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Benelux Bioinformatics Conference 2015: student fellowships
by Laukens Kris 09 Oct '15

09 Oct '15

- Benelux Bioinformatics Conference 2015 - Student fellowships - The University of Antwerp is proud to welcome you the Benelux Bioinformatics Conference 2015 (BBC 2015). The BBC 2015 will take place at Elzenveld in the heart of Antwerp, on 7-8 December 2015. To stimulate the participation of young scientists, we are pleased to announce the availability of 10 student fellowships. What is a student fellowship? A fellowship covers the registration fee for full participation to the Benelux Bioinformatics Conference, including lectures, poster sessions, lunch and coffee breaks. Note that a fellowship does NOT cover the conference dinner on Monday evening, but fellowship recipients are allowed to join the dinner at the normal rate (€ 50). Fellowships also do not cover accommodation, travel, or other costs. Who can get a fellowship? The fellowships will be preferentially awarded to students with: • a particular interest in bioinformatics; • active involvement in bioinformatics work (internship, bachelor or master thesis, …); • NO formal scientific employment (in the form of a salary or grant). Active participation with a scientific poster is strongly encouraged. Check the late poster abstract submission information on the conference website: http://bbc2015.be/submission.html How can I apply for a fellowship? Send an e-mail with a short CV (studies, grades, internships, employment), contact details, and a motivation that convincingly shows that you deserve to be awarded this fellowship to info(a)bbc2015.be<mailto:info@bbc2015.be> with the following subject line: “BBC2015 student fellowship application: first name family name”. Deadline for applications is November 10. The organising committee is responsible for the selection. Candidates will be informed about their application by the end of November. No further discussion will be held with regards to the result. Note that we will follow a strict attendance policy. Fellowship recipients who are unable to attend, are expected to inform us 7 days in advance. Without notification, fellowship recipients who do not show up at the conference notice will be charged the registration fee. Gold sponsors [cid:39348392-FFB5-410B-BD43-AC02AE426152@ua.ac.be][cid:A7C6CF3A-9AE4-4B83-A478-767908F6EA32@ua.ac.be]

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BioSB course on Managing and Integrating Life Science Information, 30 Nov - 4 Dec, Utrecht, the Netherlands
by Celia.vanGelder＠radboudumc.nl 09 Oct '15

09 Oct '15

BioSB Course on Managing and Integrating Life Science Information: Approaches using Linked Data and Semantics (4th edition) Course coordinators: Marco Roos, Katy Wolstencroft Date: 30 November - 4 December 2015 Location: SURF, Utrecht, the Netherlands Website: http://biosb.nl/education/course-portfolio/course-managing-and-integrating-…. Registration: http://biosb.nl/education/course-portfolio/course-managing-and-integrating-… .Please not that this course is free of charge for PhDs who are or will become a member of the BioSB research school, and with a reduced fee for other researchers who are or will become a member of BioSB. More information about the BioSB membership can be found here: http://biosb.nl/about/members/biosb-membership-information/ . Course flyer: http://biosb.nl/wp-content/uploads/2013/08/Wolstencroft_Roos_Course_2015_Ju… Target audience This course is for bioinformaticians who would like to learn about leading-edge data and knowledge integration solutions. You will learn (1) powerful and flexible approaches to data and information management for your bioinformatics application (Semantic Web and Linked Data), (2) how to work with data across remote locations, for instance by applying Web Services and workflows, (3) how to publish your own data to make it available and reusable for the rest of the community. We assume a basic understanding of bioinformatics programming for the hands on sessions. It would suit previous user participants of BYOD<http://www.dtls.nl/fair-data/byod/> meetings who would like more hands-on experience of data integration. It would also suit data providers who would like to explore new ways of serving their data or integrating it with other resources Description The amount of Life Science data available in the public domain is a vast and growing resource for bioinformatics research. There are over 20 million papers in PubMed and over 1600 biological databases. In many cases finding and applying the information from these resources is far from trivial. Following this course will show you techniques for working with these distributed resources, which includes using the web of Linked data and scientific workflows. It will also focus on methods for using or linking your own data into this large distributed Semantic Web of resources, in order to ensure that your data is FAIR<http://www.dtls.nl/fair-data/byod/> (Findable, Accessible, Interoperable and Reusable). This course introduces modern techniques for the management of life science data and knowledge for bioinformatics applications. After following this course students should be able to start creating their first applications based on these technologies or make more informed design decisions for their current application. In this course you will learn about: 1. Linked Data and the Semantic Web technologies that underpin it 2. How you can use Linked Data for data and knowledge integration in the Life Sciences 3. Available Linked Data resources in the public domain and large-scale projects that use these resources 4. How you can integrate your own data with Linked Data resources 5. How you can combine data integration and analysis over distributed resources, using Web Services and workflows Lecturers: Marco Roos, Katy Wolstencroft, Frank van Harmelen, Paul Groth, Simon Jupp, Jesse van Dam, and others TBC . Programme Monday - Introduction to Semantic Interoperability and the Semantic Web The Semantic Web primer, an introduction to RDF and Linked Data Tuesday - The Semantic Web in Use. Querying public Linked Data resources Querying Linked Data with SPARQL, using public Linked Data resources from the EBI Wednesday - The Semantic web in use (2) - Systems and guidelines Guidelines and best practices for Linked Data, Case study Open PHACTS - using Linked Data for research Thursday - Making Data Understandable and Searchable Methods for annotating and providing Linked Data, using and understanding ontologies Friday - Using, Integrating and Analysing Data Using scientific workflows and web services to integrate and analyse Linked Data and other kinds of data 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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[DUTCH] Vacature docent praktijkonderwijs HAN Nijmegen
by Bruggen Martijn van der 06 Oct '15

06 Oct '15

De Faculteit Techniek zoekt voor de campus in Nijmegen per direct Docent PraktijkOnderwijs Bio-informatica (0,8 - 1,0 .fte) De Faculteit Techniek (FT) verzorgt de technische opleidingen van de HAN. Studenten volgen er competentiegericht onderwijs in moderne werkvormen en in diverse trajecten, zoals in voltijd, deeltijd en duaal. Ze worden opgeleid tot gekwalificeerde bachelors/ingenieurs in het specifieke beroepenveld. Medewerkers van de faculteit zijn werkzaam in het reguliere onderwijs en mogelijk ook in post-hbo-, internationale en masteropleidingen, en voor onderzoeksopdrachten van én voor bedrijven en instellingen. Het Instituut Applied Sciences van de Faculteit Techniek leidt zijn studenten op tot (laboratorium)medewerkers in het chemische, biologische, medische en bio-informatica- beroepenveld. Een hecht team geeft hier op moderne en enthousiaste wijze gestalte aan. Wat zijn uw werkzaamheden? U begeleidt leerprocessen met name in de rol van praktijkdocent (bio)informatica, tutor voor de opleiding bio-informatica. U bent vooral werkzaam in het 1e en 2e leerjaar van de opleiding. Wat zijn uw kwaliteiten? U hebt een afgeronde HBO-opleiding op het gebied van de bio-informatica. U bent communicatief, sociaal vaardig en collegiaal. U bent enthousiast, flexibel, resultaatgericht en stressbestendig. Wat bieden wij u? Een interessante en afwisselende functie in een dynamische, informele werkomgeving. Aanstelling vindt plaats voor de duur van een jaar. De aanstelling is van tijdelijke aard. U wordt aangesteld in de functie van Instructeur PraktijkOnderwijs (IPO). Wilt u meer informatie? Voor meer informatie over deze functie kunt u contact opnemen met de heer M. van der Bruggen, opleidingscoördinator Bio-informatica T (06) 55 20 63 44 of via Martijn.vanderBruggen(a)han.nl<mailto:Martijn.vanderBruggen@han.nl> Hebt u belangstelling? Herkent u zich in bovenstaand profiel en voldoet u aan de eisen? Sollicitaties kunnen rechtstreeks naar de contactpersoon worden verstuurd. Deze dienen uiterlijk maandag 12 oktober binnen zijn.

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Edinburgh Genomics 1-day workshop: Oxford Nanopore MinION Sequencing - Data Handling, Analysis and Applications Thursday 10 Dec 2015
by Bert Overduin 06 Oct '15

06 Oct '15

To whom this may concern: Edinburgh Genomics is happy to offer a 1-day workshop "Oxford Nanopore MinION Sequencing - Data Handling, Analysis and Applications". *Description:* Nanopore sequencing is one of the newest sequence technologies, in which single DNA molecules are sequenced directly, without the need for an intervening PCR amplification step or a chemical labelling step. It offers the potential of read lengths of tens of kilo bases. The Oxford Nanopore MinION ( https://www.nanoporetech.com/products-services/minion-mki) is a portable sequencing device that already has proven its power in e.g. the rapid identification of viral pathogens, the monitoring of ebola, genome assembly improvement, and environmental and food safety monitoring. As a member of the pre-release MinION Access Programme (MAP), Edinburgh Genomics has considerable experience in both generating and analyzing MinION sequence data and also has published one of the first software tools to visualize and analyze these data [1]. This workshop will focus on the handling, analysis and applications of MinION sequence data. The workshop will be a combination of presentations, demos and hands-on tutorials. In the hands-on tutorials a wide range of software programs will be used, some of which were especially developed for the MinION. [1] M Watson et al. poRe: an R package for the visualization and analysis of nanopore sequencing data. Bioinformatics. 2015 Jan 1;31(1):114-5. *Topics:* The following topics will be covered: - Introduction to the Oxford Nanopore MinION sequencing technology - Organisation of raw reads (poRe/Poretools) - Extraction of FASTQ/A data (poRe/Poretools) - Gathering and visualization of run statistics (poRe/Poretools) - Error correction and quality control (Nanocorr, NanoOK) - Alignment of reads (Last, BWA, R) - Event alignment (Nanopolish) - Scaffolding of short reads (SSPACE-LongRead) - Hybrid de novo assembly (SPAdes) *Who should attend?* This workshop is aimed at anyone who is working with, or is planning to work with, Oxford Nanopore MinION sequence data. *Instructors:* - Mick Watson (Head of Bioinformatics) - Judith Risse (Bioinformatician, Edinburgh Genomics) - Bert Overduin (Training and Outreach Bioinformatician, Edinburgh Genomics) *Requirements:* For this workshop basic knowledge of Linux is essential, while familiarity with R would be advantageous. *Cost:* The registration fee for this workshop is £155, which includes lunch and refreshments. *Application:* You can apply for this workshop by filling in the application form at https://www.surveymonkey.com/r/8WM7SF3. Application will close on Thursday 12 November 2015 noon. Successful applicants will be notified a.s.a.p. after this date. *Information:* For more information, please contact Bert Overduin (bert.overduin(a)ed.ac.uk) Note that registration is also open for our RNA-seq, Linux and Python workshops. For more information, please see https://genomics.ed.ac.uk/events/workshops. With kind regards, Bert Overduin -- Bert Overduin, PhD TRAINING AND OUTREACH BIOINFORMATICIAN Bert.Overduin(a)ed.ac.uk EDINBURGH GENOMICS The University of Edinburgh Ashworth Laboratories The King's Buildings Charlotte Auerbach Road Edinburgh EH9 3FL Scotland, United Kingdom tel. +44(0)1316507403 http://genomics.ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Recruitment of Edinburgh ER, bioinformatics
by Lieven Sterck 06 Oct '15

06 Oct '15

Marie-Curie postdoc position in bioinformatics at Edinburgh University. best, lieven > From: Karim Gharbi [ mailto:Karim.Gharbi@ed.ac.uk ] > Sent: 04 October 2015 07:52 > To: Clark, Melody S. > Cc: angela.noble(a)ed.ac.uk ; CACHE ITN, BAS; Mark Blaxter; dpower(a)ualg.pt ; > 'Kristina Sundell' > Subject: Re: Recruitment > Hi Mel: > The ER post was advertised on Friday: > https://www.vacancies.ed.ac.uk/pls/corehrrecruit/erq_jobspec_version_4.jobs… > ESR to follow. > Cheers, > Karim > This message (and any attachments) is for the recipient only. NERC is subject to > the Freedom of Information Act 2000 and the contents of this email and any > reply you make may be disclosed by NERC unless it is exempt from release under > the Act. Any material supplied to NERC may be stored in an electronic records > management system . > The Scottish Association for Marine Science (SAMS) is registered in Scotland as > a Company Limited by Guarantee (SC009292) and is a registered charity (9206). > SAMS has two actively trading wholly owned subsidiary companies: SAMS Research > Services Ltd (SC224404) and SAMS Ltd (SC306912). All Companies in the group are > registered in Scotland and share a registered office at Scottish Marine > Institute, Oban Argyll PA37 1QA. The content of this message may contain > personal views which are not the views of SAMS unless specifically stated. > Please note that all email traffic is monitored for purposes of security and > spam filtering. As such individual emails may be examined in more detail.

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Joint postdoc position at University of Washinton and Institute for Systems Biology
by Theo Knijnenburg 05 Oct '15

05 Oct '15

Please feel free to distribute this ad among potential candidates. ___ *University of Washington — Institute for Systems Biology* *Joint Postdoctoral Fellow* *Computational Identification of Molecular Determinants of Cancer Therapeutic Response* *Contact:* Prof. Ray Monnat (UW) monnat(a)u.washington.edu Prof. Ilya Shmulevich (ISB) ilya.shmulevich(a)systemsbiology.org We are recruiting a new computationally-oriented Postdoctoral Fellow to work as part of a multidisciplinary NCI-funded Program grant focused on developing better ways to treat adult acute myelogenous leukemia (AML) and glioblastoma multiforme (GBM). See attached PDF for details.

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[Gtpb] TBHD15 - Translational Bioinformatics Training Course - Announcement / Reminder
by Pedro Fernandes 05 Oct '15

05 Oct '15

TBHD15 Translational Bioinformatics in Health and Disease with Fátima AlSharhour, Javier Perales and Elena Piñeiro IMPORTANT DATES for this Course Deadline for applications: Nov 16th 2015 Latest notification of acceptance: Nov 17th 2015 Course dates: Nov 30th 2015 to Dec 3rd 2015 Course description Implementation of cancer genomics into the clinic is becoming a reality. Personalised medicine or "Precision medicine" as some authors refer to it, uses molecular data from a specific patient to guide clinical decisions such as prevention, diagnosis and treatment. This will revolutionise healthcare and will play a dominant role in the future of cancer therapy. Bioinformatics analyses are essential to identify patients who will benefit from treatment based on their molecular profile, and to tailor chemotherapeutic regimens accordingly. The aim of this course is to present a complete computational pipeline for the analysis and interpretation of Next-Generation Sequencing (NGS) data, such as exome sequencing or targeted panels that are commonly used in the clinic. We will address the implementation of large-scale genomic sequencing in clinical practice and recently developed computational strategies for the analysis of NGS data. Particular emphasis will be placed on the interpretation of results, selection of biomarkers for drug responses and affording opportunities to match therapies with the characteristics of individual patient tumours. Case studies will be used to illustrate the principles of how genetics has influenced the refinement of diagnoses and personalised treatment of cancer disease. TBHD15 Course duration: 4 days TBHD15 Course Fee: Euro 360.00 Thank you for your interest P.Fernandes -- Pedro Fernandes Bioinformatics Training Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt ----- End forwarded message ----- _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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Job offer NGS software engineer @WIV-ISP
by Vanneste, Kevin 05 Oct '15

05 Oct '15

Dear all, The Belgian Institute of Public Health (www.wiv-isp.be<http://www.wiv-isp.be>) has one vacant position for a NGS software engineer to strengthen their NGS & bioinformatics platform. More details can be found in the job description added in attachment. Applications are possible using our job site (direct application link: http://wiv-isp.hr-technologies.com/content/jobpage.asp?a=DETAIL&jdkid=90&l=…) Please apply before 25/10/2015 if interested. Sincerely, [Description: Description: logo ISP-WIV]Kevin Vanneste Bioinformatician Platform Biotechnology and Molecular Biology Expertise, Service Provision and Customer Relations Rue Juliette Wytsmanstraat 14 | 1050 Brussels | Belgium T +32 (0)2 642 50 65 | F +32 (0)2 642 52 92 Email: kevin.vanneste(a)wiv-isp.be<mailto:kevin.vanneste@wiv-isp.be> | Skype: wiv-isp.kevin.vanneste Scientific Institute of Public Health | www.wiv-isp.be<http://www.wiv-isp.be/> ########################################################### Checked as being free of known viruses. Scientific Institute of Public Health, Brussels, Belgium Wetenschappelijk Instituut Volksgezondheid, Brussel, Belgi� Institut scientifique de Sant� publique, Bruxelles, Belgique Visit our website: http://www.wiv-isp.be ######################################################################## DISCLAIMER: Please see https://www.wiv-isp.be/Pages/EmailDisclaimer.aspx ########################################################################

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LATA 2016: 3rd call for papers
by GRLMC 02 Oct '15

02 Oct '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: Avrim Blum (CarnegieMellonUniversity), Reconstructing Preferences from Opaque Transactions Martin Grohe (RWTHAachenUniversity), Connectivity Systems, Decompositions, and Tangles Giovanni Pighizzini (University of Milan), Restricted Turing Machines and Language Recognition (tutorial) 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 the journal Information and Computation (Elsevier, 2014 JCR impact factor: 0.830) 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] CSDM15 - Bioinformatics Training Course - Announcement / Reminder
by Pedro Fernandes 02 Oct '15

02 Oct '15

CSDM15 Chromosome structure determination using modelling and Hi-C data IMPORTANT DATES for this Course Deadline for applications: November 15th 2015 Notification of acceptance within 72 hours of application (working days count) Course date: November 24th to November 27th 2015 Course description The sequence of a genome alone does not carry enough information to fully understand how genomic processes are carried out in the cell nucleus; to achieve this, the knowledge of the three-dimensional (3D) architecture of a genome is necessary. Advances in genomic technologies and the development of new analytical methods, such as 3C-based methods, have allowed getting insights at unprecedented resolution into how the genome is organized. Recently, it has been shown that chromatin is organized in Topologically Associating Domains (TADs), large interaction domains that appear to be conserved among different cell types. In this course, participants will learn to use TADbit, a software for the analysis and modeling of Hi-C data. The course will cover all the aspect of modeling with Hi-C data: Generation of Hi-C contact matrices from raw data (that is, Hi-C specific quality check of the reads, mapping, filtering and normalization) Analysis of Hi-C matrices (Hi-C map visualization, TAD identification, experiment comparison, and TAD selection) 3D modeling and analysis of TADs The 3D module of TADbit is based on a computational module of the Integrative Modeling Platform (IMP, http://www.integrativemodeling.org) that uses chromosome conformation capture data to determine the 3D architecture of genomic domains and entire genomes at unprecedented resolutions. Participants can bring-in specific biological questions and/or their on data to work on during the course. At the end of the course, participants will be familiar with the TADbit software, enabling them to fully analyze and model Hi-C data. Target Audience The course is oriented to experimental researchers and bioinformaticians at the graduate and post-graduate levels. The last edition of this course was attended by people with different backgrounds and interested in the genome organization. Moreover, Hi-C data have recently been used in metagenomics studies to accurately cluster metagenome assembly contigs into groups that contain nearly complete genomes of each species. It is likely that the participants to this course aim at getting involved in generating Hi-C data for chromosome structure determination or that they just want to be able to correctly interpret and analyze publicly available data. CSDM15 Course duration: 4 days CSDM15 Course Fee: Euro 360.00 Thank you for your interest P.Fernandes -- Pedro Fernandes Bioinformatics Training 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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