- BBClist - maillist.psb.ugent.be

Upcoming BioSB courses: Protein structures & RNA seq data analysis
by Femke Francissen 04 Oct '17

04 Oct '17

BioSB Core Course: Protein structures: production, prowess, power, promises, and problems (4th edition) Oct 30 – Nov 3, 2017, Radboudumc, Nijmegen - Course coordinator: Gert Vriend (Radboudumc) In the right hands, protein structures are a ‘power’ful tool to answer bio-molecular questions. Knowledge of the structure is a pre-requisite for rational drug design, for biotechnology, for chemical biology, and for answering a whole series of biomedical questions. In this course we will discuss the ‘production’ of protein structures by NMR, X-ray, and homology modelling. These methods all have their pro’s and cons so a certain ‘prowess’ is needed to follow all ‘promises’ and start attacking bio-medical ‘problems’ using protein structures. The course will be split in three parts: Part 1) Looking and seeing things in protein structures, learning to operate the software, understanding some of the algorithms. Part 2) Protein structure determination (prediction) with NMR, X-ray, and homology modelling, and the possibilities and problems that come with each of these three techniques. Part 3) Applying all that was learned in real-life example studies. Target audience The course is suitable for both PhD students working in structural bioinformatics as well as for PhD students in the life sciences who want to learn more about using structural information in their research. The course schedule accommodates both groups, parallel sessions for both groups will be scheduled when necessary. Read more <http://biosb.nl/education/course-portfolio/protein-structures-production-pr…> ---------------------- BioSB Specific Course: RNA-seq data analysis (7th edition) November 6-8, 2017, Leiden University Medical Center - Course coordinators: Peter-Bram 't Hoen, Leon Mei (LUMC), Jan Oosting (LUMC), Szymon Kielbasa (LUMC) The BioSB research school and partner LUMC are organizing a 3-day course on RNA-seq data analysis. This is an advanced course for people with experience in NGS. The course will consist of seminars and hands-on command line, Galaxy and R practicals and will cover the analysis pipelines for differential transcript expression and variant calling. Examples will be taken from human and mouse studies. The course does not cover prokaryotic RNA profiling nor plant- and metagenomics aspects. Course topics: RNA-seq experimental approaches and study design Quality control and alignment Statistics for differential gene expression eQTL analysis and allele specific expression Single cell RNA sequencing Fusion transcript detection Small RNA profiling Software for RNA-seq data analysis Target audience Participants for the RNA-seq course should preferably have participated in the general NGS course or otherwise have demonstrated hands-on experience with NGS data analysis. The course is aimed at PhD students and post-docs, but scientific programmers and data analysts with a background in biology and bioinformatics may also attend. Read more <http://biosb.nl/education/course-portfolio/rna-seq/>

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Bioinformatics double event: ISCB Belgium RSG and IB2 student day, 13 October in Brussels
by Tom Lenaerts 04 Oct '17

04 Oct '17

Dear all, Friday October 13, 2018, we are hosting together with the IB2 student day also the ISCB RSG Belgium student day. You’re all invited to participate. Send in your abstracts asap (the sooner the more chance you will be selected for a presentation) for oral/poster presentation toib2rgs(a)gmail.com with the following information: Your name and your Academic affiliation. Presentation/poster choice Abstract: maximum 400 words, figures not allowed. Registration is free. Please register before the 11th of October with the following link : https://goo.gl/forms/nJ2ZNCqt13URjsk03 Below you can find the program for that day. Kind regards Tom BIOINFORMATICS DOUBLE EVENT, second edition of ISCB Belgium RSG and IB2 Bioinformatics STUDENT DAY When: Friday, the 13th of October 2017, 9 am- 7 pm Where: Plenary Room, U-Residence Building, ULB-VUB La Plaine-Etterbeek campus, Brussels PROGRAM: 9.00-9.10 Welcome and Introductions 9.10-10.30 4 selected student presentations (20 min. each) 10.30-11.00 Coffee break 11.00-12.00 Keynote speaker: Prof. Gert Vriend (CMBI, Radboudumc, Nijmegen,Netherlands) Harvesting sequence information for GPCR structures 12.00-12.30 Poster flash presentations 12.30 - 2 pm Lunch and Poster session 2.00-3.00 pm Keynote speaker: Prof. Elfride De Baere (CMGG, UGent, Belgium) Why exome sequencing fails: lessons from mendelian blinding diseases 3.00-4.00 pm 3 selected student presentations (20 min. each) 4.00-4.20 pm Coffee break 4.20-5.00 pm 2 selected student presentations (20 min. each) 5.00-6.00 pm Keynote speaker: Prof. Axel Cleeremans (UNI, ULB, Brussels, Belgium) Computational principles for consciousness 6.00-7.00 pm Closing and drinks ________________________________________________________________________________ Tom Lenaerts Université Libre de Bruxelles (ULB) Boulevard du Triomphe CP 212 1050 Brussels. Belgium. Vice-president of the ULB Computer Science Department (http://www.ulb.ac.be/facs/sciences/info/) and co-head of the Machine Learning Group (mlg.ulb.ac.be) MLG Office: Campus La Plaine, Building O, room 2.O8.117 (mon, tue and thur) MLG Phone: +32 2 650 60 04 MLG Fax: +32 2 650 56 09 Director of the Interuniversity Institute for Bioinformatics in Brussels (www.ibsquare.be) IB2 Office: Campus La Plaine, Building C, room 2.C6.107 (wed and fri) IB2 Phone: +32 2 650 59 43 IB2 Fax: +32 2 650 54 25 IB2 secr: +32 2 650 20 13 Also affiliated with the Artificial Intelligence Lab Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium ai.vub.ac.be ________________________________________________________________________________

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Handle your data the tidy way: Data science using R and the tidyverse - BBC17 Workshop
by Daniele Parisi 03 Oct '17

03 Oct '17

WHERE: _LEUVEN, CAMPUS GASTHUISBERG_ WHEN: _13th December 2017, 14u00-18u00_ WHAT: _FREE WORKSHOP_ The use of R IN THE DATA SCIENCE field has increased enormously the last few years. One very useful toolkit for a wide variety of analyses is the 'TIDYVERSE': a collection of R-packages used for data manipulation, exploration and visualization that share a common design philosophy. Tidyverse packages are INTENDED TO MAKE STATISTICIANS AND DATA SCIENTISTS MORE PRODUCTIVE by guiding them through workflows that facilitate communication, and result in reproducible work products. In this workshop you will learn: * The difference between tidy and untidy data * How to create tidy datasets and manipulate them using the main tidyr and dplyr verbs * Make your results reproducible by using Rmarkdown and Rstudio * Integrate data visualisation into your workflow using ggplot2 * Apply the tidyverse to biological problems A very basic knowledge of the R programming language (or any other programming language) is expected. Please remember to bring your own laptop with the last version of R installed. FREE REGISTRATION https://bbc2017blog.wordpress.com/workshops/ -- DANIELE PARISI PhD student at ESAT - STADIUS, Yves Moreau's group President of RSG Belgium Board member of PhD Leuven society Kasteelpark Arenberg 10 - box 2446 3001 Leuven, Belgium Tel: +32488794394art

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Open position: Bioinformatician
by jeroen.crappe＠agilent.com 02 Oct '17

02 Oct '17

Dear all, Agilent inspires and supports discoveries that advance the quality of life. We provide life science, diagnostic and applied market laboratories worldwide with instruments, services, consumables, applications and expertise. Agilent enables customers to gain the answers and insights they seek –– so they can do what they do best: improve the world around us. Information about Agilent is available at www.agilent.com. Multiplicom N.V., now a part of Agilent Technologies, is a Belgian biotech company focused on human molecular diagnostics. The company develops, manufactures and commercializes leading edge and easy-to-use genetic test kits based on the latest molecular diagnostic technologies. With its easy and reliable methodology it is enabling all molecular laboratories the implementation of personalized medicine. Multiplicom is located in Niel, and Ghent, Belgium. To strengthen our team, we are looking for a passionate Bioinformatician to be based at our Ghent, Belgium site. More information can be found on the Agilent career site or via LinkedIn: https://www.agilent.apply2jobs.com/ProfExt/index.cfm?fuseaction=mExternal.s… https://www.linkedin.com/jobs/view/427303300/ Best regards, Jeroen Crappé Jeroen Crappé, Phd [cid:image001.png@01D33B5F.ACFBC770]<http://www.agilent.com/> Software R&D Manager Genomics Agilent Technologies www.agilent.com<http://www.agilent.com/>

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ELIXIR: Data-Driven Innovation in Food, Nutrition and Microbiome
by Dirk Valkenborg 27 Sep '17

27 Sep '17

Dear colleagues, The registration deadline for the ELIXIR innovation and SME forum on "Data-Driven Innovation in Food, Nutrition and Microbiome" is approaching. This event brings together companies active in the probiotics, food and health sectors to stimulate interaction between companies and academic partners. The meeting is held in Brussels, Belgium on October 9-10, 2017. If you want to contribute to this interesting discussion, please click on the link below and register for the event. Date: October 9 - 10, 2017 Venue: KVS - Brussels City Theatre, Lakensestraat 146, 1000 Brussels, Belgium Website: https://www.elixir-belgium.org/events/SMEforum_91017 We are looking forward to meet you! On behalf of the organizing committee, Dirk Valkenborg

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Registrations open: Engaging Researchers in Good Data Management - 15th November, Cambridge, UK
by Sergio Martinez Cuesta 26 Sep '17

26 Sep '17

*(Apologies for the broken links on the previous email. Many thanks for pointing out)*Dear all, Registrations are now open for this one-day conference taking place in Cambridge, UK on the 15th November 2017. It may be relevant to those interested in learning more and discussing data sharing and management in life sciences and other research disciplines. Please find more information below. All the best, Sergio Martinez Cuesta Postdoctoral research associate CRUK-CI and Department of Chemistry Cambridge, UK ------------------ *Registration Now Open* *Engaging Researchers in Good Data Management* A one-day conference 15 November 2017, St Catharine’s College, Cambridge, UK *On 15th November, Cambridge University, together with SPARC Europe and JISC, will host a one-day conference sharing the latest thinking as well as good practices around creating and promoting effective practices in research data management. Via a combination of workshops and talks, focus groups and panel discussions, participants will discover how researchers across an array of disciplines, and librarians, are finding increasing success managing and providing greater access to research data.* *Who should attend?* Researchers working to engage colleagues with Open Research and Research Data Management; librarians and scholarly communications specialists included. We invite you to find out more <https://webmail.cruk.cam.ac.uk/owa/redir.aspx?C=PWvUB2Vn2avizzCwG2YYAPYRsO8…>and secure your place by registering here <https://www.eventbrite.co.uk/e/engaging-researchers-in-good-data-management…> . *Register by 17th October for an early bird discount.* *Lightning Talks Proposal? Submissions welcome.* The conference, intended to represent a wide range of experiences and voices, will feature a series of lightning talks, 5-10 minutes in length. If you have experiences to share, we would very much like to hear from you. We welcome researchers, librarians and support professionals with exciting and innovative stories regarding good data management practices, collaborations and methods of engaging colleagues to submit an abstract <https://docs.google.com/forms/d/e/1FAIpQLScOF72wXtRWb-iGyRVi1Yj2uqOXqqBON8g…> . <https://webmail.cruk.cam.ac.uk/owa/redir.aspx?C=ZsEt7Bqka-ETzKBcbVVp89PXQUy…> *Bursary Application* Thanks to the Wellcome Trust, we are pleased to be offering a limited number of bursaries to qualified applicants based on financial need. To be considered, please submit your application <https://docs.google.com/forms/d/e/1FAIpQLSdmqdJq4Xg_tHR8acxQQFPIA2Fk3e8-EjS…> <https://webmail.cruk.cam.ac.uk/owa/redir.aspx?C=57829bS5_D7r6SZ-v2SbnNdrhMr…>by 30th September. We will contact you to let you know if you have been awarded. *If you have any questions about the conference, please contact * *info(a)osc.cam.ac.uk* <https://webmail.cruk.cam.ac.uk/owa/redir.aspx?C=A1fSjPsvtH_tSWpIo1_ILMMNTIg…>*. We look forward to seeing you in November.*

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Upcoming Edinburgh Genomics workshops for Autumn 2017: Intro RNA-seq, Intro Linux, Intro ChIP-seq, Intro Linux and Workflows
by Bert Overduin 25 Sep '17

25 Sep '17

Dear all, For the remainder of 2017 we have the following workshops planned, on all of which there are still places left. With kind regards, Bert 2-day INTRODUCTION TO RNA-SEQ DATA ANALYSIS Date: Thursday 26 & Friday 27 October 2017 Application deadline: Thursday 28 September 2017 noon Places: 12 (selection of applicants) Registration fee: £350 (includes refreshments and lunch) Details and application: http://genomics.ed.ac.uk/services/ introduction-rna-seq-data-analysis Note: - this workshop will be repeated on Thursday 30 November & Friday 1 December 2017 - if you have applied for this workshop before but were unsuccessful, please mention this in your application 1-day LINUX FOR GENOMICS Date: Wednesday 8 November 2017 Registration deadline: Wednesday 25 October 2017 noon Places: 20 (first come, first served) Registration fee: £175 (includes coffee/tea and lunch) Details and registration: http://genomics.ed.ac.uk/services/linux-genomics 2-day INTRODUCTION TO ChIP-SEQ DATA ANALYSIS AND VISUALISATION USING ENSEMBL Date: Thursday 23 & Friday 24 November 2017 Application deadline: Thursday 26 October 2017 noon Places: 12 (selection of applicants) Registration fee: £350 (includes refreshments and lunch) Details and application: http://genomics.ed.ac.uk/services/ introduction-chip-seq-data-analysis-and-visualisation-using-ensembl 5-day INTRODUCTION TO LINUX AND WORKFLOWS FOR BIOLOGISTS Date: Monday 11 - Friday 15 December 2017 Registration deadline: Monday 27 November 2017 noon Places: 20 (first come, first served) Registration fee: £525 (includes coffee/tea, but no lunch) Details and registration: http://genomics.ed.ac.uk/services/ introduction-linux-and-workflows-biologists -- Bert Overduin, PhD TRAINING AND OUTREACH BIOINFORMATICIAN Bert.Overduin(a)ed.ac.uk orcid.org/0000-0002-5281-8838 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 <+44%20131%20650%207403> http://genomics.ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Registrations open: Engaging Researchers in Good Data Management - 15th November, Cambridge, UK
by Sergio Martinez Cuesta 24 Sep '17

24 Sep '17

Dear all, Registrations are now open for this one-day conference taking place in Cambridge, UK on the 15th November 2017. It may be relevant to those interested in learning more and discussing data sharing and management in life sciences and other research disciplines. Please find more information below. Best, Sergio Martinez Cuesta Postdoctoral research associate CRUK-CI and Department of Chemistry Cambridge, UK ------------------ *Registration Now Open* *Engaging Researchers in Good Data Management* A one-day conference 15 November 2017, St Catharine’s College, Cambridge, UK *On 15th November, Cambridge University, together with SPARC Europe and JISC, will host a one-day conference sharing the latest thinking as well as good practices around creating and promoting effective practices in research data management. Via a combination of workshops and talks, focus groups and panel discussions, participants will discover how researchers across an array of disciplines, and librarians, are finding increasing success managing and providing greater access to research data.* *Who should attend?* Researchers working to engage colleagues with Open Research and Research Data Management; librarians and scholarly communications specialists included. We invite you to *find out more* <https://webmail.cruk.cam.ac.uk/owa/redir.aspx?C=PWvUB2Vn2avizzCwG2YYAPYRsO8…> and secure your place. *REGISTER * <https://webmail.cruk.cam.ac.uk/owa/redir.aspx?C=PWvUB2Vn2avizzCwG2YYAPYRsO8…> *Register by 17th October for an early bird discount.* *Lightning Talks Proposal? Submissions welcome.* The conference, intended to represent a wide range of experiences and voices, will feature a series of lightning talks, 5-10 minutes in length. If you have experiences to share, we would very much like to hear from you. We welcome researchers, librarians and support professionals with exciting and innovative stories regarding good data management practices, collaborations and methods of engaging colleagues to *submit an abstract.* <https://webmail.cruk.cam.ac.uk/owa/redir.aspx?C=ZsEt7Bqka-ETzKBcbVVp89PXQUy…> *SUBMIT AN ABSTRACT* <https://webmail.cruk.cam.ac.uk/owa/redir.aspx?C=ZsEt7Bqka-ETzKBcbVVp89PXQUy…> *Bursary Application* Thanks to the Wellcome Trust, we are pleased to be offering a limited number of bursaries to qualified applicants based on financial need. To be considered, please submit your *application* <https://webmail.cruk.cam.ac.uk/owa/redir.aspx?C=57829bS5_D7r6SZ-v2SbnNdrhMr…> by 30th September. We will contact you to let you know if you have been awarded. *APPLY FOR A BURSARY* <https://webmail.cruk.cam.ac.uk/owa/redir.aspx?C=57829bS5_D7r6SZ-v2SbnNdrhMr…> *If you have any questions about the conference, please contact * *info(a)osc.cam.ac.uk* <https://webmail.cruk.cam.ac.uk/owa/redir.aspx?C=A1fSjPsvtH_tSWpIo1_ILMMNTIg…>*. We look forward to seeing you in November.*

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Open positions
by Yao-Cheng Lin 23 Sep '17

23 Sep '17

Dear All, Multiple specialist and tenure-track research fellow positions are available in Academia Sinica southern campus. We are looking for people working in the field of bioinformatics, genomics and plant biology at all academic levels (junior and senior PIs). Come to join us !! More information at http://abrc.sinica.edu.tw/info/app_out/jobs_2014/index2017.php Best regards, Yao-Cheng Yao-Cheng Lin, PhD Bioinformatics and Computational Genomics Agricultural Biotechnology Research Center Biotechnology Center in Southern Taiwan Academia Sinica Tainan, Taiwan TEL: +886(6)510 30 70 e-mail: yalin(a)sinica.edu.tw <mailto:yalin@sinica.edu.tw>Web: http://bcg.abrc.sinica.edu.tw/

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Open position
by Joke Reumers 22 Sep '17

22 Sep '17

Dear all, Former colleagues of mine have started a microbiome-based drug discovery biotech and are in search of an enthusiastic computational biologist/biostatistician to lead their analytics department. A more detailed job description and contact information is provided in attachment. Best regards, Joke Reumers, PhD Computational Biology @ Discovery Sciences Janssen Pharmaceutical Companies of Johnson & Johnson Turnhoutseweg 32, 2340 Beerse, Belgium jreumers(a)its.jnj.com <mailto:jreumers@its.jnj.com> +32 14 60 3324

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