- BBClist - maillist.psb.ugent.be

Fwd: postdoc bioinformatics (Roscoff, France)
by Lieven Sterck 21 Sep '15

21 Sep '15

> From: "Susana Coelho" <coelho(a)sb-roscoff.fr> > To: "Lieven Sterck" <liste(a)psb.vib-ugent.be>, "Yves Van de Peer" > <yves.vandepeer(a)psb.vib-ugent.be>, "Stephane Rombauts" <strom(a)psb.vib-ugent.be> > Sent: Monday, 21 September, 2015 12:22:08 > Subject: postdoc bioinformatics > I just wanted to tell you that in the context of my ERC we are now > officially looking for a postdoc in bioinformatics ! > Please find attached the advert, if you could please forward it to anyone > potentially interested? > Thanks a million, all the best > Su > -- > Susana M Coelho > Algal Genetics Group > UMR 7139 CNRS-UPMC > Station Biologique, > Place Georges Teissier, > CS 90974 > 29688 Roscoff, France > 48° 43' 37.33" N 3° 59' 17.41" W > Tel: 33 2 98 29 23 60, Fax: 33 2 98 29 23 85 > Email: coelho(a)sb-roscoff.fr > http://www.sb-roscoff.fr/algal-genetics

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LATA 2016: 2nd call for papers
by GRLMC 19 Sep '15

19 Sep '15

*To be removed from our mailing list, please respond to this message with UNSUBSCRIBE in the subject line* **************************************************************************************** 10TH INTERNATIONAL CONFERENCE ON LANGUAGE AND AUTOMATA THEORY AND APPLICATIONS LATA 2016 PRAGUE, CZECH REPUBLIC MARCH 14-18, 2016 Organized by: Department of Theoretical Computer Science Faculty of Information Technology CzechTechnicalUniversity in Prague Research Group on Mathematical Linguistics (GRLMC) Rovira i Virgili University http://grammars.grlmc.com/lata2016/ **************************************************************************************** AIMS: LATA is a conference series on theoretical computer science and its applications. Following the tradition of the diverse PhD training events in the field developed at Rovira i VirgiliUniversity in Tarragona since 2002, LATA 2016 will reserve significant room for young scholars at the beginning of their career. It will aim at attracting contributions from classical theory fields as well as application areas. VENUE: LATA 2016 will take place in Prague, a city full of history and cultural attractions, and one of the political and economic cores of central Europe. The venue will be the campus of the CzechTechnicalUniversity in the Dejvice quarter. 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 networks automata, concurrency and Petri nets automatic structures cellular automata codes combinatorics on words computational complexity data and image compression descriptional complexity 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 mathematical and logical foundations of programming methodologies parallel and regulated rewriting parsing patterns power series string and combinatorial issues in bioinformatics string processing algorithms symbolic dynamics term rewriting transducers trees, tree languages and tree automata unconventional models of computation weighted automata STRUCTURE: LATA 2016 will consist of: invited talks invited tutorials peer-reviewed contributions INVITED SPEAKERS: (to be completed) Martin Grohe (RWTHAachenUniversity), Connectivity Systems, Decompositions, and Tangles Jean-François Raskin (Free University of Brussels), Non-zero Sum Games for Reactive Synthesis Frank Wolter (University of Liverpool), Automata for Ontologies PROGRAMME COMMITTEE: Amihood Amir (Bar-IlanUniversity, Ramat Gan, Israel) Dana Angluin (YaleUniversity, New Haven, USA) Franz Baader (Technical University of Dresden, Germany) Christel Baier (Technical University of Dresden, Germany) Hans L. Bodlaender (UtrechtUniversity, The Netherlands) Jean-Marc Champarnaud (University of Rouen, France) Bruno Courcelle (LaBRI, Bordeaux, France) Rod Downey (VictoriaUniversity of Wellington, New Zealand) Frank Drewes (Umeå University, Sweden) Ding-Zhu Du (University of Texas, Dallas, USA) Javier Esparza (Technical University of Munich, Germany) Michael Fellows (CharlesDarwinUniversity, Darwin, Australia) Mohammad Taghi Hajiaghayi (University of Maryland, College Park, USA) Yo-Sub Han (YonseiUniversity, Seoul, South Korea) Markus Holzer (University of Giessen, Germany) Juraj Hromkovič (ETH Zurich, Switzerland) Oscar H. Ibarra (University of California, Santa Barbara, USA) Costas S. Iliopoulos (King's College London, UK) Jan Janoušek (CzechTechnicalUniversity in Prague, Czech Republic) Galina Jirásková (SlovakAcademy of Sciences, Košice, Slovakia) Ming-Yang Kao (Northwestern University, Evanston, USA) Juhani Karhumäki (University of Turku, Finland) Joost-Pieter Katoen (RWTH Aachen University, Germany) Martin Kutrib (University of Giessen, Germany) Zhiwu Li (Xidian University, Xi'an, China) Andreas Malcher (University of Giessen, Germany) Oded Maler (VERIMAG, Gières, France) Carlos Martín-Vide (Rovira i Virgili University, Tarragona, Spain, chair) Bořivoj Melichar (CzechTechnicalUniversity in Prague, Czech Republic) Ugo Montanari (University of Pisa, Italy) František Mráz (CharlesUniversity in Prague, Czech Republic) Mitsunori Ogihara (University of Miami, Coral Gables, USA) Alexander Okhotin (University of Turku, Finland) Doron A. Peled (Bar-IlanUniversity, Ramat Gan, Israel) Martin Plátek (CharlesUniversity in Prague, Czech Republic) Alberto Policriti (University of Udine, Italy) Daniel Reidenbach (University of Loughborough, UK) Antonio Restivo (University of Palermo, Italy) Kai Salomaa (Queen's University, Kingston, Canada) Davide Sangiorgi (University of Bologna, Italy) Uli Sattler (University of Manchester, UK) Frits Vaandrager (RadboudUniversity, Nijmegen, The Netherlands) Pierre Wolper (University of Liège, Belgium) Zhilin Wu (Chinese Academy of Sciences, Beijing, China) Mengchu Zhou (New Jersey Institute of Technology, Newark, USA) ORGANIZING COMMITTEE: Adrian Horia Dediu (Tarragona) Jan Janoušek (Prague, co-chair) Carlos Martín-Vide (Tarragona, co-chair) Radomír Polách (Prague) Eliška Šestáková (Prague) Jan Trávníček (Prague) Bianca Truthe (Giessen) 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, references, proofs, etc.) and should be prepared according to the standard format for Springer Verlag's LNCS series (see http://www.springer.com/computer/lncs?SGWID=0-164-6-793341-0 [1]). Submissions have to be uploaded to: https://www.easychair.org/conferences/?conf=lata2016 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 substantially 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 August 28, 2015 to March 14, 2016. The registration form can be found at: http://grammars.grlmc.com/lata2016/Registration.php DEADLINES: Paper submission: October 19, 2015 (23:59 CET) Notification of paper acceptance or rejection: November 27, 2015 Final version of the paper for the LNCS proceedings: December 7, 2015 Early registration: December 7, 2015 Late registration: February 29, 2016 Submission to the journal special issue: June 18, 2016 QUESTIONS AND FURTHER INFORMATION: florentinalilica.voicu (at) urv.cat POSTAL ADDRESS: LATA 2016 Research Group on Mathematical Linguistics (GRLMC) Rovira i Virgili University Av. Catalunya, 35 43002 Tarragona, Spain Phone: +34 977 559 543 Fax: +34 977 558 386 ACKNOWLEDGEMENTS: České vysoké učení technické v Praze Universitat Rovira i Virgili Links: ------ [1] http://www.springer.com/computer/lncs?SGWID=0-164-6-793341-0

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[Gtpb] GACT15 - Genomic Architecture of Complex Traits
by Pedro Fernandes 16 Sep '15

16 Sep '15

Reminder Dear GTPB subscriber Please note that applications for the Bioinformatics training Course GACT15 Genomic Architecture of Complex Traits are still possible. This course has been advertised during the summer, and some of you may have missed it. http://gtpb.igc.gulbenkian.pt/bicourses/GACT15 with Arcadi Navarro, Juan A. Rodriguez and David Allen Hughes IMPORTANT DATES for this Course Deadline for applications: Sept 19th 2015 <-------------- Approaching Latest notification of acceptance: Sept 20th 2015 Course date: Sept 28th - Oct 1st 2015 Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. Overview Genome-Phenome analysis is both a challenging biological problem and a key component of precision medicine. This course aims to introduce current methods and concepts used to link genomes and phenomes. Emphasis will be placed on mapping disease susceptibility genes. Course topics will be presented as lectures each followed by illustrative practical sessions. Topics will cover technological and design issues as well as current data analysis and interpretation strategies. A variety of approaches to Genome-Phenome analysis will be covered ranging from array and targeted re-sequencing of (Epi-)Genome-Wide Association Studies to full genome re-sequencing. The main focus of this course will be on complex traits, however, the genetic architectures of cancer and rare diseases will also be considered. Methods: The course is comprised of practical exercises preceded by short lectures. There will be opportunities to hold group discussions on specific case studies. Target Audiences: (1) Individuals with knowledge about bioinformatics and/or genomics, that aim at using modern methods to address population variation or genotype phenotype association studies. (2) Individuals interested in some particular phenotype(s) (MDs, veterinarians, biologists) and wishing to commence investigation of the genetics of their trait(s) of interest. (3) All individuals, graduate or professional, wishing to expand on their working knowledge of the genetics of complex traits. Pre-requisites: In addition to a reasonable level of computer literacy, a minimal familiarity with the basics of bioinformatics, statistics, genomics and biology will be assumed. An acquaintance with studies of population variation or genotype phenotype association would be an advantage but not essential. Course duration / fee: 4 days / Euro 360.00 Thank you for your interest in GTPB courses. 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 _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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Workshop Life Sciences with Industry - Leiden, November 16 - 20, 2015
by Gokhan Ertaylan 15 Sep '15

15 Sep '15

Invitation to participate in the Life Sciences with Industry 2015 Lorentz workshop Leiden, November 16 - 20, 2015 We invite PhD students and postdocs from all branches of the life sciences that like to participate in the one-week Life Sciences with Industry 2015 Lorentz workshop in Leiden: November 16 – 20, 2015. During the workshop, the about 40 participants tackle in groups of eight six scientifically challenging and commercially important problems formulated by six companies. The workshop will take place in Leiden in the building of the Lorentz Center, an organisation that is specialised in organising scientific workshops (http://www.lorentzcenter.nl/ <http://www.lorentzcenter.nl/>). To create multi-disciplinary teams, participants will be selected based on their (i) specific background in the life sciences, (ii) motivation to participate, and (iii) date of registration. Registration on the workshop website: http://www.lorentzcenter.nl/lc/web/2015/762/info.php3?wsid=762&venue=Oort <http://www.lorentzcenter.nl/lc/web/2015/762/info.php3?wsid=762&venue=Oort> Deadline: Sunday October 18, 2015. Participation is free of charge, including hotel accommodation during the workshop. Also lunches and two workshop dinners are covered. The workshop is sponsored by the Lorentz Center, the Research School BioSB (http://biosb.nl/ <http://biosb.nl/>), STW (http://www.stw.nl/ <http://www.stw.nl/>) and the companies involved. Need more information? Contact Yousra Jaddour at the Lorentz Center: jaddour(a)lorentzcenter.nl <mailto:jaddour@lorentzcenter.nl> or +31-71-527 5578. The organisers Dr. Ellen Feddes (STW) Dr. Gökhan Ertaylan (MaCSBio, Maastricht University) Dr. Jurgen R. Haanstra (VU University Amsterdam) prof. em. Dr. Roel van Driel (University of Amsterdam) ********************************************************************* Six industrial challenges Life Sciences with Industry 2015 1. New possibilities for developing disease-resistant plants Bejo Zaden B.V. (www.bejo.nl <http://www.bejo.nl/>) 2. Technologies to modulate galactosylation and fucosylation in human antibodies production in clonal cell lines Bioceros B.V. (www.bioceros.com <http://www.bioceros.com/>) 3. Isolation of phospholipids from fresh cow milk Nutricia Danone (www.nutricia.nl/ <http://www.nutricia.nl/>) 4. Applications of a novel low-cost/disposable high resolution and sensitive detector in health and biotechnology NXP Semiconductors B.V. (www.nxp.com <http://www.nxp.com/>) 5. Quantifying the quality of light for human-centric lighting solutions: how to objectively measure (visual) comfort and well-being Philips Research (www.research.philips.com <http://www.research.philips.com/>) 6. Automated 3D imaging and analysis systems to measure plant volume and other critical parameters of seed germination and seedling establishment Syngenta (www3.syngenta.com/country/nl/nl/Pages/home.aspx) Gökhan Ertaylan, PhD Maastricht Centre for Systems Biology (MaCSBio) - Maastricht University http://macsbio.maastrichtuniversity.nl/ <http://macsbio.maastrichtuniversity.nl/> Universiteitssingel 60, 6229 ER Maastricht ( +31 (0) 43 38 81123

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[Gtpb] REMINDER: GACT15 - Genomic Architecture of Complex Traits
by Pedro Fernandes 14 Sep '15

14 Sep '15

Reminder We are happy to announce that applications for the Bioinformatics training Course GACT15 Genomic Architecture of Complex Traits are now *OPEN* http://gtpb.igc.gulbenkian.pt/bicourses/GACT15 with Arcadi Navarro, Juan A. Rodriguez and David Allen Hughes IMPORTANT DATES for this Course Deadline for applications: Sept 19th 2015 Latest notification of acceptance: Sept 20th 2015 Course date: Sept 28th - Oct 1st 2015 Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. Overview Genome-Phenome analysis is both a challenging biological problem and a key component of precision medicine. This course aims to introduce current methods and concepts used to link genomes and phenomes. Emphasis will be placed on mapping disease susceptibility genes. Course topics will be presented as lectures each followed by illustrative practical sessions. Topics will cover technological and design issues as well as current data analysis and interpretation strategies. A variety of approaches to Genome-Phenome analysis will be covered ranging from array and targeted re-sequencing of (Epi-)Genome-Wide Association Studies to full genome re-sequencing. The main focus of this course will be on complex traits, however, the genetic architectures of cancer and rare diseases will also be considered. Methods: The course is comprised of practical exercises preceded by short lectures. There will be opportunities to hold group discussions on specific case studies. Target Audiences: (1) Individuals with knowledge about bioinformatics and/or genomics, that aim at using modern methods to address population variation or genotype phenotype association studies. (2) Individuals interested in some particular phenotype(s) (MDs, veterinarians, biologists) and wishing to commence investigation of the genetics of their trait(s) of interest. (3) All individuals, graduate or professional, wishing to expand on their working knowledge of the genetics of complex traits. Pre-requisites: In addition to a reasonable level of computer literacy, a minimal familiarity with the basics of bioinformatics, statistics, genomics and biology will be assumed. An acquaintance with studies of population variation or genotype phenotype association would be an advantage but not essential. Course duration / fee: 4 days / Euro 360.00 Thank you for your interest in GTPB courses. 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 _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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BigDat 2016: early registration deadline 22 September
by GRLMC 12 Sep '15

12 Sep '15

*To be removed from our mailing list, please respond to this message with UNSUBSCRIBE in the subject line* ******************************************************** 2ND INTERNATIONAL WINTER SCHOOLON BIG DATA BIGDAT 2016 BILBAO, SPAIN FEBRUARY 8-12, 2016 Organized by: Deusto University Rovira i Virgili University http://grammars.grlmc.com/BigDat2016/ ******************************************************** --- Early registration deadline: September 22, 2015 --- ******************************************************** AIM: BigDat 2016 will be a research training event addressed to graduates and postgraduates in the first steps of their academic career. With a global scope, it aims at updating them about the most recent advances in the critical and fast developing area of big data, which covers a large spectrum of current exciting research and industrial innovation with an extraordinary potential for a huge impact on scientific discoveries, medicine, engineering, business models, and society itself. Renowned academics and industry pioneers will lecture and share their views with the audience. Most big data subareas will be displayed, namely: foundations, infrastructure, management, search and mining, security and privacy, and applications. Main challenges of analytics, management and storage of big data will be identified through 5 keynote lectures, 16 six-hour courses, and 1 round table, which will tackle the most active and promising topics. The organizers are convinced that outstanding speakers will attract the brightest and most motivated students. Interaction will be a main component of the event. An open session will give participants the opportunity to present their own work in progress in 5 minutes. ADDRESSED TO: Graduates and postgraduates from around the world. There are no formal pre-requisites in terms of academic degrees. However, since there will be differences in the course levels, specific knowledge background may be assumed for some of them. BigDat 2016 is also appropriate for more senior people who want to keep themselves updated on recent developments and future trends. All will surely find it fruitful to listen and discuss with major researchers, industry leaders and innovators. REGIME: In addition to keynotes, at least 2 courses will run in parallel during the whole event. Participants will be able to freely choose the courses they will be willing to attend as well as to move from one to another. VENUE: BigDat 2016 will take place in Bilbao, the capital of the Basque Country region, famous for its gastronomy and the seat of the GuggenheimMuseum. The venue will be: DeustoTech, School of Engineering DeustoUniversity Avda. Universidades, 24 48014 Bilbao KEYNOTE SPEAKERS: tba PROFESSORS AND COURSES: (to be completed) Nektarios Benekos (European Organization for Nuclear Research), [introductory/intermediate] Exploring the Mysteries of our Cosmos: the Big Deal between Big Data and Big Science Hendrik Blockeel (KU Leuven), [intermediate] Decision Trees for Big Data Analytics Edward Y. Chang (HTC Health, Taipei), [introductory/intermediate] Big Data Analytics for Healthcare: Scalable Algorithms and Applications Nello Cristianini (University of Bristol), [introductory] THINKBIG: Towards Large Scale Computational Social Sciences, History and Digital Humanities Ernesto Damiani (University of Milan), tba Francisco Herrera (University of Granada), [introductory] Big Data Preprocessing George Karypis (University of Minnesota), [intermediate/advanced] Scaling Up Recommender Systems Chih-Jen Lin (NationalTaiwanUniversity), [introductory/intermediate] Large-scale Linear Classification Geoff McLachlan (University of Queensland), tba Wladek Minor (University of Virginia), [introductory/intermediate] Big Data and Structural Biology and Chemistry Sankar K. Pal (Indian Statistical Institute), [introductory/advanced] Machine Intelligence and Granular Mining: Relevance to Big Data Hanan Samet (University of Maryland), [introductory/intermediate] Sorting in Space Jeffrey Ullman (StanfordUniversity), [introductory] Big Data Algorithms that Aren't Machine Learning Alexandre Vaniachine (Argonne National Laboratory), [introductory/advanced] Big Data: Comparison with Computational Models Xiaowei Xu (University of Arkansas, Little Rock), [introductory/advanced] Big Data Analytics for Social Networks Mohammed J. Zaki (Rensselaer Polytechnic Institute), [introductory/advanced] Large Scale Graph Analytics and Mining OPEN SESSION An open session will collect 5-minute presentations of work in progress by participants. They should submit a half-page abstract containing title, authors, and summary of the research to adrian.dediu(a)urv.cat by February 5, 2016. ORGANIZING COMMITTEE: Adrian Horia Dediu Carlos Martín-Vide (co-chair) Borja Sanz (co-chair) Florentina Lilica Voicu REGISTRATION: It has to be done at http://grammars.grlmc.com/bigdat2016/registration.php The selection of up to 8 courses requested in the registration template is only tentative and non-binding. For the sake of organization, it will be helpful to have an approximation of the respective demand for each course. Since the capacity of the venue is limited, registration requests will be processed on a first come first served basis. The registration period will be closed and the on-line registration facility disabled when the capacity of the venue will be complete. It is much recommended to register prior to the event. FEES: Participants are expected to attend full-time. Fees are a flat rate allowing the attendance to all courses during the week. There are several early registration deadlines. Fees depend on the registration deadline. ACCOMMODATION: Suggestions of accommodation will be available on the webpage in due time. CERTIFICATE: Participants will be delivered a certificate of attendance. QUESTIONS AND FURTHER INFORMATION: florentinalilica.voicu(a)urv.cat ACKNOWLEDGEMENTS: DeustoUniversity Rovira i VirgiliUniversity

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[Gtpb] GACT15 - Genomic Architecture of Complex Traits - details
by Pedro Fernandes 11 Sep '15

11 Sep '15

The detailed timetable for the CAT15 course has been updated Best, Pedro Fernandes Mon, Sept 28th Day #1 09:30 - 11:00 Introduction. Genotypes and Phenotypes - Examples from the literature. 11:00 - 11:30 Coffee Break 11:30 - 12:30 Overview of Genetic Variation. 12:30 - 14:00 Lunch Break 14:00 - 16:00 Technologies to acquire data: genotyping, sequencing, aCGH 16:00 - 16:30 Tea Break 16:30 - 18:00 Practical: Databases of human variation - Functional Annotation. Tue, Sept 29th Day #2 09:30 - 11:00 Morning Wrap-up (what have we done so far?) How to link phenotypes and genotypes. Linkage mapping and association. 11:00 - 11:30 Coffee Break 11:30 - 12:30 Practical: PLINK. Association Studies - GWAS - WTCCC 12:30 - 14:00 Lunch Break 14:00 - 16:00 Practical: PLINK continued and GCTA 16:00 - 16:30 Tea Break 16:30 - 18:00 Discussions - Open topics (Privacy, Replication, Most findings are false) Wed, Sept 30th Day #3 09:30 - 11:00 Morning Wrap-up (what have we done so far?) Intorducion to SAM, BAM, VCFtools 11:00 - 11:30 Coffee Break 11:30 - 12:30 Practical: SAM, BAM, VCFtools 12:30 - 14:00 Lunch Break 14:00 - 16:00 Predicting Phenotypes. Mendelian vs. Complex. Practical: Genetic Risk Scores. 16:00 - 16:30 Tea Break 16:30 - 18:00 Discussions - Open topics (Privacy, Replication, most findings are false) Thu, Oct 1st Day #4 09:30 - 11:00 Morning Wrap-up (what have we done so far?) Introduction to Epigenome Roadmap 11:00 - 11:30 Coffee Break 11:30 - 12:30 Epigenome Roadmap. Examples and Discussion. 12:30 - 14:00 Lunch Break 14:00 - 16:00 Practical: EWAS and eQTLs with R 16:00 - 16:30 Tea Break 16:30 - 18:00 Final wrap-up session -- 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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BioSB Course Matlab, 20 October 2015, Wageningen
by Celia.vanGelder＠radboudumc.nl 08 Sep '15

08 Sep '15

BioSB Course Matlab, 20 October 2015, Wageningen Website: http://biosb.nl/education/course-portfolio-2/course-matlab/ . Coordinators: Hans Stigter (WUR), Celia van Gelder (BioSB, celia.van.gelder(a)biosb.nl<mailto:celia.van.gelder@biosb.nl>) Registration: http://biosb.nl/education/course-portfolio-2/course-matlab/enrollment-cours… Please note that if you are (or become) a member of BioSB this course is free of charge for PhD students and with reduced fee for other researchers! Goal The main goal of this course is to get acquainted with Matlab software for use within Systems Biology. After this introductory course you will have gained the basic knowledge to pursue further use via self-study of Matlab in order to apply more advanced programming techniques within Matlab in your own research. In summary, the sub-goals are: 1. To learn the philosophy behind Matlab and its syntax 2. To program simple Systems Biology models in Matlab (in ordinary differential equation format) and to solve these differential equations with Matlab Programme 09:45 Coffee/Tea 10:00 Welcome 10:05 Introduction Matlab Basics (functions, variables, matrices, etc) 10:45 Advanced Programming (vectorised thinking, solving dynamic ordinary differential equation models in Matlab, parameter estimation for ODE-models) 12:00 Afternoon: Solving basic and advanced problems in Matlab - hands-on experience on a PC. Exercises will be provided, but you can also bring your own problems that you have encountered in your own research. 12:30 Lunch 15:00 Coffee/tea 16:30 End Target audience Primarily targeting researchers from academia, but participants from the private sector are also welcome. The course focusses on the use of Matlab for building dynamic Systems Biology Models in terms of ordinary differential equations. Course Description This is a one-day introduction to the possibilities of Matlab as a programming environment for simulation and analysis of biological models. We will start with a simple introduction of the basics of Matlab (matrices, vectors, manipulation of matrices and presentation of data). Having obtained some basic programming knowledge (writing of simple scripts and functions in Matlab), we will move on to more advanced topics. These include programming and solving ordinary differential equation models (ODEs) and the concept of "vectorized thinking" while writing Matlab-code. Finally, calibration of parameters in ODE type of models using measured data will be discussed and examples will be given. The course also includes the basics of presenting your results (graphing) in various types of plots that can easily be drawn in Matlab. Participants will, of course, get hands-on experience with Matlab and write code themselves in a practical. BioSB Education Programme 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/> or via education(a)biosb.nl<mailto:education@biosb.nl>. Dr. Celia W.G. van Gelder Education Manager BioSB Coordinator Education CMBI Programme Manager Learning DTL/ELIXIR-NL tel. +31613375327 e-mail: Celia.vanGelder(a)radboudumc.nl<mailto:Celia.vanGelder@radboudumc.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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[Gtpb] GACT15 - Genomic Architecture of Complex Traits
by Pedro Fernandes 01 Sep '15

01 Sep '15

Announcement/Reminder We are happy to announce that applications for the Bioinformatics training Course GACT15 Genomic Architecture of Complex Traits are now *OPEN* http://gtpb.igc.gulbenkian.pt/bicourses/GACT15 with Arcadi Navarro, Juan A. Rodriguez and David Allen Hughes IMPORTANT DATES for this Course Deadline for applications: Sept 19th 2015 Latest notification of acceptance: Sept 20th 2015 Course date: Sept 28th - Oct 1st 2015 Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. Overview Genome-Phenome analysis is both a challenging biological problem and a key component of precision medicine. This course aims to introduce current methods and concepts used to link genomes and phenomes. Emphasis will be placed on mapping disease susceptibility genes. Course topics will be presented as lectures each followed by illustrative practical sessions. Topics will cover technological and design issues as well as current data analysis and interpretation strategies. A variety of approaches to Genome-Phenome analysis will be covered ranging from array and targeted re-sequencing of (Epi-)Genome-Wide Association Studies to full genome re-sequencing. The main focus of this course will be on complex traits, however, the genetic architectures of cancer and rare diseases will also be considered. Methods: The course is comprised of practical exercises preceded by short lectures. There will be opportunities to hold group discussions on specific case studies. Target Audiences: (1) Individuals with knowledge about bioinformatics and/or genomics, that aim at using modern methods to address population variation or genotype phenotype association studies. (2) Individuals interested in some particular phenotype(s) (MDs, veterinarians, biologists) and wishing to commence investigation of the genetics of their trait(s) of interest. (3) All individuals, graduate or professional, wishing to expand on their working knowledge of the genetics of complex traits. Pre-requisites: In addition to a reasonable level of computer literacy, a minimal familiarity with the basics of bioinformatics, statistics, genomics and biology will be assumed. An acquaintance with studies of population variation or genotype phenotype association would be an advantage but not essential. Course duration / fee: 4 days / Euro 360.00 Thank you for your interest in GTPB courses. 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 _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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LATA 2016: 1st call for papers
by GRLMC 29 Aug '15

29 Aug '15

*To be removed from our mailing list, please respond to this message with UNSUBSCRIBE in the subject line* **************************************************************************************** 10TH INTERNATIONAL CONFERENCE ON LANGUAGE AND AUTOMATA THEORY AND APPLICATIONS LATA 2016 PRAGUE, CZECH REPUBLIC MARCH 14-18, 2016 Organized by: Department of Theoretical Computer Science CzechTechnicalUniversity in Prague Research Group on Mathematical Linguistics (GRLMC) Rovira i Virgili University http://grammars.grlmc.com/lata2016/ [1] **************************************************************************************** AIMS: LATA is a conference series on theoretical computer science and its applications. Following the tradition of the diverse PhD training events in the field developed at Rovira i VirgiliUniversity in Tarragona since 2002, LATA 2016 will reserve significant room for young scholars at the beginning of their career. It will aim at attracting contributions from classical theory fields as well as application areas. VENUE: LATA 2016 will take place in Prague, a city full of history and cultural attractions, and one of the political and economic cores of central Europe. The venue will be the campus of the CzechTechnicalUniversity in the Dejvice quarter. 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 networks automata, concurrency and Petri nets automatic structures cellular automata codes combinatorics on words computational complexity data and image compression descriptional complexity 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 parallel and regulated rewriting parsing patterns power series string and combinatorial issues in bioinformatics string processing algorithms symbolic dynamics term rewriting transducers trees, tree languages and tree automata unconventional models of computation weighted automata STRUCTURE: LATA 2016 will consist of: invited talks invited tutorials peer-reviewed contributions INVITED SPEAKERS: tba PROGRAMME COMMITTEE: (to be completed) Dana Angluin (YaleUniversity, New Haven, USA) Franz Baader (Technical University of Dresden, Germany) Christel Baier (Technical University of Dresden, Germany) Hans L. Bodlaender (UtrechtUniversity, The Netherlands) Jean-Marc Champarnaud (University of Rouen, France) Rod Downey (VictoriaUniversity of Wellington, New Zealand) Frank Drewes (Umeå University, Sweden) Ding-Zhu Du (University of Texas, Dallas, USA) Michael Fellows (CharlesDarwinUniversity, Darwin, Australia) Mohammad Taghi Hajiaghayi (University of Maryland, College Park, USA) Yo-Sub Han (Yonsei University, Seoul, South Korea) Oscar H. Ibarra (University of California, Santa Barbara, USA) Jan Janoušek (CzechTechnicalUniversity in Prague, Czech Republic) Galina Jirásková (SlovakAcademy of Sciences, Košice, Slovakia) Ming-Yang Kao (Northwestern University, Evanston, USA) Juhani Karhumäki (University of Turku, Finland) Joost-Pieter Katoen (RWTH Aachen University, Germany) Martin Kutrib (University of Giessen, Germany) Zhiwu Li (Xidian University, Xi'an, China) Oded Maler (VERIMAG, Gières, France) Carlos Martín-Vide (Rovira i Virgili University, Tarragona, Spain, chair) Ugo Montanari (University of Pisa, Italy) František Mráz (CharlesUniversity in Prague, Czech Republic) Mitsunori Ogihara (University of Miami, Coral Gables, USA) Alexander Okhotin (University of Turku, Finland) Doron A. Peled (BarIlanUniversity, Ramat Gan, Israel) Martin Plátek (CharlesUniversity in Prague, Czech Republic) Daniel Reidenbach (University of Loughborough, UK) Antonio Restivo (University of Palermo, Italy) Kai Salomaa (Queen's University, Kingston, Canada) Davide Sangiorgi (University of Bologna, Italy) Uli Sattler (University of Manchester, UK) Pierre Wolper (University of Liège, Belgium) Zhilin Wu (Chinese Academy of Sciences, Beijing, China) Mengchu Zhou (New Jersey Institute of Technology, Newark, USA) ORGANIZING COMMITTEE: Adrian Horia Dediu (Tarragona) Jan Janoušek (Prague, co-chair) Carlos Martín-Vide (Tarragona, co-chair) Radomír Polách (Prague) Eliška Šestáková (Prague) Jan Trávníček (Prague) Bianca Truthe (Giessen) 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, references, proofs, etc.) and should be prepared according to the standard format for Springer Verlag's LNCS series (see http://www.springer.com/computer/lncs?SGWID=0-164-6-793341-0 [2]). Submissions have to be uploaded to: https://www.easychair.org/conferences/?conf=lata2016 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 substantially 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 August 28, 2015 to March 14, 2016. The registration form can be found at: http://grammars.grlmc.com/lata2016/Registration.php [3] DEADLINES: Paper submission: October 19, 2015 (23:59 CET) Notification of paper acceptance or rejection: November 27, 2015 Final version of the paper for the LNCS proceedings: December 7, 2015 Early registration: December 7, 2015 Late registration: February 29, 2016 Submission to the journal special issue: June 18, 2016 QUESTIONS AND FURTHER INFORMATION: florentinalilica.voicu(a)urv.cat POSTAL ADDRESS: LATA 2016 Research Group on Mathematical Linguistics (GRLMC) Rovira i Virgili University Av. Catalunya, 35 43002 Tarragona, Spain Phone: +34 977 559 543 Fax: +34 977 558 386 ACKNOWLEDGEMENTS: České vysoké učení technické v Praze Universitat Rovira i Virgili Links: ------ [1] http://grammars.grlmc.com/lata2014/ [2] http://www.springer.com/computer/lncs?SGWID=0-164-6-793341-0 [3] http://grammars.grlmc.com/lata2014/Registration.php

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