- BBClist - maillist.psb.ugent.be

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.

1 0

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

1 0

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

1 0

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. > > >

1 0

[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

1 0

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/

1 0

FW: BioJS Conference 3-4 July, Norwich, UK - preceding Galaxy Community Conference
by Celia.vanGelder＠radboudumc.nl 16 May '15

16 May '15

Van: mc.admin(a)manuelcorpas.com [mailto:mc.admin@manuelcorpas.com] Namens Manuel Corpas Verzonden: vrijdag 15 mei 2015 21:52 Aan: Manuel Corpas Onderwerp: BioJS Conference 3-4 July, Norwich, UK - preceding Galaxy Community Conference BioJS CONFERENCE 3-4 JULY, NORWICH, UK http://conf.biojs.net/ Are you - a researcher interested in interactive visualisation of massive biological datasets on the web? - a developer interested in data visualisation? - interested to understand current industry-based end user needs? Would you like to meet recognised leaders in the field of visualisation in bioinformatics, including representatives from a variety of SMEs, big pharma and for profit organisations? It is our pleasure to invite you to join us for the 1st Annual BioJS Conference (BioJS.conf)<http://conf.biojs.net/> and hackathon on 3-4 July 2015, hosted at The Genome Analysis Centre (TGAC), Norwich, UK. As part of the conference we will have an industry-led session organised by the Repositive.io<http://repositive.io/> SME. The aim of this session is to understand the needs, wants, and limitations of front-end interfaces applied to industry-based end users. Current confirmed speakers include: Suzi Lewis (Berkeley) Henning Hermjakob (EBI) Ian Mulvany (eLife) Michiel Helvensteijn (Leiden) Jessie Kennedy (Napier University, Edinburgh) Registration open NOW!<http://conf.biojs.net/#register> Please help us spread the word! The BioJS.conf Organising Committee<http://conf.biojs.net/#organisers> 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.

1 0

Vacature praktijkdocent bio-informatica Hogeschool van Arnhem en Nijmegen
by Bruggen Martijn van der 15 May '15

15 May '15

De Hogeschool van Arnhem en Nijmegen heeft een vacature voor een praktijkdocent bio-informatica. Meer informatie is terug te vinden op onze website: http://ssl1.peoplexs.com/Peoplexs22/CandidatesPortalNoLogin/Vacancy.cfm?Vac… Met vriendelijke groet, Martijn. Drs. M.H.H. van der Bruggen Lecturer bioinformatics / Programme director bioinformatics HAN University of Applied Sciences Institute of Applied Sciences (www.han.nl/appliedsciences) Postal address: P.O. Box 6960 | 6503 GL NIJMEGEN | The Netherlands | Martijn.vanderBruggen(a)han.nl<mailto:Martijn.vanderBruggen@han.nl> Visiting Address: Laan van Scheut 2 | Room 0.06 | 6525 EM NIJMEGEN | The Netherlands | +31-6-55206344 Present: Monday - Tuesday - Wednesday - Thursday - Friday [untitled]

1 0

Vacancy for PhD student in bioinformatics
by Christian.Gilissen＠radboudumc.nl 11 May '15

11 May '15

Dear all, We're looking for a PhD student in biofinformatics at the department of Human Genetics and the Centre for Molecular and Biomolecular Informatics, Radboud university medical centre Nijmegen. Job description Project title: A holistic approach to the analysis of genetic variation in patients. Interpretation of the thousands of single nucleotide variants identified in a single individual is one of the most profound challenges in genetics today, both from a research as well as from a diagnostic perspective. This project will combine the strengths of the CMBI on protein structures together with the knowledge on genome-wide variation from the genetics department to develop novel bioinformatic methods that improve the interpretation of genomic variation in patients. The position is that of a shared PhD student between the CMBI and the department of human genetics. See also http://www2.cmbi.ru.nl/ and http://genomicdisorders.nl Key words: Bioinformatics, genomics, genetic variation, intellectual disability Profile We are looking for a bioinformatics scientist with a strong drive to pursue a carrier in science, and the ability to work in a team. A strong background in computer science and programming is required. Some background in genetics is preferred as well as experience with statistical techniques and machine learning techniques. Organization The protein structure bioinformatics group from Prof. Vriend is part of the Centre for Molecular and Biomolecular Informatics and located within the Radboud Institute for Molecular Life Sciences. The department of Human Genetics is one of the largest human genetics departments in Europe performing both high quality research and patient care. The translational genomics group of Prof. Veltman consists of about 20 people with a background in genetics and bioinformatics and applies novel genomic technologies for basic research as well as patient care. We regularly publish in high-ranking journals. Comments and contact information Include your curriculum vitae, description of research experience and names and addresses of 2 references in your application. For more information you can contact Dr. Christian Gilissen, christian.gilissen(a)radboudumc.nl<mailto:christian.gilissen@radboudumc.nl>, +31 24 36 68940, Prof. Gert Vriend, vriend(a)cmbi.ru.nl<mailto:G.Vriend@cmbi.ru.nl> , +31 24 3619521, or Prof. Joris Veltman joris.veltman(a)radboudumc.nl<mailto:joris.veltman@radboudumc.nl> 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.

1 0

Registration open: Advanced de novo assembly and resolving complex genomic regions, 1-3 June 2015, Leiden
by Celia.vanGelder＠radboudumc.nl 09 May '15

09 May '15

BioSB Course Advanced de novo assembly and resolving complex genomic regions Date: 1-3 June, 2015 Location: Leiden Course Coordinators: Yahya Anvar (LUMC), Johan den Dunnen (LUMC) Website: http://biosb.nl/education/course-portfolio-2/course-advanced-de-novo-assemb… Registration: http://biosb.nl/education/course-portfolio-2/enrollment-advanced-de-novo-as… This course is targeted at PhD students and Postdocs in Life Sciences or Bioinformatics with basic knowledge of next-generation sequencing (NGS) technology and data analysis. This course covers topics on what every biologist should know about de novo assembly and study design, overview of available technologies and sampling strategies, methodologies and framework for de novo assembly (haploid and polyploid genomes), gap closure, quality assessment and functional annotation. In addition, we will showcase recent achievements, novel discoveries and current limitations in resolving complex genomes. The practical sessions are designed in such a way to promote lively discussions on how to design your study, the best practices, dos and don'ts, and provide you with an outlook on how to move from sequencing data to high-quality assembly and meaningful biological interpretation. After following this course, participants will gain insights on how to design a genome assembly study and will have an overview of challenges and various techniques to choose the most fitting strategy in order to produce a high-quality genome assembly. This course is primarily targeted at academic researchers such as PhD students and Postdocs in Life Sciences or Bioinformatics with experience in genomics or NGS data analysis. However, participants from private sector are also welcome. Participants are expected to have experience in NGS data analysis or to have followed the NGS data analysis course. This course is part of the Education Programme of BioSB, the Netherlands Bioinformatics and Systems Biology Research School, which offers training and education for in bioinformatics and systems biology. More information about BioSB can be found at www.biosb.nl<http://www.biosb.nl>. Best regards Celia van Gelder 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:C.vanGelder@umcn.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.

1 0