- BBClist - maillist.psb.ugent.be

BioVis 2015 - 10 & 11 July 2015 @ ISMB/ECCB
by Westenberg, M.A. 26 May '15

26 May '15

Dear colleagues, There is still time to submit posters to BioVis until May 29! BioVis 2015 is a SIG at ISMB/ECCB, and provides an excellent opportunity to meet with data visualization experts. Please find more information below in the CFP, or go directly to http://www.biovis.net. We look forward to meeting you in Dublin! On behalf of the organizing committee, Michel Westenberg and Alexander Lex (BioVis 2015 poster chairs) Call for Participation -- BioVis 2015 ------------------------------------------------ Compact ======= July 10 - 11 , 2015 Dublin, Ireland http://www.biovis.net Call === BioVis 2015, hosted by ISMB in Ireland, is the 5th Symposium on Biological Data Visualization, an interdisciplinary event covering all aspects of visualization in biology. The Symposium brings together researchers from the visualization, bioinformatics, and biology communities with the purpose of educating, inspiring, and engaging visualization researchers in problems in biological data visualization as well as bioinformatics and biology researchers in state-of-the-art visualization research. We invite submissions of original research articles, poster submissions, as well as submissions for data visualization and design contests. We invite contributions on all aspects of data visualization in biology, from molecular to cell, tissue, organism and population biology. All papers accepted into the conference will be considered for publication in the BMC Bioinformatics journal, using a two-stage review process. All conference papers will also be made available through the IEEE Digital Library and/or BMC Proceedings. Important Dates: ============= Poster submission: May 29, 2015 [done] Paper submission: February 15, 2015 [done] Data Analysis Contest entry submission: May 1, 2015 [done] Design Contest entry submission: May 1, 2015 (All deadlines are at 5:00 pm Pacific Time - PDT. )

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Thematic day 3rd generation sequencing (Lille, 9 june)
by Marc Lensink 25 May '15

25 May '15

Bilille, the bioinformatics platform on the Lille region, organises a scientific day dedicated to third generation sequencing (pacbio, oxford nanopore, ...) The entire day will be in English and is open for everybody. Registration required, since the number of places is limited. http://www.cristal.univ-lille.fr/~touzet/bilille/third_generation.html Program below. cheers, marc -- Marc F. Lensink, CR1, PhD marc.lensink(a)iri.univ-lille1.fr Computational Molecular Systems Biology - CNRS UMR8576 UGSF Parc de la Haute Borne, 50 Avenue de Halley, BP 70478 F-59658 Villeneuve d'Ascq, France tel: +33 3 62 53 17 28 fax: +33 3 62 53 17 01 ----- Forwarded message from Helene Touzet <helene.touzet(a)univ-lille1.fr> ----- Bilille, la plateforme de bio-informatique de Lille, organise le 9 juin prochain une journée scientifique consacrée au séquençage de troisième génération (PAcBio, Oxford Nanopore et plus). Le formulaire d'inscription est disponible à l'adresse : http://www.cristal.univ-lille.fr/~touzet/bilille/third_generation.html --------------------------- * * * PROGRAMME * * * --------------------------- 9:30-10:00 Registration, welcome 10:00-10:15 Opening 10:15-11:15 The latest methods and devices for nanopore sensing Clive Brown (Oxford Nanopore Technologies) 11:15-12:15 Bioinformatics approaches for real-time nanopore sequencing Nick Loman (University of Birmingham) 12:15-13:30 Lunch 13:30-14:10 Genome assembly using Nanopore-guided long and error-free DNA reads Amin Madoui (Genoscope) 14:10-14:50 Hybrid error correction for long sequencing reads using maximal exact matches Jan Fostier (Ghent University) 14:50-15:30 Looking for mutations in PacBio cancer data: an alignment free method Justine Rudewicz (LaBRI and CBiB Bordeaux) 15:30-15:50 Coffee break 15:50-16:30 Precise breakpoint localization of large genomic deletions using PacBio and Illumina next-generation sequencers Janine Meienberg (Center for Cardiovascular Genetics and Gene Diagnostics, Zurich) 16:30-17:10 Single molecule detection of DNA sequences and epigenetic markers using unzipping rezipping assay Vincent Croquette (Laboratoire de Physique Statistique, ENS) ----- End forwarded message -----

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RSG Belgium Symposium
by Cuypers Bart 23 May '15

23 May '15

Dear All, I would like to invite you to the RSG Belgium Symposium 2015. It will take place, next week, Thursday, 28th of May 2015, 14:00 in the University of Hasselt (Campus Diepenbeek, Building D, room C109) . The event is focused around young bioinformaticians (master students, PhD student, young post-docs), who will get the opportunity to present their work in a broad research context and network with one another. You can find the program attached. You are most welcome to send this invitation to anyone that might be interested. Do not forget your students. We only ask a brief notification if you are coming. Unfortunately, there will be trains strikes, so we do not advice to take the train that day. Best Regards, Bart Cuypers ADReM<http://adrem.ua.ac.be/> & Biomina<http://www.biomina.be/> University Of Antwerp Middelheimlaan 1 2020 Antwerp Belgium Mail: bart.cuypers(a)uantwerpen.be<mailto:bart.cuypers@uantwerpen.be> Tel.: 0032 32 65 34 07 Skype: bart-cuypers [image002]<http://www.linkedin.com/pub/bart-cuypers/57/b50/547>[image003]<https://twitter.com/cuypersb>

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German Conference on Bioinformatics 2015 (GCB'15) - Call for submissions
by Yves Moreau 22 May '15

22 May '15

On behalf of the organizers of the German Conference on Bioinformatics. Best regards, Yves Moreau KU Leuven Call for submissions German Conference on Bioinformatics 2015 (GCB'15) ================================================= Please distribute this call to interested colleagues, and please excuse us if you receive multiple copies of this call. GCB 2015 invites the submission of papers on all aspects of bioinformatics. The conference language is English. Areas of interest include, but are not limited to: * Methods for genomics and metagenomics * Methods for transcriptomics and metatranscriptomics * Methods for metabolomics * Poly-omics analyses * Personalized medicine * Network and pathway analysis * Bioimage informatics * Structural modeling * Visualization of large biological datasets * Workflow management for big data GCB invites contributions of the following types, with detailed information below: * Workshops and tutorials (31.05.2015) * Proceedings papers (30.06.2015), published at PeerJ PrePrints * Highlight abstracts (30.06.2015) * Junior research group presentations (30.06.2015), new! * Poster abstracts (31.07.2015) See also http://www.gcb2015.de <http://www.gcb2015.de/> Call for Workshops and Tutorials by May 31, 2015 ================================================ A whole day of GCB (Sunday, September 27, 2015) is devoted to tutorials and workshops on current hot topics of bioinformatics. This is an excellent opportunity for new PhD students (or more experienced scientists entering a new research area) to get up to speed with new methods, techniques and tools. While tutorials provide an in-depth introduction to a particular method, technique or tool (e.g., a collection of R/BioConductor packages, or multiple testing in bioinformatics), workshops should provide a broad overview of a current hot topic, where the workshop organizers invite or call for contributions from experts in the field. Both workshop and tutorials can be half-day (3 hrs, morning or afternoon), or full-day (2x 3hrs). Please clearly indicate the duration in the proposal. Prospective workshop or tutorial organizers are encouraged to contact the GCB program chairs and submit a workshop proposal until 31.05.2015. Please submit your proposal electronically as a pdf file to tutorial-@-gcb2015-dot-de with the subject line "GCB workshop proposal: yourworkshoptitle". Workshop organizers will be responsible for advertising the workshop, inviting and selecting the contributions and guaranteeing a high quality worthy of the prestige and range of the conference. Workshop papers will not be published in the GCB conference proceedings, but may be published in other formats chosen by the workshop organizers. Both tutorial and workshop submissions must include * name and affiliations of the organizers, * a one-page description of the topic and its relevance and value to the GCB community, * a brief description of the submitters' qualification/experience with the topic. Workshop submission must further include * a draft time schedule for the workshop (CFP, deadlines, etc.), * a list of potential members of the workshop's program committee, * an estimation of the number of attendees, * a draft list of potential authors / presenters. Tutorial submissions must include * proof of the submitters' pedagogical qualifications Important: Workshop organizers and speakers must pay their expenses, including GCB registration, to participate in the meeting. The GCB organizers will help in the administrative aspects of assigning the rooms, announcements and adding the detailed schedule to the conference program. Note that the GCB cannot financially support the speakers or the workshop organizers. (Exceptions due to unusual circumstances can be discussed with the program chairs.) Call for Proceedings Papers (Extended Abstracts) by June 30, 2015 ================================================================= Proceedings papers are like regular computer science conference papers. These submissions will be peer-reviewed by the program committee and judged by quality, originality and relevance. Accepted papers will be published as a special collection at PeerJ PrePrints with a unique "GCB 2015" label. Authors of accepted papers will have the additional option to submit them (or an extended version) to the regular PeerJ journal (either PeerJ Computer Science, or PeerJ the biology journal, depending on which journal is more appropriate) immediately or later, together with the conference reviews to facilitate speedier review at the journal. Accepted papers which are published at PeerJ will also appear in the "GCB 2015" Collection (a virtual collection of all the "GCB 2015" output which is published at PeerJ). Of course, authors may alternatively submit their work to any other journal of their choice that allows existing preprints. Accepted papers must be presented at the conference, and at least one author of each accepted paper must register before the early registration deadline. Proceedings papers must be submitted via EasyChair and should be 8-10 pages long using the provided template (see the submissions page). Call for Highlight Abstracts by June 30, 2015 ============================================= Highlight abstracts should refer to one or two of the authors' recent papers that report on work of high importance and were published during the present or past year. Typical topics might include biological findings with bioinformatics methods, new computational methods or new software tools. The general topics of interest correspond to those for proceedings papers. The abstracts should summarize the findings of the referenced paper(s), explain their importance and mention which areas of the paper(s) the talk will focus on, as opposed to presenting the whole paper(s). Highlight abstract submissions will be reviewed by the program committee and judged by the importance and novelty of the findings and by relevance to the conference audience. Accepted highlight abstracts will collected into one document "Highlight Abstracts of GCB 2015" that will be published at PeerJ Preprints in the "GCB 2015" Collection. Accepted highlight abstracts must be presented at the conference, and at least one author of each accepted abstract must register before the early registration deadline. Highlight abstracts must be submitted via EasyChair, should be at most 4 pages long and use the provided abstract template. Call for Junior Research Group Presentations (New!) by June 30, 2015 ==================================================================== This new track calls for abstracts from junior group leaders (definition: have their own (small) group, do not have a permanent position) to present their area of research and to highlight recent findings from their group. These abstracts should be similar to highlight abstracts, but may reference more of the group's papers, giving a good and complete picture of the group's research focus as a whole. Accepted highlight abstracts will collected into one document "Junior Research Group Presentations of GCB 2015" that will be published at PeerJ Preprints in the "GCB 2015" Collection. Accepted junior research group presentations must be given at the conference, and the group leader must register before the early registration deadline. Junior research group abstracts must be submitted via EasyChair, should be at most 4 pages long and use the provided abstract template. Call for Posters by July 31, 2015 ================================= Posters should present recent scientific work in any area of bioinformatics. Poster abstracts will be reviewed by the organizing committee for clarity and novelty. Accepted poster abstracts will collected into one document "Poster Abstracts of GCB 2015" that will be published at PeerJ Preprints in the "GCB 2015" Collection. Accepted posters must be brought to and presented at the conference. The designated poster presenter must register before the early registration deadline and indicate whether she or he wants to give a flash presentation (1 slide, 1 minute). Poster abstracts must be submitted via EasyChair, can be at most a single page long (including references) and use the provided abstract template. Detailed Information ==================== Please visit http://www.gcb2015.de <http://www.gcb2015.de/> for details and submission information. At this time, LaTeX templates for submissions are online, but EasyChair submission is not yet open. Best regards, Axel Mosig Sven Rahmann -- The GCB 2015 organizers contact(a)gcb2015.de <mailto:contact@gcb2015.de>

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Registration open: Data Carpentry Workshop - Data management beyond Excel, 24-25 June 2015, Utrecht
by Celia.vanGelder＠radboudumc.nl 22 May '15

22 May '15

A Data Carpentry Workshop - Data Management beyond Excel 24-25 June 2015, Utrecht, the Netherlands Instructors: Karthik Ram (Berkeley Institute for Data Science, SC/DC), Aleksandra Pawlik (ELIXIR-UK, SC/DC) Organisers: Mateusz Kuzak (NLeSC, ELIXIR-NL), Philip Lijnzaad (UMC Utrecht, ELIXIR-NL), Celia van Gelder (DTL, ELIXIR-NL) Registration fee: 50 euro. Website, including registration information: http://apawlik.github.io/2015-06-24-dc-utrecht/ More information: celia.van.gelder(a)dtls.nl<mailto:celia.van.gelder@dtls.nl> Data Carpentry In many domains of research the rapid generation of large amounts of data is fundamentally changing how research is done. The deluge of data presents great opportunities, but also many challenges in managing, analyzing and sharing data. Data Carpentry is designed to teach basic concepts, skills and tools for working more effectively with data. The workshop is aimed at researchers in the life sciences at all career stages and is designed for learners with little to no prior knowledge of programming, shell scripting, or command line tools. Workshop Learning objectives & programme Researchers should be able to retrieve, view, manipulate, analyze and store their's and other's data in an open and reproducible way. The workshop will cover the following topics: * How to use spreadsheet programs (such as Excel) more effectively, and the limitations of such programs. * Getting data out of spreadsheets and into more powerful tools (R). * Using databases, including managing and querying data in SQL. * Workflows and automating repetitive tasks, in particular using the command line shell. Acknowledgements & Support The workshop is supported by the ELIXIR programme (http://www.elixir-europe.org/ ). Data Carpentry (http://www.datacarpentry.org/ ) is a sibling organization of Software Carpentry (http://www.software-carpentry.org/ ) and is designed to teach basic concepts, skills and tools for working more effectively with data. The structure and objectives of the curriculum as well as the teaching style are informed by Software Carpentry. Dr. Celia W.G. van Gelder Education Manager NBIC/BioSB Coordinator Education CMBI Programme Manager Learning DTL/ELIXIR-NL tel. +31-(0)24-3666120 e-mail: Celia.vanGelder(a)radboudumc.nl<mailto:Celia.vanGelder@radboudumc.nl> websites: www.nbic.nl<http://www.nbic.nl/>, www.biosb.nl<UrlBlockedError.aspx>, www.cmbi.ru.nl<http://www.cmbi.ru.nl/>, www.dtls.nl<UrlBlockedError.aspx> Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre PO Box 9101 6500 HB Nijmegen The Netherlands Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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PhD position Data Mining for Biomedicine
by Celine Vens 21 May '15

21 May '15

Dear all, At KU Leuven KULAK we are looking for a PhD student in 'Data mining for biomedicine’. The job description can be found at the following webpage: https://icts.kuleuven.be/apps/jobsite/vacatures/53318198. Thank you for forwarding this vacancy to any potential candidates. Best regards, Celine Vens — prof. Celine Vens KU Leuven Kulak www.kuleuven-kulak.be/~celine.vens

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BioKDD 2015 - Call for Papers, deadline June 5 - Please distribute
by Joana Gonçalves 21 May '15

21 May '15

Apologies for potential cross posting. -------------------------------------- ****CALL FOR PAPERS**** 15th International Workshop on Data Mining in Bioinformatics (BIOKDD'15) August 10 2015 Sydney, Australia http://home.biokdd.org/biokdd15/ http://www.facebook.com/Biokdd The goal of the 15th International Workshop on Data Mining in Bioinformatics (BIOKDD'15) is to encourage KDD researchers to take on the numerous challenges that Bioinformatics offers. This year, the workshop will feature the theme of “Knowledge Discovery on Complex Biological and Medical Data”. This field focuses on the use of data mining and machine learning approaches for the analysis of the large amount of heterogeneous complex biological and medical data being generated. The goal here is to build accurate predictive or descriptive models from these data enabling novel discoveries in basic biology and medicine. We encourage papers that propose novel data mining techniques for areas including but not limited to: * Building predictive models for complex phenotypes from large-scale biological data * Discovering biological networks and pathways underlying biological processes and diseases * Processing of new/next-generation sequencing (NGS) data for genome structural variation analysis, discovery of biomarkers and mutations, and disease risk assessment * Discovery of genotype-phenotype associations * Novel methods and frameworks for mining and integrating big biological data * Comparative genomics * Metagenome analysis using sequencing data * RNA-seq and microarray-based gene expression analysis * Genome-wide analysis of non-coding RNAs * Genome-wide regulatory motif discovery * Structural bioinformatics * Correlating NGS with proteomics data analysis * Functional annotation of genes and proteins * Cheminformatics * Special biological data management techniques * Information visualization techniques for biological data * Semantic web and ontology-driven data integration methods * Privacy and security issues in mining genomic databases **Important Dates** June 5th, 2015 Deadline for Submission of Papers June 30th, 2015 Notification of Acceptance; Workshop Registration Open July 10th, 2015 Submission of Camera-ready Papers August 10th, 2015 Workshop Presentation **Submissions** Papers should be at most 10 pages long, single-spaced, in font size 10 or larger with one-inch margins on all sides. Using the ACM Proceedings Format is highly recommended. Papers should be submitted in PDF format through EasyChair (see webpage for details). Papers will be published in the webpage. A selection of accepted papers will also be invited to be submitted to a special section of the reputed IEEE Transactions on Computational Biology and Bioinformatics. **Workshop Organizers** Program Chairs: Sara C. Madeira, Instituto Superior Técnico, sara.madeira(a)tecnico.ulisboa.pt Jieping Ye, University of Michigan, Ann Arbor, jpye(a)umich.edu General Chairs: Mohammed J. Zaki, Rensselaer Polytechnic Institute, zaki(a)cs.rpi.edu Jake Y. Chen, Indiana University - Purdue University Indianapolis, jakechen(a)iupui.edu

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fwd:Post-doctoral position available in Human Microbiome Research and Women's Health
by Karoline Faust 19 May '15

19 May '15

Forwarded message: >From: jravel(a)som.umaryland.edu >To: (Ravel, Jacques) jravel(a)som.umaryland.edu >Cc: "Brotman, Rebecca" <rbrotman(a)som.umaryland.edu> >Date: Tue, 19 May 2015 16:04:17 +0000 >Subject: Post-doctoral position available in Human Microbiome Research and Women's Health > >Dear Colleagues, > >I am looking to fill two postdoctoral positions to work on collaborative projects with Dr. Rebecca Brotman related to the Human Microbiome and Women?s Health. I would really appreciate it if you could pass along the attached advertisement to any potential candidates. > >Thanks again! > >Best, > >Jacques > >Jacques Ravel, PhD | Professor and Associate Director for Genomics | Institute for Genome Sciences | University of Maryland School of Medicine | 410-706-5674 | www.igs.umaryland.edu<http://www.igs.umaryland.edu> | jravel(a)som.umaryland.edu<mailto:jravel@som.umaryland.edu> > >This electronic message transmission contains information which may be confidential. The information is intended for the use of the individual or entity named above. If you are not the intended recipient, and have received this electronic transmission in error, please notify sender then delete immediately. > > >

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[Gtpb] Bioinformatics Training Course MEVR15 Molecular Epidemiology DEADLINE EXTENSION
by Pedro Fernandes 18 May '15

18 May '15

Dear All, The deadline for applications to the Training Course MEVR15 Molecular Epidemiology of Viruses using R has been extended, due to some tech issues with the e-mail delivery in the last few days. IMPORTANT DATES for this Course Deadline for applications: May 20th 2015 <--- NEW Latest notification of acceptance: May 21st 2015 Course date: May 25th - May 28th 2 with Simon Frost from the University of Cambridge, Cambridge, UK Details at: http://gtpb.igc.gulbenkian.pt/bicourses/MEVR15 PLEASE make sure that you read the description and the detailed program, as reading only the title may convey a different idea about the content. Duration: 4 days Course fee: Euro 360.00 Note: Travelling to Portugal is relatively cheap. Oeiras is 15 km away from Lisboa International Airport (LIS). Subsistence in Oeiras can cost as low as Euro 30 (Lodging and dinner) the rest is covered by the course fee. Thanks for your interest, Pedro -- Pedro Fernandes GTPB Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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2015 Galaxy Community Conference, 4-8 July, Norwich UK
by Dave Clements 18 May '15

18 May '15

Hello all, The 2015 Galaxy Community Conference (GCC2015, http://gcc2015.tsl.ac.uk/) is being held at the Sainsbury Lab in Norwich, United Kingdom, 4-8 July. GCC2015 is an opportunity to meet with 200+ others working at the forefront data-intensive biomedical research. The 2015 edition of GCC includes more than ever before (http://gcc2015.tsl.ac.uk/programme/) - Coding and Data Wrangling Hackathons (and a colocated BioJS Hackathon too) - Two days of training offering 18 sessions on 15 topics in up to 5 parallel tracks, covering topics ranging from analysis to administration to tool development. - A two day meeting featuring accepted talks, poster presentations, keynote talks, vendor exhibits, lightning talks, birds-of-a-feather meetups, and plenty of networking. Early registration is now open (but closes Friday, 22 May, *which is this Friday)*. Registering early saves you 40%. Registering now ensures you'll get a spot in the hackathon and training sessions of your choice. Finally, there are also many other events going on before and after GCC2015, and GCC itself ends right before ISMB / ECCB starts in Dublin. See https://wiki.galaxyproject.org/News/NearGCC2015 for a complete list. Hope to see you in Norwich! Dave Clements, on behalf of the GCC2015 Organising Committee -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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