September 2018 - BBClist - maillist.psb.ugent.be

Invitation: Life Sciences with Industry Workshop 2018 @ Lorentz Center, Leiden
by Gokhan Ertaylan 19 Sep '18

19 Sep '18

********************************************************************************************** Invitation to participate in the Life Sciences with Industry 2018 Lorentz workshop: Leiden, November 19 – 23, 2018 ********************************************************************************************** We invite researchers (especially PhD students and postdocs) from all branches of the life sciences to participate in the one-week* Lorentz workshop* *Life Sciences with Industry 2018* in Leiden: November 19 – 23, 2018. During the workshop, 24 participants will tackle, three *scientifically challenging* and *commercially important* problems formulated by the following three companies. *Heineken* *Selective recovery of ethanol and aroma compounds from alcoholic solutions* *Solynta* *Quality Matters: how to monitor frying quality of potato tubers?* *VITO* *A Serious Game on Preventive Health* For a full description of these challenges https://www.lorentzcenter.nl/lc/web/2018/1055/info.php3?wsid=1055&venue=Sne… The workshop will take place in Leiden in the building of the Lorentz Center, an organisation that is specialised in organising scientific workshops (http://www.lorentzcenter.nl/) To create multi-disciplinary teams, participants will be selected based on their (i) specific background, (ii) motivation to participate, and (iii) date of registration (*first come first served).* *Register on the workshop website*: https://www.lorentzcenter.nl/lc/web/2018/1055/info.php3?wsid=1055&venue=Sne… *Deadline: Friday October 19, 2018. * Participation is free of charge, including hotel accommodation, lunches and two dinners during the workshop. The workshop is sponsored by the Lorentz Center, the Research School BioSB (http://biosb.nl/) and the three companies involved. Need for more information? Contact (Carey Batenburg-Einthoven <batenburg(a)lorentzcenter.nl>) at the Lorentz Center (phone +31 715 275 578). We hope to welcome you on November 19th 2018. *Scientific organizers:* Dennis Botman, Vrije Universiteit Amsterdam Em. prof. dr. Roel van Driel, Universiteit van Amsterdam Dr. Gökhan Ertaylan, VITO, Mol, Belgium Eunice van Pelt-KleinJan, Vrije Universiteit Amsterdam Klara Scupakova, Maastricht University Prof. dr. Bas Teusink, Vrije Universiteit Amsterdam *Organizers (NWO): * Dr. Ansa Baykus-Fiaz, NWO-Domain Science, Den Haag Dr. Margot Beukers, NWO-Domain Applied and Engineering Sciences, Utrecht Drs. Lisette Krul, NWO-Domain Applied and Engineering Sciences, Utrecht **********************************************************************************************

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byteMAL2018 Bioinformatics conference for young researchers
by Loïc 18 Sep '18

18 Sep '18

Dear all, We are pleased to announce that byteMAL2018 (Bioinformatics for Young inTernational researchers Maastricht - Aachen - Liège) will take place on the 5th of October 2018 at the University of Liège, in Belgium. This conference aims to provide an opportunity for young researchers in the fields of bioinformatics and computational biology to meet and network together. The keynote speaker list is available on the website (http://www.bytemal.org/2018/) Information desks will also be provided, where PIs/representatives of Bioinformatics and related fields are open to answer questions about research opportunities or potential vacancies for the master’s/PhD students. The subscription is free but mandatory, please subscribe before the 4th of October on our website (http://www.bytemal.org/2018/#Registration) Also a poster session and flash talks (selected among poster abstracts) will be organized! Date: October 5th, 9.30 AM Location: B22, Chemin de la Vallée 4 (Sart Tilman Campus) 4000 Liège https://www.campus.uliege.be/cms/c_5799509/en/b22-institut-de-botanique We are looking forward to welcoming you! The Liège byteMAL team

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Registration Open for ELIXIR-NL Course Bioinformatics for Translational Medicine using Galaxy - 17- 19 October 2018, Amsterdam
by Celia van Gelder 17 Sep '18

17 Sep '18

ELIXIR-NL Course: Bioinformatics for Translational Medicine using Galaxy Please circulate this email to those who might be interested. Date: 17-19 October, 2018 Location: VU Amsterdam ( <https://goo.gl/maps/CphwJEFDegt> O|2 Lab Building, Gustav Mahlerlaan 665, 1082 MK, 1082 MK Amsterdam) Organizers: Chao (Cico) Zhang (VU), Sanne Abeln (VU), Anton Feenstra (VU), Saskia Hiltemann (ErasmusMC), Mateusz Kuzak (DTL) and Celia van Gelder (DTL). Course page: <https://www.biosb.nl/education/course-portfolio/bioinformatics-for-translat ional-medicine-using-galaxy/> https://www.biosb.nl/education/course-portfolio/bioinformatics-for-translati onal-medicine-using-galaxy/ Application form: <https://www.biosb.nl/education/course-portfolio/bioinformatics-for-translat ional-medicine-using-galaxy/enrollment-galaxy-workshop-2018/> https://www.biosb.nl/education/course-portfolio/bioinformatics-for-translati onal-medicine-using-galaxy/enrollment-galaxy-workshop-2018/ TARGET AUDIENCE This course consists of two parts, each of which you could register separately in the <https://www.biosb.nl/education/course-portfolio/bioinformatics-for-translat ional-medicine-using-galaxy/enrollment-galaxy-workshop-2018/> application form. Part 1 (Day 1 and 2): biomedical & translational medicine researchers/students who are keen on bioinformatics Part 1 and 2 (Day 1, 2 and 3): educators in the bio domain who would like to start using Galaxy in their courses as an introduction to bioinformatics. COURSE DESCRIPTION Analysing molecular data in translational medicine involves a multitude of computational steps. Here, we introduce the basics of how to design and run these steps within Galaxy, a free and easy-to-use web platform that enables users to connect bioinformatics tools into a workflow without any prior programming expertise. This course consists of two parts, each of which you could register separately. Part 1 will let you get familiar with Galaxy; it will introduce some bioinformatics workflows used for RNAseq, variant detection and metagenomics; and how to easily connect different computational steps in Galaxy. Part 2 will focus on how to teach bioinformatics with Galaxy and to design bioinformatics courses using Galaxy. Participants can register for both parts separately. This course is also interspersed with a few keynotes, from recognized researchers in the fields of biomedicine, bioinformatics education, and Galaxy workflows. The confirmed speakers include Remond Fijneman (Day 1), a scientist in oncology from NKI; Björn Grüning (Day 2), the leader of Galaxy training network, who is also actively involved in Bioconda, and Jaap Heringa (Day 3), the scientific director of the Netherlands Bioinformatics Centre. PREREQUISITE KNOWLEDGE The attendees of Part I are assumed to have the basic knowledge of biomedicine (molecular biology and genomics) and be interested in analyzing patient-derived sequencing data. The attendees of Part II are assumed to have some teaching experience in the relevant field (e.g., bioinformatics, computational biology, systems biology, quantitative biology, etc.) COURSE SCHEDULE The course consists of six modules, as the table below shows, covering a list of topics as follows: * Introduction to Galaxy. Run bioinformatics tools and workflows in Galaxy without the need for any programming expertise. * Reference-based RNA-Seq data analysis * Module detection in differential gene expression in meta transcriptomics samples. * Microbiota Analysis: 16S rRNA sequencing analysis in Galaxy * How to teach bioinformatics workflows. * How to prepare training material development. Day 1 - Wed Oct 17 Day 2 - Thu Oct 18 Day 3 - Fri Oct 19 Morning <http://galaxyproject.github.io/training-material/topics/introduction/> Introduction to Galaxy <https://www.ncbi.nlm.nih.gov/pubmed/26342232> Network analysis with microbiota metatranscriptome Teaching bioinformatics workflows <https://shiltemann.github.io/> Saskia Hiltemann <https://hi-it.org/> Chao Zhang <http://www.few.vu.nl/~feenstra/> Anton Feenstra Keynote I: About bioinformatics workflows II: About Galaxy and ELIXIR III: About bioinformatics teaching <https://www.nki.nl/people/fijneman-remond/> Remond Fijneman <https://galaxyproject.org/people/bjoern-gruening/> Björn Grüning <https://www.cs.vu.nl/~heringa/> Jaap Heringa Afternoon <http://galaxyproject.github.io/training-material/topics/transcriptomics/> RNAseq <http://galaxyproject.github.io/training-material/topics/metagenomics/> 16S rRNA sequencing with mothur <http://galaxyproject.github.io/training-material/> Galaxy training material development <https://galaxyproject.org/people/bjoern-gruening/> Björn Grüning <https://shiltemann.github.io/> Saskia Hiltemann <https://shiltemann.github.io/> Saskia Hiltemann Evening Social dinner About the instructor: Each session is led by one instructor listed in the table above but strongly supported by multiple co-instructors, including, but not limited to, Saskia Hiltemann (ErasmusMC), Björn Grüning, Chao Zhang (VU), Leon Mei (LUMC), Ruben Vorderman (LUMC) and Sanne Abeln (VU). Correction: An earlier version of this announcement mentioned that you dont need to bring your own laptop, this is NOT TRUE. We regret the error. You do need to bring your own laptop. COURSE FEE Course participation is free of charge. A workshop dinner will be organized on Thursday (at participants own expenses) Should you have any question about this course, please contact Celia van Gelder ( <mailto:celia.van.gelder@dtls.nl> celia.van.gelder(a)dtls.nl) Dr. Celia W.G. van Gelder Programme Manager DTL Learning Training Coordinator ELIXIR-NL ELIXIR Training Platform Leader tel. +31613375327 e-mail: <mailto:celia.van.gelder@dtls.nl> celia.van.gelder(a)dtls.nl websites: <http://www.dtls.nl/> www.dtls.nl, <http://www.biosb.nl/> www.biosb.nl skype: celia.van.gelder Office: DTL | Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht Postal address: Postbus 8500 | 3503 RM Utrecht While I may be sending this email outside my normal office hours, I have no expectation to receive a reply outside yours.

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OLA'2018 @Thailand on Optimization and Learning
by El-Ghazali Talbi 16 Sep '18

16 Sep '18

Apologies for cross-posting. Appreciate if you can distribute this CFP to your network. **************************************************************************************** OLA'2019 International Conference on Optimization and Learning: Challenges and Applications 29-31 Jan 2019 Bangkok Thailand http://ola2019.sciencesconf.org/ **************************************************************************************** OLA is a conference focusing on the future challenges of optimization and learning methods and their applications. The conference OLA'2019 will provide an opportunity to the international research community in optimization and learning to discuss recent research results and to develop new ideas and collaborations in a friendly and relaxed atmosphere. OLA'2019 welcomes presentations that cover any aspects of optimization and learning research such as optimization for learning, learning for optimization, optimization and learning under uncertainty, new high-impact applications, parameter tuning, 4th industrial revolution, hybridization issues, optimization-simulation, meta-modeling, high-performance computing, parallel and distributed optimization and learning, surrogate modeling, multi-objective optimization ... Submission papers: We will accept submissions in two different formats: - S1: Extended abstracts of work-in-progress and position papers of a maximum of 3 pages - S2: Original research contributions of a maximum of 10 pages Important dates: =============== Submission deadline Oct 19 2018 Notification of acceptance Nov 9, 2018 Proceedings: Accepted papers in categories S1 and S2 will be published in the proceedings that will be available at the conference. In addition, a post-conference indexed Springer book and special issue of Journal (ITOR International Transaction on Operational Research) is planned to be published. Participants will be invited to submit extended versions of their work for consideration.

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Fwd: I'm looking for a new colleague
by Stephane Rombauts 12 Sep '18

12 Sep '18

JOB > From: "Dauchot, Nicolas" <nicolas.dauchot(a)thermofisher.com> > To: "stephane rombauts" <stephane.rombauts(a)ugent.vib.be> > Sent: Wednesday, September 12, 2018 10:47:19 AM > Subject: I'm looking for a new colleague > Dear Stephane, > I hope you’re doing fine. > Find bellow a job offer that might interest some of your contacts. > [ > http://jobs.thermofisher.com/ShowJob/Id/350126/Field%20Applications%20Speci… > | > http://jobs.thermofisher.com/ShowJob/Id/350126/Field%20Applications%20Speci… > ] > Thermo Fisher Scientific is currently looking for a talented scientist to > support ABi capillary electrophoresis (sequencing and fragment analysis) and > Ion Torrent NGS platform. > That person would replace my current colleague (Dutch/English speaking, > currently based in Amsterdam) who moved to a new position within Thermo. > If you think that this job offer could interest some of your contacts, do not > hesitate to share the link or forward this email. > I’m also always available if he/she needs further information. > Have a nice day, > Cheers, > Nicolas > Nicolas Dauchot, PhD > Field Application Scientist > Next Generation & Capillary Electrophoresis Sequencing Solutions > Thermo Fisher Scientific > Guldensporenpark 26 | 9820 Merelbeke | Belgium > T 00 800 5345 5345 • F 00 32 (0) 2 582 1886 > [ mailto:Nicolas.Dauchot@thermofisher.com | Nicolas.Dauchot(a)thermofisher.com ] | > [ http://www.thermofisher.com/ | www.thermofisher.com ] > [ > https://www.thermofisher.com/uk/en/home/life-science/sequencing/next-genera… > ] > For any support inquery being answered swiftly, please submit them through (in > English) to [ http://www.thermofisher.com/askaquestion | > http://www.thermofisher.com/askaquestion ] > This email and its attachments are confidential. If you received this email in > error, please notify the sender and delete.

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Announcement: Conference Systems Epigenetics - Towards Precision Cancer Medicine, Amsterdam, 27-30 Nov 2018
by Moerland, P.D. (Perry) 11 Sep '18

11 Sep '18

Dear colleagues, I would like to invite you to submit an abstract and register for the upcoming conference on Systems Epigenetics - Towards Precision Cancer Medicine in Amsterdam, 27-30 November 2018. Abstracts on novel methods and applications of computational approaches to the analysis of epigenomics data are especially welcomed. Systems Epigenetics - Towards Precision Cancer Medicine · Date: 27-30 November, 2018 · Location: Amsterdam, the Netherlands · Website: http://www.SystemsEpigenetics2018.eu · Registration: http://systemsepigenetics2018.eu/registration (early bird till September 23) · Call for abstracts (short talks/posters): http://www.systemsepigenetics2018.eu/call-for-abstracts (deadline October 14) We will discuss various aspects of epigenetic regulation (e.g. higher order chromatin folding, chromatin enhancer regulation, dynamics of chromatin and nuclear organization and epigenomics) in the context of cancer initiation, progression and treatment. The latest scientific developments to studying epigenetic regulation will be presented by keynote and invited speakers setting ground for precision medicine in cancer treatment. This conference brings together scientists from multidisciplinary fields employing different research strategies providing a platform for scientists focusing on fundamental and biomedical research, clinicians and private sector scientists. We aim to create a vibrant environment to promote cross-talk between different disciplines. Confirmed speakers Geneviève Almouzni, Institut Curie, FR Jonathan Chubb, University College London, MRC, GB Martin Fussenegger, ETH Zürich, CH Pamela Munster, University of California, San Francisco, US Lucia Altucci, Institute of Genetics and Biophysics, IT Pilar Blancafort, University of Western Australia, AU Tiziana Bonaldi, European Institute of Oncology, SRSI, IT Maria Carmo-Fonseca, Instituto de Medicina Molecular Lisbon, PT Toni Cathomen, University Medical Center Freiburg, DE Luciano Di Croce, Centre for Genomic Regulation, ES Wouter de Laat, Hubrecht Institute, NL Massimo Loda, Harvard Cancer Center, US Luca Magnani, Imperial College London, GB Christoph Plass, German Cancer Research Center, DE Maria Rodriguez Martinez, IBM Research, CH Paola Scaffidi, Francis Crick institute London, GB Vahid Shahrezaei, Imperial College London, GB Henk Stunnenberg, Radboud University Nijmegen, NL Lodewyk Wessels, Netherlands Cancer Institute, NL Call for Abstracts Abstracts can be submitted<http://www.systemsepigenetics2018.eu/call-for-abstracts> for a short talk or poster within one of the following session categories: · Epigenetic regulatory mechanisms: 'State-of-the-art epigenetics' · Epigenetics and clinical cancer: A systems medicine view · Epigenetics and clinical cancer: metabolic reprogramming · Epigenetics, cell heterogeneity and cancer stem cells · Innovative epigenetic interference tools and synthetic biology --- Perry Moerland, PhD Room J1B-210-1 Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics Academic Medical Center, University of Amsterdam Postbus 22660, 1100 DD Amsterdam, The Netherlands tel: +31 20 5666945 p.d.moerland(a)amc.uva.nl<mailto:p.d.moerland@amc.uva.nl>, http://www.bioinformaticslaboratory.nl/ ________________________________ AMC Disclaimer : https://www.amc.nl/disclaimer ________________________________

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NETTAB 2018: Call for posters and software demoes - deadline is approaching
by Frederik Coppens 11 Sep '18

11 Sep '18

On behalf of Paolo Romano Dear all, this is reminder that the deadline for the submission of abstracts for posters for next NETTAB 2018 workshop is set to next Sunday September 16, 2018. See the Instructions for authors here below. The NETTAB 2018 workshop, devoted to the FAIR approach, tools, implementations for bioinformatics, has an impressive scientific programme. 10 invited speakers, two tutorials and one satellite event makes this workshop one of the most relevant scientific event on this topic. See the programme at http://www.igst.it/nettab/2018/programme/scientific-programme/ <http://www.igst.it/nettab/2018/programme/scientific-programme/> . Tutorials are listed at http://www.igst.it/nettab/2018/programme/tutorials/ <http://www.igst.it/nettab/2018/programme/tutorials/> . I hope that many of you will take this occasion to present their work and I’m looking forward to meeting you in Genoa soon. All the best. Paolo Romano Frederik Coppens - Project leader & IT manager Applied Bioinformatics And Biostatistics I.T. Support VIB-UGent Center for Plant Systems Biology Ghent University Technologiepark 927 - 9052 Ghent - Belgium Tel. +32(0)9 331 38 12 www.psb.ugent.be <http://www.psb.ugent.be/>

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First Announcement NSBM Fall Meeting
by Nicolaes, G (BIOCH) 10 Sep '18

10 Sep '18

Save the Date [ogo.png] NETHERLANDS SOCIETY ON BIOMOLECULAR MODELLING Fall meeting 3D Protein Structures: what sequences cannot tell you November 16th 2018 Venue: Boothzaal, University Library De Uithof, Utrecht The Netherlands Society on Biomolecular Modelling (NSBM) is an independent society that brings people together in The Netherlands and beyond, that work on three dimensional structures of biomolecules and biomolecular simulations. This is a first announcement of our Fall meeting to which you are cordially invited. During the meeting, the floor will be given to students, PhD students, post-docs and a number of invited guest speakers who study protein structure and/or structural bioinformatics or related topics. Location and dates * Date: November 16th, 2018, 10:00-17:00 * Venue: Boothzaal, University Library De Uithof, Heidelberglaan 3, 3584 CS Utrecht * http://www.uu.nl/universiteitsbibliotheek/locaties<http://www.uu.nl/universiteitsbibliotheek/locaties%20> Deadlines * Registration deadline for posters or to be considered for a short talk: November 5th * Registration deadline (including lunch): November 9th Application procedure * Participants should send an email to register (required but free registration) to: g.nicolaes(a)maastrichtuniversity.nl<mailto:g.nicolaes@maastrichtuniversity.nl> * Submission of an abstract is required if you want to present a poster. * Indicate in your email if you want to be selected for a short oral presentation. Note: The maximum number of participants is limited to 75! So please register on time. Lead contact * Dr. Gerry Nicolaes - g.nicolaes(a)maastrichtuniversity.nl<mailto:g.nicolaes@maastrichtuniversity.nl> http://www.3dstructure-function.nl/nsbm-fall-meeting/<http://www.3dstructure-function.nl/?page_id=912&preview=true> A programme will be sent as soon as possible Costs Attendance is free of charge but registration is required. Lunch and coffee will be provided thanks to the financial support of the Nijmegen Centre for Molecular and Biomolecular Informatics. A flyer is enclosed. With kind regards, Gerry Nicolaes [cid:image001.jpg@01CC2F5C.EA047880] Gerry Nicolaes, PhD Associate Professor Cardiovascular Research Institute Maastricht Biochemistry Department g.nicolaes(a)maastrichtuniversity.nl<mailto:g.nicolaes@maastrichtuniversity.nl> www.maastrichtuniversity.nl <http://www.maastrichtuniversity.nl/> Universiteitssingel 50, 6229 ER Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 3881688 F +31 43 3884159 http://www.3dstructure-function.nl<http://www.3dstructure-function.nl/> [cid:image002.jpg@01CC2F5C.EA047880]Please consider your environmental responsibility before printing this e-mail.

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Call for group leader position in computational biology at institut Curie
by Yvan Saeys 09 Sep '18

09 Sep '18

-------- Forwarded Message -------- Subject: call for group leader position in computational biology at institut Curie Date: Sun, 9 Sep 2018 12:31:34 +0200 From: Emmanuel Barillot <Emmanuel.Barillot(a)curie.fr> To: Emmanuel Barillot <Emmanuel.Barillot(a)curie.fr> Dear colleague, We are recruiting group leader in computational biology at institut Curie (see attachment). Could you please spread the word as widely as possible? I also add an URL in case you want to tweet it or share it this way: http://sysbio.curie.fr/texts/Call4GroupLeaderCurieU900-2018.pdf Many thanks for your help Best wishes Emmanuel Barillot - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Dr Emmanuel Barillot Director of U900 Institut Curie - INSERM - PSL Research University / Mines ParisTech: "Bioinformatics and Computational Systems Biology of Cancer" Institut Curie 26 rue d'Ulm 75248 PARIS cedex 05 FRANCE Mail: Emmanuel.Barillot(a)curie.fr

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Data Science Opportunities at Janssen
by Tim Van den Bulcke 07 Sep '18

07 Sep '18

*Data Science Opportunities at Janssen* Janssen Pharmaceuticals, one of the Pharmaceutical Companies of Johnson & Johnson, is accepting applications for their R&D Data Science team. Janssen develops treatments that improve the health and lifestyles of people worldwide. Research and development areas encompass oncology, cardiovascular and metabolic disorders, immunology, neuroscience, and infectious disease, with the ultimate goal of helping people live longer, healthier lives. Janssen has produced and marketed many first-in-class prescription medications and is poised to serve the broad needs of the healthcare market – from patients to practitioners and from clinics to hospitals. To learn more about Janssen, please visit www.janssen.com. The R&D Data Science team within Janssen is looking for outstanding candidates who are interested in designing, developing, and fielding impactful data science solutions. We are a dynamic, accomplished team that supports innovative projects in multiple R&D therapeutic areas, spanning from discovery through late development. For more information about each position and to apply, please visit: · Senior Analyst: https://jobs.jnj.com/jobs/00001DJM · Scientist: https://jobs.jnj.com/jobs/00001DJO <https://jobs.jnj.com/jobs/00001DJO?lang=en-us> · Senior Scientist: https://jobs.jnj.com/jobs/00001DJP Depending on applicant's location and preferences, these positions are open both in Belgium (Beerse) as well as in the United States. Kind regards, Tim Van den Bulcke. Link: https://www.linkedin.com/feed/update/urn:li:activity:6443758701026295808

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