November 2019 - BBClist - maillist.psb.ugent.be

VIB Applied Bioinformatics Conference 2020 - deadline for travel grant and abstract submission are approaching fast
by Alexander Botzki 12 Nov '19

12 Nov '19

?Dear All, I would like to let you know that the deadline for the travel grant (15/11/2019) and the abstracts (2/12/2019) for our VIB Applied Bioinformatics Conference 2020 are approaching fast. More information and the submission details could be found here: https://www.vibconferences.be/events/applied-bioinformatics-in-life-science… Thanks a lot for your consideration. Best regards, Alex Alexander Botzki - Head of VIB Bioinformatics Core | Training Coordinator ELIXIR-BE VIB Bioinformatics Core Rijvisschestraat 126, 9052 GENT, Belgium | +32 9 248 16 00 www.bits.vib.be<http://www.bits.vib.be/> | @vibbioinfocore | https://corefacilities.vib.be<https://corefacilities.vib.be/> ?

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Data analysis with python courses
by Blanckenburg, Bo 11 Nov '19

11 Nov '19

Dear colleagues, Looking for a python-upgrade, to beautify your data analysis? At the Hogeschool Leiden we’re offering one-day courses on python data analysis with Pandas data-frames<https://www.hsleiden.nl/nascholingen/bioscience-en-diagnostiek/eng-python-d…)> and making beautiful dynamic interactive graphs with Bokeh<https://www.hsleiden.nl/nascholingen/bioscience-en-diagnostiek/eng-schilder…> to convince all your (biological) collaboration partners. Join us in Leiden on February 7th for Pandas data-frames or on March 4th for ‘paint your data with Bokeh’! Kind regards, Bo Blanckenburg Coordinator Bachelor Bioinformatics Hogeschool Leiden +31 (0) 648133872 Pandas: https://www.hsleiden.nl/nascholingen/bioscience-en-diagnostiek/eng-python-d… Bokeh: https://www.hsleiden.nl/nascholingen/bioscience-en-diagnostiek/eng-schilder… Op deze e-mail zijn de voorwaarden van toepassing als vermeld op: The following conditions apply to this e-mail: http://www.hsleiden.nl/disclaimer-email

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Molecular Dynamics Simulations in Biophysics School April 26-May 1, 2020
by Nicolaes, G (BIOCH) 09 Nov '19

09 Nov '19

Forwarded message on behalf of NSBM: Dear friends and colleagues In April 26 - May 1, 2020, we organize a Physics-School on “Molecular Dynamics Simulations in Biophysics” at the Physikzentrum Bad Honnef, Germany. Molecular Dynamics simulations have become a widely used tool for studying molecular systems (biomolecule dynamics, biomolecule binding, drug design) and are of interest for research in theoretical or computational biosciences but also for experimental biophysics and related fields. The School provides a forum for young researchers (primarily Master and PhD students) to become acquainted with the topic, deepen their knowledge and to initiate further discussions. It is also possible to present and discuss own research. More information and registration at: https://www.dpg-physik.de/veranstaltungen/2020/molecular-dynamics-simulatio… A flyer of the Physics-School is attached. Please forward this message to potentially interested students and coworkers in your group. With best regards, Martin Zacharias, Dominik Horinek Prof. Dr. Martin Zacharias Physik-Department T38 Technische Universität München James Franck Str. 1 85747 Garching Tel. ++49(0)89 28912335 Fax.++49(0)89 28912444 e-mail: zacharias(a)tum.de<mailto:zacharias@tum.de>

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VIB training course on Variant Analysis - 20 & 21 January 2020 - still open seats
by Alexander Botzki 08 Nov '19

08 Nov '19

Dear All, On 20th and 21st of January 2020, a hands-on introduction to NGS variant analysis is taking place in Ghent (Technologiepark 126, 9052 Ghent, Belgium). For more information and registration, please visit https://training.vib.be/hands-introduction-ngs-variant-analysis In case you would like to distribute the announcement, please feel free to share with your network. Best regards, Alex Alexander Botzki - Head of VIB Bioinformatics Core | Training Coordinator ELIXIR-BE VIB Bioinformatics Core Rijvisschestraat 126, 9052 GENT, Belgium | +32 9 248 16 00 www.bits.vib.be<http://www.bits.vib.be/> | @vibbioinfocore | https://corefacilities.vib.be<https://corefacilities.vib.be/> [signatureFooter (002)] [ELIXIR logo]

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[ELIXIR-IIB] Winter School: Disorder in Disorders: Pathogenic mechanisms of Intrinsically Disordered Proteins - 27-31 January - Bressanone-Brixen, Italy
by Celia van Gelder 06 Nov '19

06 Nov '19

On behalf of ELIXIR-Italy: Dear colleague Please find below information about a Winter School in Italy and spread in your organisation as you see fit. Best Celia COURSE ANNOUNCEMENT Please circulate this email to those who might be interested. ELIXIR-IIB (ELIXIR Italy) is pleased to announce the upcoming Winter School “Disorder in Disorders: Pathogenic mechanisms of Intrinsically Disordered Proteins”, organised by MSCA-RISE IDPfun. IMPORTANT DATES Course dates: 27-31 January 2020 Deadline for applications: 15 Jan 2020 Deadline for trainee grant applications: 15 Nov 2019 VENUE Università degli Studi di Padova - Casa della Gioventù, Via Rio Bianco,12 39042 Bressanone-Brixen (BZ), Italy. The venue can be easily reached by train, travelling on the international railway line between Verona and Innsbruck/Munich. The closest airports are Innsbruck, Verona, Munich, Venice and Milan (with increasing distance). COURSE DESCRIPTION During lectures and practicals, experts of the field will provide students with an overview of IDP biological mechanisms that develop pathogenic phenotypes. They will explore the concepts of folding, unfolding and misfolding, highlighting their differences and similarities. Practical exercises aim at transferring to students basic skills for the study of IDPs using bioinformatic tools to solve complex problems. The school includes a half-day workshop on ELIXIR interoperability services and support for the IDP community. REGISTRATION FEE 300€ - Early bird till 15Nov 2019 400€ - Late registration till 15 Jan 2020 Registration fee includes course material, coffee breaks, lunches and dinners for five days. TRAINEE GRANTS A limited number of fellowships will be available covering registration fee and hostel accommodation. Participants will be selected based on their background in protein bioinformatics and a motivation statement. Full details at <http://disprotcentral.org/idpschool20> disprotcentral.org/idpschool20. A flyer of the event is attached and available here for download <http://disprotcentral.org/assets/docs/Flyer-Brixen20.pdf> . Should you have any questions, do not hesitate to contact the organisers at: idpfun(a)ngp-net.bio.unipd.it <mailto:idpfun@ngp-net.bio.unipd.it> . Thank you for your interest, kind regards -- ELIXIR-IIB Training https://elixir-iib-training.github.io/website/ <https://docs.google.com/uc?export=download&id=0B0c7_C2GRNsQTEpVMXRDeDBiQnM&…>

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Job: PhD student Computational Tools for Network Biology in Plants
by Michiel Van Bel 06 Nov '19

06 Nov '19

The Comparative Network Biology lab, led by Klaas Vandepoele, of the VIB Center for Plant Systems Biology is home to an enthusiastic, diverse and international group of researchers in the field of plant bioinformatics. Beyond our expertise in plant genomics, comparative genomics and scientific creativity, we are looking for a new team member: PhD student ‘Computational Tools for Network Biology in Plants’ Job description * Fully funded PhD position with the aim to obtain a doctorate at Ghent University. In this project, the candidate is expected to * i. develop new computational methods to accurately build gene regulatory networks in different plants (model species & crops) with varying levels of genome complexity * ii. develop and evaluate methods to translate networks between model and crop species using different experimental data sources * * Reporting of results through publications in peer-reviewed international journals. * Attending and presenting your results at international scientific events. * Access to a diverse set of training programs at UGent / VIB (both scientific & soft skills) Profile * MSc in Bioinformatics, Computer Science, Engineering, or similar. * Good programming (Python, JavaScript and/or PHP) and Linux skills are a must * Experience with tool/web-development (for example, JavaScript frameworks like React, Vue, of Angular) is a plus. * You are enthusiastic about scientific research, computational biology, and want to learn more about advanced biological concepts. * You have good communication and writing skills. * You are proficient in English. How to apply? Submit your application online ( [ https://vibvzw.jobsoid.com/j/23481/phd-student-computational-tools-for-netw… | https://vibvzw.jobsoid.com/j/23481/phd-student-computational-tools-for-netw… ] ) and please include a letter of motivation, a detailed CV and contact info of 2 references (including e-mail addresses and phone numbers). Applications will be accepted until the position is filled. Michiel Van Bel - Postdoctoral fellow Applied Bioinformatics And Biostatistics VIB-UGent Center for Plant Systems Biology Ghent University Technologiepark-Zwijnaarde 71 - 9052 Ghent - Belgium Tel. +32(0)9 331 36 95 [ http://www.psb.ugent.be/ | www.psb.ugent.be ] Genome editing, cutting-edge technology for a sustainable agriculture

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BioSB Course - Modelling & optimization for bioinformatics and systems biology, 9-13 December 2019, Wageningen
by Femke Francissen 05 Nov '19

05 Nov '19

*BioSB Course - Modelling & optimization for bioinformatics and systems biology* *Website: *Modelling & optimization <https://www.biosb.nl/archive-courses/modeling-and-optimization-2019/> for bioinformatics and systems biology *Date: *9-13 December 2019 *Location: * Wageningen University & Research, the Netherlands *Coordinators: * Jaap Molenaar, WUR *Registration: * Register now via the website! <https://www.biosb.nl/archive-courses/modeling-and-optimization-2019/> *Course overview* In this course the participants learn how to describe the dynamic behavior of biological systems, and how to use optimization techniques to solve a variety of problems in bioinformatics and systems biology. Concepts of modelling in terms of differential equations are introduced via a great variety of case studies taken from diverse practices. This course also provides you with the main ideas underlying classical optimization, such as *steepest descent methods, Levenberg-Marquardt approach, genetic algorithms, global and local search methods*, and to get you acquainted with the optimization techniques that are nowadays available and widely used. Examples of optimization problems in life sciences will be presented and discussed. The course is a mixture of theory sessions and computer practicals. During the practicals we will work with the easy-to-use package *PPlane* for phaseplane analysis and most of the time with *Matlab*. Participants not acquainted with Matlab will get the opportunity to follow an introduction module. The course offers a math refresher to help those participants who are not (yet) involved in modelling on a daily basis. The course is completed with assignments in the form of practical exercises as homework afterwards. *Teachers:* - Aalt-Jan van Dijk, Wageningen University & Research - Hans Stigter, Wageningen University & Research - Natal van Riel, TU Eindhoven - Aljoscha Wahl, TU Delft *Target audience* PhDs and Postdocs interested in the fundamental modeling concepts and techniques of Systems Biology and Optimization. Basic knowledge of mathematics is assumed, Programming experience and knowledge of Matlab is preferable but not required. *Learning objectives* The students will be provided with a theoretical basis, a variety of methods and a computational hands-on experience to handle differential equation modelling and numerical optimization. In the course the students will learn: - To understand the common ground and the differences for applications of dynamic modeling in metabolic, regulatory, signaling, population and multi-scale biological processes; - How to set-up a dynamic model to represent biological networks using different interaction mechanisms; - To implement, simulate and analyze dynamic network models; - To apply different types of numerical optimization methods; - The combination of dynamic modeling and optimization to estimate model parameters and design experiments; - Design of experiments to minimize the uncertainty in parameter estimates. *Course credits* The study load of this course is 3 ECTS credits. Participants will get a certificate after successfully completing this course. *Registration fee* The registration fees for this 5-day course are: PhD student: 400 euro (excl. VAT), Academic researcher (PI/Postdoc): 600 euro (excl. VAT), Industry: 900 euros (excl.VAT) ------------------------- *About the BioSB research school* BioSB <https://www.biosb.nl/> is the Bioinformatics and Systems Biology community in the Netherlands. We are committed to train the next generation of computational life scientists. Our challenging and inspiring education programme covers essential topics in bioinformatics and systems biology, taught by teams of experts. *Upcoming BioSB courses* Registration is open for the following BioSB courses: - Constraint based modelling <https://www.biosb.nl/archive-courses/constraint-based-modelling-introductio…> - 25-29 November 2019, Leiden, the Netherlands For more information you can visit our website <http://www.biosb.nl/> or contact us via: education(a)biosb.nl

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Bioinformatics Post-doc Position
by Gaurav Dube 05 Nov '19

05 Nov '19

BIOINFORMATICS POSTDOC for EPIGENOMICS *Job description**: * A *postdoctoral *position is available for a highly motivated researcher that wishes to join the Laboratory of Cancer Epigenetics headed by *Prof. François Fuks* (ULB-Cancer Research Center, Brussels). The research goal will be the analysis of transcriptomic and epigenomic changes (*e.g.* DNA methylation) that arise in cancers. Our major focus is particularly on the analysis of next generation sequencing data concerning a novel RNA epigenetic modification, which our lab recently investigated, will be one of the main challenging tasks of the candidate (Delatte et al.,* Science 2016*). He/she will participate in several projects with high impact publication potentials. *Working environment:* The candidate will have the possibility to analyse many types of sequencing methods (RNA-seq, ChIP-seq, RIP-seq, CLIP-seq, Oxford Nanopore, …), while having a direct interaction with the wet lab biologists generating the data. The host lab is part of the ULB-Cancer Research Center (U-CRC) ( http://ucrc.ulb.be/) providing opportunity to interact with high profile scientific community. The candidate will *join other **experienced bioinformaticians* working on transcriptomics and epigenomics. The lab has collaborations in Belgium and abroad, while being international, the working language is English. *Profile:* The candidate should hold a PhD (or submitted) in bioinformatics, computational biology, bio-engineering or computer sciences. He/She should demonstrate proficiency in statistics and programming with R, Python, and/or Bash. Pipeline development and automation will be a plus. Experience with next-generation sequencing (esp. RNA-seq, ChIP-seq) and clinical data will be assets. The applicant should have good organizational skills, a taste for interdisciplinary research, excellent scientific writing and presenting skills and abilty to work independently and with team. The interaction with the biologists in the lab will be key and genuine interest for biology and clinical researches is required. This position is *funded for 2 years*, with the possibility of further renewal. Screening of applications begins immediately and continues until an outstanding candidate is selected (*f**lexible starting date*). *How to apply?* Informal enquiries, a motivation letter, a CV and names of two referees should be sent to: Gaurav DUBE (Gaurav.Dube(a)ulb.ac.be) Lab website: *http://fukslab.ulb.be/* <http://fukslab.ulb.be/> *Selected publications:* - Bonvin et al., *Cancer Res.* 2019 - Collignon et al., *Science Adv.* 2018 - Jeschke*, Bizet* et al., *J. Clin. Invest.* 2017 - Van Grembergen et al., *Science Adv.* 2016 - Delatte et al. *Science* 2016 - Boumahdi et al. *Nature* 2014 - Deplus et al. *Cell Rep*. 2014 - Dedeurwaerder*, Defrance* et al. * Briefings in Bioinformatics* 2014 - Delatte et al. *EMBO J.* 2014 - Deplus et al. *EMBO J.* 2013 - Volkmar et al. *EMBO J.* 2012 - Dedeurwaerder et al. *EMBO Mol Med.*2011 - Dedeurwaerder*, Defrance* et al. * Epigenomics* 2011 - Fuks F. *Nature* 2010 - Villa et al. *Cancer Cell* 2007 - Viré et al. *Nature* 2006

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