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NBIC advanced NGS course: RNA-seq data analysis course (3rd edition), October 30 - Nov 1 2013, Leiden, the Netherlands
by C.vanGelder＠umcn.nl 14 Sep '13

14 Sep '13

RNA-seq data analysis course (3th edition) Date: October 30- Nov 1, 2013 Course coordinators: Peter-Bram 't Hoen, Marieke Simonis Location: Leiden, the Netherlands Website: http://www.nbic.nl/education/course-overview/pages3/1/coursedetails/advance… Registration: http://www.nbic.nl/education/nbic-phd-school/enrolment/ Course Description This is an expert course for people with experience in NGS. 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 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. 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 project RD-Connect<http://www.rd-connect.eu/> and Marie Curie European Training Network TranCYST<http://www.trancyst.eu/>. NBIC PhD School The Life Sciences Track of the NBIC PhD School (http://www.nbic.nl/education/nbic-phd-school/nbic-phd-school-course-portfol…) currently offers six bioinformatics courses focussing on application and data-analysis of Next-generation sequencing (NGS). All NBIC NGS 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 For more information about the course you can contact Celia van Gelder (NBIC Education) at celia.van.gelder(a)nbic.nl<mailto:celia.van.gelder@nbic.nl>. -- Dr. Celia W.G. van Gelder Coordinator Education CMBI Projectleader Education NBIC tel. +31-(0)24-3666120 e-mail: C.vanGelder(a)umcn.nl<mailto:C.vanGelder@umcn.nl> websites: www.cmbi.ru.nl<http://www.cmbi.ru.nl>, www.nbic.nl<http://www.nbic.nl> Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre /NCMLS PO Box 9101, 6500 HB Nijmegen The Netherlands Het UMC St Radboud staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud University Nijmegen Medical Centre is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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NBIC PhD course Protein Structures: production, prowess, power, promises, and problems
by C.vanGelder＠umcn.nl 14 Sep '13

14 Sep '13

NBIC PhD course Protein Structures: production, prowess, power, promises, and problems Date: 4 – 8 Nov 2013 Course coordinator: Gert Vriend Location: Center for Molecular and Biomolecular Informatics (CMBI), UMC Radboud, Nijmegen, the Netherlands Website: http://www.nbic.nl/education/nbic-phd-school/course-schedule/protein-struct… Registration: http://www.nbic.nl/education/nbic-phd-school/enrolment/ Target audience The course is suitable for both PhD students working in structural bioinformatics as well as for PhD students in the life sciences who want to learn more about using structural informatioin in their research. The course schedule accommodates both groups, parallel sessions for both groups will be scheduled when necessary. Course Description In the right hands, protein structures are a 'power'ful tool to answer bio-molecular questions. Knowledge of the structure is a pre-requisite for rational drug design, for biotechnology, for chemical biology, and for answering a whole series of biomedical questions. In this course we will discuss the 'production' of protein structures by NMR, X-ray, and homology modelling. These methods all have their pro's and cons so a certain 'prowess' is needed to follow all 'promises' and start attacking bio-medical 'problems' using protein structures. The course will be split in three parts. Part 1) Looking and seeing things in protein structures, learning to operate the software, understanding some of the algorithms. Part 2) Protein structure determination (prediction) with NMR, X-ray, and homology modelling, and the possibilities and problems that come with each of these three techniques. Part 3) Applying all that was learned in real-life example studies. Course topics Day 1: Homology modelling Day 2: Protein structure determination and validation Day 3: Electrostatics and molecular dynamics Day 4: Protein structure comparison Day 5: Own project executed with help from CMBI staff. Examples of questions you will be able to answer after following the course: · Why is a person with this mutation sick? Or in other words, how does the molecular phenotype cause a disease state? · This enzyme converts mannose. Can I make is specificity broader? · This enzyme doesn't function in my in vitro assay. Should I add some ions? · I want to add a tag to my enzyme, should I put it on the N-terminus, the C-terminus, or is something different needed? · This receptor binds a ligand, but if I look at the structure, that ligand doesn't fit at all. Can I predict motions that take place upon ligand binding? NBIC PhD School This course is part of the Education Programme of the NBIC PhD School. The NBIC PhD School offers training and education for PhD students in bioinformatics. More information about the NBIC PhD School can also be found on http://www.nbic.nl => Education => NBIC PhD School. More information For more information about the course you can contact Celia van Gelder (NBIC Education) at celia.van.gelder(a)nbic.nl<mailto:celia.van.gelder@nbic.nl>. -- Dr. Celia W.G. van Gelder Coordinator Education CMBI Projectleader Education NBIC tel. +31-(0)24-3666120 e-mail: C.vanGelder(a)umcn.nl<mailto:C.vanGelder@umcn.nl> websites: www.cmbi.ru.nl<http://www.cmbi.ru.nl>, www.nbic.nl<http://www.nbic.nl> Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre /NCMLS PO Box 9101, 6500 HB Nijmegen The Netherlands Het UMC St Radboud staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud University Nijmegen Medical Centre is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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LATA 2014: 3rd call for papers
by GRLMC 14 Sep '13

14 Sep '13

*To be removed from our mailing list, please respond to this message with UNSUBSCRIBE in the subject line* ************************************************************************* 8th INTERNATIONAL CONFERENCE ON LANGUAGE AND AUTOMATA THEORY AND APPLICATIONS LATA 2014 Madrid, Spain March 10-14, 2014 Organized by: Research Group on Implementation of Language-Driven Software and Applications (ILSA) Complutense University of Madrid Research Group on Mathematical Linguistics (GRLMC) Rovira i Virgili University http://grammars.grlmc.com/lata2014/ ********************************************************************* AIMS: LATA is a yearly conference on theoretical computer science and its applications. Following the tradition of the diverse PhD training events in the field developed at Rovira i Virgili University in Tarragona since 2002, LATA 2014 will reserve significant room for young scholars at the beginning of their career. It will aim at attracting contributions from both classical theory fields and application areas (bioinformatics, language technology, artificial intelligence, etc.). VENUE: LATA 2014 will take place in Madrid, the capital of Spain. The venue will be the School of Informatics of Complutense University. SCOPE: Topics of either theoretical or applied interest include, but are not limited to: algebraic language theory algorithms for semi-structured data mining algorithms on automata and words automata and logic automata for system analysis and programme verification automata, concurrency and Petri nets automatic structures cellular automata codes combinatorics on words compilers computability computational complexity data and image compression decidability issues on words and languages descriptional complexity DNA and other models of bio-inspired computing digital libraries and document engineering foundations of finite state technology foundations of XML fuzzy and rough languages grammars (Chomsky hierarchy, contextual, unification, categorial, etc.) grammatical inference and algorithmic learning graphs and graph transformation language varieties and semigroups language-based cryptography language-theoretic foundations of artificial intelligence and artificial life natural language and speech automatic processing parallel and regulated rewriting parsing patterns power series quantum, chemical and optical computing semantics string and combinatorial issues in computational biology and bioinformatics string processing algorithms symbolic dynamics symbolic neural networks term rewriting transducers trees, tree languages and tree automata weighted automata STRUCTURE: LATA 2014 will consist of: invited talks invited tutorials peer-reviewed contributions INVITED SPEAKERS: Javier Esparza (Munich Tech, DE), On Trees and Fixed Point Equations (tutorial) Leslie A. Goldberg (Oxford, UK), The Complexity of Approximate Counting Oscar H. Ibarra (Santa Barbara, US), tba Sanjeev Khanna (Philadelphia, US), tba Helmut Seidl (Munich Tech, DE), tba PROGRAMME COMMITTEE: Dana Angluin (Yale, US) Eugene Asarin (Paris Diderot, FR) Jos Baeten (Amsterdam, NL) Christel Baier (Dresden, DE) Jan Bergstra (Amsterdam, NL) Jin-Yi Cai (Madison, US) Marek Chrobak (Riverside, US) Andrea Corradini (Pisa, IT) Mariangiola Dezani (Turin, IT) Ding-Zhu Du (Dallas, US) Michael R. Fellows (Darwin, AU) Jörg Flum (Freiburg, DE) Nissim Francez (Technion, IL) Jürgen Giesl (Aachen, DE) Annegret Habel (Oldenburg, DE) Kazuo Iwama (Kyoto, JP) Sampath Kannan (Philadelphia, US) Ming-Yang Kao (Northwestern, US) Deepak Kapur (Albuquerque, US) Joost-Pieter Katoen (Aachen, DE) S. Rao Kosaraju (Johns Hopkins, US) Evangelos Kranakis (Carleton, CA) Gad M. Landau (Haifa, IL) Andrzej Lingas (Lund, SE) Jack Lutz (Iowa State, US) Ian Mackie (École Polytechnique, FR) Carlos Martín-Vide (Tarragona, ES, chair) Giancarlo Mauri (Milan, IT) Faron G. Moller (Swansea, UK) Paliath Narendran (Albany, US) Enno Ohlebusch (Ulm, DE) Helmut Prodinger (Stellenbosch, ZA) Jean-François Raskin (Brussels, BE) Wolfgang Reisig (Humboldt Berlin, DE) Marco Roveri (Bruno Kessler, Trento, IT) Michaël Rusinowitch (LORIA, Nancy, FR) Yasubumi Sakakibara (Keio, JP) Davide Sangiorgi (Bologna, IT) Colin Stirling (Edinburgh, UK) Jianwen Su (Santa Barbara, US) Jean-Pierre Talpin (IRISA, Rennes, FR) Andrzej Tarlecki (Warsaw, PL) Rick Thomas (Leicester, UK) Sophie Tison (Lille, FR) Rob van Glabbeek (NICTA, Sydney, AU) Helmut Veith (Vienna Tech, AT) ORGANIZING COMMITTEE: Adrian Horia Dediu (Tarragona) Ana Fernández-Pampillón (Madrid) Carlos Martín-Vide (Tarragona, co-chair) Antonio Sarasa (Madrid) José-Luis Sierra (Madrid, co-chair) Bianca Truthe (Magdeburg) Florentina Lilica Voicu (Tarragona) SUBMISSIONS: Authors are invited to submit non-anonymized papers in English presenting original and unpublished research. Papers should not exceed 12 single-spaced pages (including eventual appendices) and should be formatted according to the standard format for Springer Verlag's LNCS series (see http://www.springer.com/computer/lncs?SGWID=0-164-6-793341-0) Submissions have to be uploaded to: https://www.easychair.org/conferences/?conf=lata2014 PUBLICATIONS: A volume of proceedings published by Springer in the LNCS series will be available by the time of the conference. A special issue of a major journal will be later published containing peer-reviewed extended versions of some of the papers contributed to the conference. Submissions to it will be by invitation. REGISTRATION: The period for registration is open from July 15, 2013 to March 10, 2014. The registration form can be found at: http://grammars.grlmc.com/lata2014/Registration.php DEADLINES: Paper submission: October 14, 2013 (23:59 CET) Notification of paper acceptance or rejection: November 25, 2013 Final version of the paper for the LNCS proceedings: December 2, 2013 Early registration: December 9, 2013 Late registration: February 24, 2014 Starting of the conference: March 10, 2014 End of the conference: March 14, 2014 Submission to the post-conference journal special issue: June 14, 2014 QUESTIONS AND FURTHER INFORMATION: florentinalilica.voicu(a)urv.cat POSTAL ADDRESS: LATA 2014 Research Group on Mathematical Linguistics (GRLMC) Rovira i Virgili University Av. Catalunya, 35 43002 Tarragona, Spain Phone: +34-977-559543 Fax: +34-977-558386 ACKNOWLEDGEMENTS: Departament dEconomia i Coneixement, Generalitat de Catalunya Universidad Complutense de Madrid Universitat Rovira i Virgili

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postdocs wanted to work in Pretoria, South Africa
by Yves Van de Peer 14 Sep '13

14 Sep '13

The Van de Peer lab (http://bioinformatics.psb.ugent.be/beg/) is setting up a joint lab in Bioinformatics and Systems Biology at the University of Pretoria (http://web.up.ac.za) Recently, the University of Pretoria founded a new Genomics Research Center, focusing on five major themes, namely Microbial and Environmental Genomics, Plant Genomics, Fungal Genomics, Animal and protozoon genomics, and Human Genomics. To support research in these respective fields, we are setting up a new Bioinformatics and Systems Biology research group at the University of Pretoria, which will be closely interconnected with the Bioinformatics group at Ghent University. In this respect, we are currently looking for 3 Postdoctoral Fellows (to be working in Pretoria). We seek creative, skilled and highly motivated candidates with a PhD in bioinformatics or computational biology. We do require strong analytical, computational skills proven by an excellent publication record. Experience with next generation sequence and whole genome sequence data is also required. Applicants should be proficient in programming (Perl, Python, C++ or Java) and knowledge in statistics and/or mathematical modeling would be an asset. Good communication skills are essential and applicants should be proficient in English, both speaking and writing. Funding is secured for at least three years, and may be extended. Contact Yves Van de Peer (yves.vandepeer(a)psb.ugent.be) for more information and/or to apply. To apply, please send a single PDF file that contains a cover letter describing your research interests and experience, full C.V., and contact information for three references. Review of applications will begin on October 1st and continue until the positions are filled. Start: As soon as possible. -- Check out http://www.plantgenomeevolution.com/ Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Group Leader Bioinformatics and Systems Biology, Department of Plant Systems Biology Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer(a)psb.vib-ugent.be http://bioinformatics.psb.ugent.be/

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NBIC PhD course Protein Structures: production, prowess, power, promises, and problems
by C.vanGelder＠umcn.nl 13 Sep '13

13 Sep '13

NBIC PhD course Protein Structures: production, prowess, power, promises, and problems Date: 4 - 8 Nov 2013 Course coordinator: Gert Vriend Location: Center for Molecular and Biomolecular Informatics (CMBI), UMC Radboud, Nijmegen, the Netherlands Website: http://www.nbic.nl/education/nbic-phd-school/course-schedule/protein-struct… Registration: http://www.nbic.nl/education/nbic-phd-school/enrolment/ Target audience The course is suitable for both PhD students working in structural bioinformatics as well as for PhD students in the life sciences who want to learn more about using structural informatioin in their research. The course schedule accommodates both groups, parallel sessions for both groups will be scheduled when necessary. Course Description In the right hands, protein structures are a 'power'ful tool to answer bio-molecular questions. Knowledge of the structure is a pre-requisite for rational drug design, for biotechnology, for chemical biology, and for answering a whole series of biomedical questions. In this course we will discuss the 'production' of protein structures by NMR, X-ray, and homology modelling. These methods all have their pro's and cons so a certain 'prowess' is needed to follow all 'promises' and start attacking bio-medical 'problems' using protein structures. The course will be split in three parts. Part 1) Looking and seeing things in protein structures, learning to operate the software, understanding some of the algorithms. Part 2) Protein structure determination (prediction) with NMR, X-ray, and homology modelling, and the possibilities and problems that come with each of these three techniques. Part 3) Applying all that was learned in real-life example studies. Course topics Day 1: Homology modelling Day 2: Protein structure determination and validation Day 3: Electrostatics and molecular dynamics Day 4: Protein structure comparison Day 5: Own project executed with help from CMBI staff. Examples of questions you will be able to answer after following the course: * Why is a person with this mutation sick? Or in other words, how does the molecular phenotype cause a disease state? * This enzyme converts mannose. Can I make is specificity broader? * This enzyme doesn't function in my in vitro assay. Should I add some ions? * I want to add a tag to my enzyme, should I put it on the N-terminus, the C-terminus, or is something different needed? * This receptor binds a ligand, but if I look at the structure, that ligand doesn't fit at all. Can I predict motions that take place upon ligand binding? NBIC PhD School This course is part of the Education Programme of the NBIC PhD School. The NBIC PhD School offers training and education for PhD students in bioinformatics. More information about the NBIC PhD School can also be found on http://www.nbic.nl => Education => NBIC PhD School. More information For more information about the course you can contact Celia van Gelder (NBIC Education) at celia.van.gelder(a)nbic.nl<mailto:celia.van.gelder@nbic.nl>. -- Dr. Celia W.G. van Gelder Coordinator Education CMBI Projectleader Education NBIC tel. +31-(0)24-3666120 e-mail: C.vanGelder(a)umcn.nl<mailto:C.vanGelder@umcn.nl> websites: www.cmbi.ru.nl<http://www.cmbi.ru.nl>, www.nbic.nl<http://www.nbic.nl> Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre /NCMLS PO Box 9101, 6500 HB Nijmegen The Netherlands Het UMC St Radboud staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud University Nijmegen Medical Centre is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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Symposium - New Genomics toward personalized medicine - 10/10/2013 Lille
by Olivier Sand 13 Sep '13

13 Sep '13

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10th Network Biology Symposium and Cytoscape Workshop 2013 in Paris, France, October 9-10
by P. Molenaar 09 Sep '13

09 Sep '13

The 10th annual Network Biology Symposium and Cytoscape Workshop brings together an international Network Biology community, including Cytoscape users and developers, for an update to the field of Network Biology, and Cytoscape tutorials and workshops. PROGRAM The meeting will kick off with the public symposium (Wednesday Oct. 9th) and poster session on the latest developments in Network Biology on the campus of the Pasteur Institute. Confirmed speakers include: - Patrick Aloy (IRB Barcelona) - Andreas Beyer (Univ. Cologne) - Nils Blüthgen (Charité Berlin) - Trey Ideker (UC San Diego) - Julio Saez-Rodriguez (Cambridge) - Esti Yeger-Lotem (Ben-Gurion University, Negev) Thursday, October 10th: Cytoscape User and Developer Workshop REGISTER NOW DEADLINE: September 23, 2013 http://nrnb.org/cyretreat2013 Reduced student rate available! REGISTER FOR A POSTER AND/OR A FLASH TALK Posters will be available all day 5-minute flash talks Cytoscape is a free, open-source software platform for visualizing and analyzing complex networks and associated data. Find out more at http://cytoscape.org<http://cytoscape.org/> For any questions, e-mail cyretreat2013(a)gmail.com<mailto:cyretreat2013@gmail.com> Piet Molenaar piet.amc(a)gmail.com<mailto:piet.amc@gmail.com> Department of Oncogenomics, M1-131 Academic Medical Center University of Amsterdam Meibergdreef 9 1105 AZ Amsterdam the Netherlands tel (+31) 20-5666592 fax (+31) 20-6918626 ________________________________ AMC Disclaimer : http://www.amc.nl/disclaimer ________________________________

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TPNC 2013: call for posters
by GRLMC 07 Sep '13

07 Sep '13

The 2nd International Conference on the Theory and Practice of Natural Computing (TPNC 2013) invites authors to submit poster presentations. TPNC 2013 will be held in Cáceres (Spain) on 3-5 December, 2013. See http://grammars.grlmc.com/tpnc2013/ Poster presentations are intended to enhance informal interactions with the conference participants, at the same time permitting in-depth discussion. TOPICS Authors are encouraged to submit presentations that discuss novel work in progress on: - nature-inspired models of computation, - synthesis of nature by means of computation, - nature-inspired materials, - information processing in nature, - applications of natural computing. Posters do not need to present final research results. Work that may lead to new interesting developments is welcome. KEY DATES Submission deadline: October 20, 2013 Notification of poster acceptance or rejection: October 27, 2013 SUBMISSION Please submit a .pdf abstract through: https://www.easychair.org/conferences/?conf=tpnc2013 It should contain the title, author(s) and affiliation, and should not exceed 500 words. PRESENTATION Posters will be allocated 8 minutes each in the programme for oral presentation. Moreover, they will remain hanging during the whole conference for discussion. PUBLICATION Posters will not appear in the LNCS proceedings volume of TPNC 2013. However, they will be eligible for submission to the post-conference Soft Computing journal special issue. REGISTRATION Authors of accepted posters have to register to the conference. Their registration fare is reduced: 150 Euro (appr. one third of the fare for PhD students).

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BBC 2013 abstract submission deadline is approaching
by BBC2013 06 Sep '13

06 Sep '13

BBC2013 – BeNeLux Bioinformatics Conference 2013 Date: December 9 & 10, 2013 Venue: Salle Dupréel (Université Libre de Bruxelles), Brussels, Belgium Website: http://bbc2013.ibsquare.be Abstract submission deadline: October 1, 2013 Early registration deadline: November 1, 2013 Dear Colleagues, We are happy to announce the 8th edition of the BeNeLux Bioinformatics Conference, which will take place in Brussels on the 9th and 10th of December 2013. The theme of this year's conference is: "Bioinformatics at all scales of life". Since 2005, the BeNeLux Bioinformatics Conference gives bioinformaticians, from the BeNeLux and beyond, the opportunity to discuss their results and build new collaborations, in a relaxed and friendly atmosphere. This year's edition will be enhanced by the presence of three distinguished keynote speakers: Alfonso Valencia (Spanish National Cancer Research Center, http://bit.ly/14SAITQ) Anna Tramontano (University of Rome "La Sapienza", http://www.biocomputing.it) and Jim Haseloff (Plant Synthetic Biology, University of Cambridge, http://www.haseloff-lab.org) Call for abstracts We invite you to submit an abstract for an oral presentation (20 available slots: 6 long, 14 short) and/or a poster presentation. Contributions from all fields of bioinformatics are welcome and encouraged. We have provided a template to use for submission. Details on the submission procedure can be found at http://bbc2013.ibsquare.be/content/call-abstracts . We hope to see you all in Brussels! -- The BBC 2013 organising committee BeNeLux Bioinformatics Conference 2013 December 9-10, 2013 (Brussels)

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Fwd: opening for bioinformatics post-doc in mycobacteriology
by Laukens Kris 06 Sep '13

06 Sep '13

Dear colleagues, please find attached the details for a job opening for a post-doc bioinformatics in mycobacteriology, in Antwerpen. Best regards, Kris Laukens Dear colleagues, friends, We are advertising for a bioinformatics specialist. Please pass the attached job description on to those you think might be interested. Kind regards, Bouke de Jong, MD PhD Head, Mycobacteriology Unit Institute of Tropical Medicine Nationalestraat 155 2000 Antwerp Belgium Phone: 00-32-3 247 6590 P Please consider the environment before printing this e-mail Disclaimer<http://www.itg.be/disclaimer> Directions to our location(s)<http://g.co/maps/ua89b>

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