Biomedical Engineering. Participants from private sector are also welcome. Participants are expected to have some experience in modelling with differential equations or to have followed Introductory courses from the BiosB Course Portfolio<http://biosb.nl/education/course-portfolio-2/>, e.g. E-course modelling , E-course calculus, Discovering Systems Biology Principles or Applications for Systems Biology and Bioinformatics in the Medical Sciences. The course will start with a session to refresh the basic elements of modelling with differential equations. 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>. Best regards Celia van Gelder Dr. Celia W.G. van Gelder Education Manager BioSB Coordinator Education CMBI Programme Manager Learning DTL/ELIXIR-NL tel. +31-(0)24-3666120 e-mail: Celia.vanGelder(a)radboudumc.nl<mailto:C.vanGelder@umcn.nl> websites: www.nbic.nl<http://www.nbic.nl/>, www.biosb.nl<UrlBlockedError.aspx>, www.cmbi.ru.nl<http://www.cmbi.ru.nl/>, www.dtls.nl<UrlBlockedError.aspx> Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre PO Box 9101 6500 HB Nijmegen The Netherlands 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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vacancy PhD student
by Willem Waegeman 29 May '15

29 May '15

Fully funded PhD studentship in constructive machine learning for the life sciences at Ghent University --- Duration of studentship: 4 years Studentship start date: September 2015 Application closing date: July 1st (will be extended if no suitable candidate is found). Apply as soon as possible to avoid disappointment! --- Project description: Constructive machine learning describes a class of related machine learning problems where the ultimate goal of learning is not to find a good model of the data but instead to find one or more particular instances of the domain which are likely to exhibit desired properties. While traditional approaches choose these domain instances from a given set/databases of unlabeled domain instances, constructive machine learning is typically iterative and searches an infinite or exponentially large instance space. Interesting applications in the life sciences are in the domains of chemistry (e.g. de novo drug design), biology (e.g. gene design, metabolic path design, RNA polymer design), food sciences (e.g. generation of novel food recipes or cocktails) and spatio-temporal modelling (e.g. prediction of spatio-temporal maps that evolve in time, as in climate analysis and ecology). This project will focus on the development of novel constructive machine learning methods with a particular emphasis on large output spaces, streaming data and decomposition techniques for output spaces. Background information: The studentship is available in the research unit KERMIT of Ghent University (acronym for Knowledge Extraction and Representation Management by means of Intelligent techniques) under supervision of Prof. Willem Waegeman. KERMIT is a young interdisciplinary team of mathematicians, engineers and computer scientists, and it draws upon intelligent techniques resulting from the cross-fertilization between the fields of computational intelligence and operations research. The main focus is on mathematical and computational aspects of relational structures as knowledge instruments, with emphasis on the fields of fuzzy set theory and machine learning. KERMIT serves as an attraction pole for applications in the applied biological sciences, and serves colleagues in hydrology, ecology, bacterial taxonomy, genome analysis, integrated water management, geographical information systems, forest management, metabolic engineering, soil science, bioinformatics, systems biology, etc. The ideal candidate for the position has the following profile: - An MSc degree in (Bio-)Engineering, Computer Science, Mathematics, Statistics, Bio-informatics, Physics, or equivalent – candidates from outside Belgium are welcome. - An interest in fundamental machine learning research, as well as practical applications in the life sciences - In-depth experience with at least one programming language (Matlab, R, Python, Java, etc.) - An interest for applied mathematics, data management and data analysis in general - Good knowledge of machine learning and statistical methods is a strong asset - Fluent in English (speaking and writing, as demonstrated by personal texts) - Knowledge of Dutch is an asset, but not a must - Team player with good communication skills How to apply: Send your c.v., a motivation letter and a copy of your MSc.-thesis and/or any relevant publications to Mrs. Ruth Van Den Driessche (ruth.vandendriessche(a)ugent.be) -- Prof. dr. Willem Waegeman Research Unit Knowledge-Based Systems (KERMIT) Department of Mathematical Modelling, Statistics and Bioinformatics Coupure links 653 9000 Ghent, Belgium Phone: + 32 9 264 59 87 www.kermit.ugent.be users.ugent.be/~wwaegemn

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Last chance for registration: Advanced de novo assembly and resolving complex genomic regions, 1-3 June 2015, Leiden
by Celia.vanGelder＠radboudumc.nl 27 May '15

27 May '15

BioSB Course Advanced de novo assembly and resolving complex genomic regions Date: 1-3 June, 2015 Location: Leiden Course Coordinators: Yahya Anvar (LUMC), Johan den Dunnen (LUMC) Website including link to full programme: http://biosb.nl/education/course-portfolio-2/course-advanced-de-novo-assemb… Registration: http://biosb.nl/education/course-portfolio-2/enrollment-advanced-de-novo-as… . Please note that members of BioSB get a reduction on the course fee. Programme: See attached pdf This course is targeted at PhD students and Postdocs in Life Sciences or Bioinformatics with basic knowledge of next-generation sequencing (NGS) technology and data analysis. This course covers topics on what every biologist should know about de novo assembly and study design, overview of available technologies and sampling strategies, methodologies and framework for de novo assembly (haploid and polyploid genomes), gap closure, quality assessment and functional annotation. In addition, we will showcase recent achievements, novel discoveries and current limitations in resolving complex genomes. The practical sessions are designed in such a way to promote lively discussions on how to design your study, the best practices, dos and don'ts, and provide you with an outlook on how to move from sequencing data to high-quality assembly and meaningful biological interpretation. After following this course, participants will gain insights on how to design a genome assembly study and will have an overview of challenges and various techniques to choose the most fitting strategy in order to produce a high-quality genome assembly. This course is primarily targeted at academic researchers such as PhD students and Postdocs in Life Sciences or Bioinformatics with experience in genomics or NGS data analysis. However, participants from private sector are also welcome. Participants are expected to have experience in NGS data analysis or to have followed the NGS data analysis course. 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>. Best regards Celia van Gelder Dr. Celia W.G. van Gelder Education Manager BioSB Coordinator Education CMBI Programme Manager Learning DTL/ELIXIR-NL tel. +31-(0)24-3666120 e-mail: Celia.vanGelder(a)radboudumc.nl<mailto:C.vanGelder@umcn.nl> websites: www.nbic.nl<http://www.nbic.nl/>, www.biosb.nl, www.cmbi.ru.nl<http://www.cmbi.ru.nl/>, www.dtls.nl Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre PO Box 9101 6500 HB Nijmegen The Netherlands 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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