May 2013 - BBClist - maillist.psb.ugent.be

2013 Galaxy Community Conference (GCC2013) Early Registration ends Friday, 24 May
by Dave Clements 20 May '13

20 May '13

Hello all, Early registration <http://bit.ly/GCC2013Reg> for the 2013 Galaxy Community Conference (GCC2013) <http://bit.ly/gcc2013> ends this Friday, 24 May. Early registration saves *up to 75% off regular registration costs*, and is downright affordable, with combined registration (Training Day<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> + main meeting <http://wiki.galaxyproject.org/Events/GCC2013/Program>) starting at ~ €95 for post-docs and students. Registering early also assures you a spot in the Training Day workshops you want to attend. Once a Training Day session becomes full, it will be closed to new registrations. GCC2013 <http://wiki.galaxyproject.org/Events/GCC2013> is an opportunity to participate in two full days of presentations, discussions, poster sessions, keynote, and lightning talks, all about high-throughput biology and the tools that support it. The conference also includes a Training Day<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> with in-depth topic coverage of twelve different topics in 15 sessions across 5 tracks. An early program is available<http://wiki.galaxyproject.org/Events/GCC2013/Program> featuring 25 oral presentations, lightning talks and poster sessions, and the just added Birds-of-a-Feather <http://wiki.galaxyproject.org/Events/GCC2013/BoF> gatherings. If you are a biologist or bioinformatician performing or enabling high-throughput biological research, then this conference is for you. Thanks, GCC2013 Organizing Committee<http://wiki.galaxyproject.org/Events/GCC2013/Organizers> PS: And please help get the word out<http://wiki.galaxyproject.org/Events/GCC2013/Promotion> ! On Tue, Mar 12, 2013 at 3:18 PM, Dave Clements <clements(a)galaxyproject.org>wrote: > Hello all, > > We are pleased to announce that early registration<http://wiki.galaxyproject.org/Events/GCC2013/Register> > and paper and poster abstract submission<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts> are > now open for the 2013 Galaxy Community Conference (GCC2013)<http://wiki.galaxyproject.org/Events/GCC2013> > . GCC2013 will be held 30 June through July 2 in Oslo Norway, at the University > of Oslo <http://uio.no/>. > > GCC2013 <http://wiki.galaxyproject.org/Events/GCC2013> is an opportunity > to participate in two full days of presentations, discussions, poster > sessions, keynotes, lightning talks and breakouts, *all about > high-throughput biology and the tools that support it*. The conference > also includes a Training Day<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> for > the second year in a row, this year with more in-depth topic coverage, more > concurrent sessions, and more topics. > > If you are a biologist or bioinformatician performing or enabling > high-throughput biological research, then please consider attending. > GCC2013 is aimed at: > > - Bioinformatics tool developers and data providers > - Workflow developers and power bioinformatics users > - Sequencing and Bioinformatics core staff > - Data archival and analysis reproducibility specialists > > *Early registration<http://wiki.galaxyproject.org/Events/GCC2013/Register> > * *saves up to 75% off regular registration costs,* and is very > affordable, with combined registration (Training Day<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> + > main meeting) starting at ~ €95 for post-docs and students. Registering > early also assures you a spot in the Training Day workshops you want to > attend. Once a Training Day session becomes full, it will be closed to new > registrations. Early registration closes 24 May. > > *Abstract submission<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts> > * for oral presentations closes 12 April, and for posters on 3 May. > Please consider presenting your work. If you are working with big > biological data, then the people at this meeting want to hear about your > work. > > Thanks, and hope to see you in Oslo! > > The GCC2013 Organizing Committee<http://wiki.galaxyproject.org/Events/GCC2013/Organizers> > > PS: And please help get the word out<http://wiki.galaxyproject.org/Events/GCC2013/Promotion> > ! > -- > http://galaxyproject.org/GCC2013 > http://galaxyproject.org/ > http://getgalaxy.org/ > http://usegalaxy.org/ > http://wiki.galaxyproject.org/ > -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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NBIC advanced NGS course "Variant Detection and Interpretation in a Diagnostic Context"
by Patrick Koks 17 May '13

17 May '13

Apply now for the : NBIC advanced NGS course on Genomic Resequencing: "Variant Detection and Interpretation in a Diagnostic Context" Course coordinators: Christian Gilissen (UMCN), Terry Vrijenhoek (UMCU) & Jasper Saris (EMC) Date: May 27th - 29th, 2013 Location: Erasmus Medical Centre (EMC), Rotterdam, the Netherlands course-website: http://www.nbic.nl/education/nbic-phd-school/course-schedule/ngsresequencin… Registration: http://www.nbic.nl/education/nbic-phd-school/enrolment/ Contact for information: Patrick Koks (education(a)NBIC.nl) description: The NBIC advanced NGS course "Genomic Resequencing" focuses on the application of exome or whole genome sequencing as a research and diagnostic tool for the detection of mutations and variants with a clinical relevance. This is a three-day course with a 'shifting focus' from the bioinformaticians' and molecular geneticists' practice on day 1 to the daily routine of the clinical geneticist on day 3. We will cover sample preparation methods and updates in sequencing techniques, data analysis steps from quality control and mapping till variant calling and annotation. Furthermore we will zoom in on the clinical relevance of NGS results, application in the clinic, legal issues, etc. On day 1 & 2 the afternoons are devoted to (hands-on) workshops in analysing NGS data and on day 3 we will have a panel discussion on the impact of NGS on research, diagnostics and clinical practice as it is now. confirmed teachers: Johan den Dunnen (Leiden UMC) Robert Hofstra (Erasmus MC) Victor Guryev (UMC Groningen) Helger Yntema (UMC St. Radboud) Laurent Francioli (UMC Groningen) Helger Yntema (UMC St. Radboud) Lisenka Vissers (UMC St. Radboud) Frank Baas (AMC) Ewart de Bruijn (Hubrecht) Chris Mattocks (Salisbury) Julien Tarabeux (Institut Curie) a.o. This course is part of the Education Programme of the NBIC PhD School. The PhD School is an initiative of NBIC together with a number of universities to organise high level education and training for PhD-students in bioinformatics and life sciences. All NBIC courses are co-developed and co-organised by experts in the field and in close collaboration with leading research groups throughout the Netherlands. All NBIC courses are taught in English and are open to PhD students and researchers worldwide. More information about the latest developments of the NBIC PhD School can also be found on the NBIC website (www.nbic.nl -> Education -> NBIC PhD School). For more information, you can send e-mail to Patrick Koks (education(a)NBIC.NL) Regards, The NBIC BioWise team Patrick Koks, NBIC BioWise – Education Tuesday – Wednesday - Thursday tel: #31-(0)24-3615210 e-mail: Patrick.koks(a)nbic.nl web: www.nbic.nl, www.ebiomics.org Postal Address: CMBI 260 Radboud University / UMC / NCMLS PO Box 9101, 6500 HB Nijmegen, The Netherlands Patrick Koks, NBIC BioWise – Education Tuesday – Wednesday - Thursday tel: #31-(0)24-3615210 e-mail: Patrick.koks(a)nbic.nl web: www.nbic.nl, www.ebiomics.org Postal Address: CMBI 260 Radboud University / UMC / NCMLS PO Box 9101, 6500 HB Nijmegen, The Netherlands

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PhD position at CRI-FEM, Trento
by Kristof Engelen 16 May '13

16 May '13

Dear, The Research and Innovation Centre (CRI) of the Fondazione Edmund Mach (http://cri.fmach.eu/) located in Trentino in the northern part of Italy, is offering a PhD position in cooperation with the Bioinformatics and Systems Biology division (Prof. Yves Van de Peer), VIB / Ghent University. More details can be found in the attached file and at http://cri.fmach.eu/education/selection . Please feel free to forward to any potentially interested candidates. Kind regards, Kristof Engelen __________________________________ Centro di Ricerca e Innovazione Fondazione Edmund Mach

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Vacancy Senior Scientist Systems Biology
by karen.lemmens＠cropdesign.com 16 May '13

16 May '13

Dear All, We are currently looking for a Senior Scientist Systems Biology at CropDesign NV, BASF Plant Science, Ghent. Details can be found at: http://www.cropdesign.com/jobs.php?jid=2012060702 Best regards, Karen Karen Lemmens, PhD Group leader -- Systems Biology Ghent Phone: +32 9 242 3-464, Fax: +32 9 242 3-489, E-Mail: karen.lemmens(a)cropdesign.com Postal Address: CropDesign N.V., 1190 GBR/KY- CD2, 9052 Gent (Zwijnaarde), Belgium CropDesign N.V. - A BASF Plant Science Company Technologiepark 3 - B-9052 Gent - Belgium - General Telephone: +32-9-242 34 00 - Fax: +32-9-242 34 89 Confidentiality notice: The information contained in this e-mail is confidential and may be the subject of legal professional privilege. It is intended for the authorized use of the individual or entity addressed. If the receiver or reader of this message is not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is prohibited. If this email is received in error, please accept our apologies, delete all copies from your system, and notify us at info(a)cropdesign.com.

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International Chemical Discovery & Design Course. 1-12 July 2013. Nijmegen.
by Celia van Gelder 14 May '13

14 May '13

International Chemical Discovery & Design Course, 1-12 July 2013, Nijmegen. We would like to draw your attention to the 9th annual International Chemical Discovery & Design Course (http://www.cmbi.ru.nl/ICDD2013) which will be held from July 1st till July 12^th at the Radboud University Nijmegen. The course is jointly organized by the Computational Drug Discovery (CDD) group of the Centre for Molecular and Biomolecular Informatics (CMBI), The Netherlands eScience Center, and The Netherlands Bioinformatics Centre (NBIC). This course covers the recent advances in discovery informatics, with a focus on the application of escience to real life problems. The course, combining practicals and lectures, will introduce and discuss different scientific concepts as well as providing an opportunity to gain practical experience using industry standard software. You can expect lectures and practicals on the following topics (see also the attachment for the complete programme): * Introduction to Computational Discovery & Design. * Comparative Protein Modelling. * Sequence Retrieval, Analysis and Alignment Techniques. * Computational Medicinal Chemistry; Molecular Descriptors & Library Design. * The Application of Computational Drug Design to Real Life Problems. * Molecular Docking and Virtual Screening. * Advanced 3D Database Searches and Scaffold Hopping. * QSAR and COMFA methods. * Structure Based Drug Design Techniques. * Text Mining. The course is targeted to MSc students, PhD students and post-docs. A basic background in bioinformatics or computational chemistry is a prerequisite for attendance. Registration is now open at: http://www.nbic.nl/education/nbic-phd-school/enrolment/application-internat… Furthermore, as part of this course, on July 5, there will be the *Dutch Computers in Chemistry Symposium, in Amsterdam (*http://esciencecenter.nl/event-page/dutch-computers-in-chemistry-symposium-2013). Best regards Tina Ritschel (CDD/CMBI/UMC Nijmegen)// Celia van Gelder (CMBI/RUN & Netherlands Bioinformatics Centre) -- Dr. Celia W.G. van Gelder Coordinator Education CMBI Projectleader Education NBIC tel. +31-(0)24-3666120 e-mail:C.vanGelder@cmbi.ru.nl websites:www.cmbi.ru.nl,www.nbic.nl Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre /NCMLS PO Box 9101, 6500 HB Nijmegen The Netherlands

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Symposium Boundaries of Bioinformatics
by Frank de Kievit 08 May '13

08 May '13

On the 4th of June, study association Exon (uni of applied sciences Leiden) will host a symposium for bioinformaticians called Boundaries of Bionformatics. On this symposium, different speakers will talk about their work or research on the edges of bio-informatics. Wifi and lunch will be supplied. Do you want to experience how broad bio-informatics really is? Register yourself now on www.exonleiden.nl/bob !

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[Gtpb] GTPB announcement Bioinformatics using Pythonm for Biologists
by Pedro Fernandes 07 May '13

07 May '13

Course Announcement Applications are OPEN until May 28th 2013 (latest deadline for applicants) Early decisions available for thos who request them. *BPB13* *Bioinformatics using Python for Biologists* with Allegra Via and Kristian Rother Is OPEN for applications Course poster available at: http://gtpb.igc.gulbenkian.pt/bicourses/posters/BPB13.pdf IMPORTANT DATES for this Course Deadline for applications: May 28th 2013 Notification of acceptance dates: EARLY: May 13th 2013 (on special request, see Application) NORMAL: May 29th 2013 Course date: June 3rd to June 7th 2013 Course website http://gtpb.igc.gulbenkian.pt/bicourses/BPB13 Suitability: This course is suitable for scientists that feel the need to overcome the difficulty of not knowing how to program. Since 2010, it has been highly successful. Description Python Python is an object-oriented programming language that is ideal for biological data analysis. The course will start from zero knowledge, and will cover all basic concepts of Python, including variables, calculating, reading and writing files, control flow, modules, functions, exceptions. All examples and practical sessions will focus on solving biological problems. In particular the sessions will cover: - working with DNA and protein sequences - data retrieval from files and their manipulation - running applications, such as BLAST, locally and from a scrip - finding motifs in sequence - parsing Swiss-Prot files, PDB files, ENSEMBL records, blast output files, etc. - Biopython The course will be highly interactive and the students will continuously put theory into practice while learning. By the end of the course, the participants will have a good understanding of Python basics and will have acquired the skills to manage any type of bioinformatics database record and to run applications from scripts. Basic Unix/linux skills will be provided at the beginning of the course. Target Audience End-users of bioinformatics databases and tools that aim at developing hands-on capabilities for biological data analysis, ie writing their own or adapting somebody else's Python scripts in an autonomous way. Course Pre-requisites Basic familiarity with bioinformatics data resources such as Uniprot/Swiss-Prot, Blast, ENSEMBL, PDB, etc. The course is directed to biologists with little or no programming experience and aims at making them capable to use Python to autonomously manage and analyse biological data. Pedro Fernandes GTPB Coordinator -- -- 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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Probabilistic Cellular Automata: Theory, Applications and Future Perspectives, 10-12 June 2013, Eindhoven, Netherlands
by Roeland Merks 05 May '13

05 May '13

-- Extended deadline for contribution: 12/05/2013 -- Probabilistic Cellular Automata: Theory, Applications and Future Perspectives Event to be held at Eurandom, Eindhoven, The Netherlands. Date 10-11-12 June, 2013 Further information on this event to be found at:http://www.eurandom.nl/events/workshops/2013/PCA/PCA.html * Computer Science and Discrete Dynamical Systems e.g. robustness of PCA when going from synchronous to asynchronous updating scheme, deterministic CA with random initial condition, density classification, synchronous / asynchronous updating. * Probability and Statistical Mechanics, e.g. PCA as discrete-time interacting particle system, non-equilibrium statistical mechanics, metastability, cut-off phenomena and abrupt convergence, phase transitions, Gibbs/Non--Gibbs transitions, PCA and stochastic algorithms * Applications mainly in computational (cell) biology e.g. Cellular Potts Model and stability of emerging patterns, time to stationarity in simulation algorithms, transient regimes

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PLOS Computational Biology T-shirt competition
by Umesh Nandal 03 May '13

03 May '13

*PLOS Computational Biology T-shirt competition* For the fourth year in a row, PLOS Computational Biology is calling on scientists and designers to send eye-catching designs that appeal to the computational biology community and encapsulate a recent advance or innovation in the field. The creator(s) of the winning design will receive a free t-shirt and a write-up of their design and research on PLOS Biologue. This year’s PLOS Computational Biology t-shirt will debut at *July’s ISMB/ECCB 2013 meeting in Berlin*. To enter the competition, send your design to ploscompbiol[at]plos.org by *Tuesday May 14th 2013*. For more details and design requirements for the competition go the following link: http://blogs.plos.org/biologue/2013/04/12/we-want-you-to-design-the-2013-pl… Regards, ISCB Student Council for PLOS Computational Biology

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NBIC PhD course on Managing Life Science Information: registration is open!
by Celia van Gelder 01 May '13

01 May '13

*NBIC PhD Course on Managing Life Science Information (2nd edition) *Course coordinators: Marco Roos, Scott Marshall _Date:_ 17-21 October 2011 (one week of tutorials) and a final workshop on Friday 28 October 2011 to discuss project results _Location:_ Science Park, Amsterdam _Registration:_ http://www.nbic.nl/education/nbic-phd-school/enrolment/ _Website: _http://www.nbic.nl/education/nbic-phd-school/course-schedule/managing-life-science-information/ Did you ever suspect that the data that you need is somewhere but neither discoverable nor accessible? Have you ever produced valuable data that nobody can use anymore, including yourself? Have you ever wondered how to create a federation of distributed data sources? If you do not want your data to end up in a data graveyard, and for many other information management issues, we have organised a course for you. In this course we will teach you methods to make data shareable and self-describing. You will learn how: 1. the 'Linked Data' principle works and how it can be applied for 'meaningful' data integration 2. to expose your local data (including relational databases) for use in other systems. 3. Web Services can be used to analyse data from anywhere. 4. text mining can be applied to link resources such as biobanks. 5. human knowledge can be made computable and associated with data. 6. to make your data publishable artifacts for which you can get scientific credit. 7. to use tools such as MolGenis <http://www.molgenis.org/>, Taverna <http://www.taverna.org.uk/>, SPARQL <http://www.w3.org/TR/sparql11-query/>, D2RQ <http://www4.wiwiss.fu-berlin.de/bizer/d2rq/>, SWObjects <http://tinyurl.com/swobjects-swat4ls>, NCBO's BioPortal <http://bioportal.bioontology.org/>, Anni <http://www.biosemantics.org/index.php?page=anni-2-0>, LarKC <http://larkc.org/>(Large Knowledge Collider). 8. to collaboratively solve an information management problem _Program_ (tentative) Monday: Introduction by leading Semantic Web expert Prof. Dr. Frank van Harmelen; Hands-on with RDF and SPARQL (Scott Marshall) Tuesday: XML, RDF, Minimal information models, and exposing data from local databases (Scott Marshall); hands-on with MolGenis (Erik Roos) Wednesday: Data integration with Web Services (Katy Wolstencroft); hands-on with Taverna (Katherine Wolstencroft) Thursday: Knowledge management and nano-publication (Andrew Gibson); hands-on federated queries with SWObjects (Scott Marshall) Friday: Text mining for linking biobanks and hands-on with Anni (Marco Roos, Kristina Hettne); Hands-on with LarKC (Spyros Kotoulas); DRINKS!!! -- Dr. Celia W.G. van Gelder Coordinator Education CMBI Projectleader Education NBIC tel. +31-(0)24-3666120 e-mail: C.vanGelder(a)cmbi.ru.nl websites: www.cmbi.ru.nl, www.nbic.nl Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre /NCMLS PO Box 9101, 6500 HB Nijmegen The Netherlands

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