- BBClist - maillist.psb.ugent.be

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

1 0

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

1 0

PhD Candidate (m/f/d) in Computational Systems Medicine
by Lenz, Michael 28 Oct '19

28 Oct '19

The Clinical Epidemiology and Systems Medicine group at the UMC Mainz invites applications for a PhD position in Computational Systems Medicine: PhD Candidate (m/f/d) in Computational Systems Medicine Topic: Multi-omics data integration for studying complex cardiovascular diseases and their associated comorbidities in large human cohort studies Employer: University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany Your tasks: * Investigation of molecular processes and markers associated with complex cardiovascular diseases (e.g. heart failure), their heterogeneity, comorbidities, and molecular progression paths based on repeatedly sampled disease-specific human cohort studies * Multi-dimensional and pathway-integrating analysis of multifaceted data (proteomics, metabolomics/lipidomics, transcriptomics, genomics, phenotypic/clinical) using state-of-the-art and newly developed algorithms * Detection and comparison of disease subtypes for the development of personalized medicine in prevention, prognosis, and treatment Your profile: * Master degree in Computational Biology, Bioinformatics, Systems Biology, Biomathematics, Biostatistics, Epidemiology, Biomedical engineering or a related area * Strong interests in human biomedicine (cardiovascular diseases, diabetes, obesity) and multi-dimensional data analysis * Programming experience in R, python, or similar programming languages * Sound statistical knowledge and experience in handling bioinformatics databases and tools * Good communication skills and fluency in English * Structured and independent work attitude We offer: * An interesting research project at the forefront of computational biomedicine related to cardiometabolic diseases. * Access to several large and deeply phenotyped human cohort studies with high level of standardization and extensive multi-omics datasets * A professional and cooperative work environment in a highly interdisciplinary research team * A three year employment with salary according to the German public service salary scale TV-L E13, 65% * A stimulating scientific environment with excellent facilities for professional and personal development * Opportunities for child care (limited places available) * Job ticket for public transport For further information please contact Dr. rer. nat. Michael Lenz (mlenz(a)uni-mainz.de<mailto:mlenz@uni-mainz.de>) or Univ.-Prof. Dr. med. Philipp Wild (philipp.wild(a)unimedizin-mainz.de<mailto:philipp.wild@unimedizin-mainz.de>). Did we catch your interest? Please submit your application, including motivation letter, CV, recommendation letters, and copies of your diploma(s) and transcripts (high-school, bachelor, master) by e-mail to mlenz(a)uni-mainz.de<mailto:mlenz@uni-mainz.de>.

1 0

ELIXIR Survey: Identifying gaps in current training
by Celia van Gelder 27 Oct '19

27 Oct '19

[apologies for multiple postings] Dear all, The ELIXIR Training Platform surveyed the training needs of its scientific communities in 2013 and 2016, and consequently took measures to fill the gaps identified with appropriate training. In order to identify potential gaps in current training in Life Sciences across Europe, we would like your input as well. The deadline for this survey is Friday, November 1st 2019. The survey [https://forms.gle/rtMoWFtnmC5D4jPF6] should take no more than 5-10 minutes of your time to complete; questions with an asterisk require a response and it would be immensely helpful if you could spare the time to respond fully to all questions. Participants who share their contact details with us will gain early access to the results and will play a vital role in helping us to optimize the training programme. We value your contribution and look forward to sharing the outcomes with you. Please, feel free to forward this email to whomever you think is relevant. Kind regards, Fotis E. Psomopoulos (ELIXIR-GR), Brane L. Leskosek (ELIXIR-SI), Jessica Lindvall (ELIXIR-SE), Patricia Palagi (ELXIR-CH), Celia van Gelder (ELIXIR-NL) and Pascal Kahlem (TrP) on behalf of the ELIXIR Training Platform -- Fotis E. Psomopoulos Assistant Research Professor INAB - Institute of Applied Biosciences CERTH - Center for Research and Technology Hellas Thermi 57001, Greece Phone: +30 2310 498 478 Fax : +30 2310 498 270 Email: fpsom(a)certh.gr <mailto:fpsom@certh.gr> Site : https://fpsom.github.io <https://fpsom.github.io/> ORCID: 0000-0002-0222-4273 While I may be sending this email outside my normal office hours, I have no expectation to receive a reply outside yours. Η επικοινωνία αυτή είναι εμπιστευτική και ενδεχομένως να προστατεύεται από νομικά πλαίσια. Εάν λάβατε αυτό το e-mail, ενώ δεν προορίζεται για εσάς, σας ενημερώνουμε ότι απαγορεύεται οποιαδήποτε διανομή, αντιγραφή ή χρήση της επικοινωνίας ή/ και των πληροφοριών που περιέχονται σε αυτό. Σας παρακαλούμε να ενημερώσετε κατάλληλα τον αποστολέα και να σβήσετε ή να καταστρέψετε τυχόν αντίγραφά της. Οι επικοινωνίες μέσω του Διαδικτύου δεν είναι ασφαλείς και για τον λόγο αυτό το ΙΝ.Ε.Β./ΕΚΕΤΑ δεν αποδέχεται νομική ευθύνη για τα περιεχόμενα του παρόντος μηνύματος και για οποιαδήποτε ζημιά προκληθεί από ιούς που είναι δυνατόν να εισαγάγει. This communication is confidential and It may also be protected by legal rules. If you are not an intended recipient please note that any form of distribution, copying or use of this communication or the information in it, is prohibited. Please inform the sender appropriately and delete or destroy any copies of it from your system. Internet communications are not secure and therefore INAB/CERTH does not accept legal responsibility for the contents of this message and for any damage whatsoever that is caused by viruses being passed. -- Fotis E. Psomopoulos Assistant Research Professor INAB - Institute of Applied Biosciences CERTH - Center for Research and Technology Hellas Thermi 57001, Greece Phone: +30 2310 498 478 Fax : +30 2310 498 270 Email: fpsom(a)certh.gr <mailto:fpsom@certh.gr> Site : https://fpsom.github.io <https://fpsom.github.io/> ORCID: 0000-0002-0222-4273 While I may be sending this email outside my normal office hours, I have no expectation to receive a reply outside yours. Η επικοινωνία αυτή είναι εμπιστευτική και ενδεχομένως να προστατεύεται από νομικά πλαίσια. Εάν λάβατε αυτό το e-mail, ενώ δεν προορίζεται για εσάς, σας ενημερώνουμε ότι απαγορεύεται οποιαδήποτε διανομή, αντιγραφή ή χρήση της επικοινωνίας ή/ και των πληροφοριών που περιέχονται σε αυτό. Σας παρακαλούμε να ενημερώσετε κατάλληλα τον αποστολέα και να σβήσετε ή να καταστρέψετε τυχόν αντίγραφά της. Οι επικοινωνίες μέσω του Διαδικτύου δεν είναι ασφαλείς και για τον λόγο αυτό το ΙΝ.Ε.Β./ΕΚΕΤΑ δεν αποδέχεται νομική ευθύνη για τα περιεχόμενα του παρόντος μηνύματος και για οποιαδήποτε ζημιά προκληθεί από ιούς που είναι δυνατόν να εισαγάγει. This communication is confidential and It may also be protected by legal rules. If you are not an intended recipient please note that any form of distribution, copying or use of this communication or the information in it, is prohibited. Please inform the sender appropriately and delete or destroy any copies of it from your system. Internet communications are not secure and therefore INAB/CERTH does not accept legal responsibility for the contents of this message and for any damage whatsoever that is caused by viruses being passed.

1 0

Postdoc position in bioinformatics: Gene regulatory network inference of RNA binding proteins - Stockholm
by Yves Moreau 25 Oct '19

25 Oct '19

On behalf of Prof. Sonnhammer. -Yves Moreau ====== http://sonnhammer.org/download/ads/PostDoc_RBPGRN.pdf <http://sonnhammer.org/download/ads/PostDoc_RBPGRN.pdf> Postdoc position in bioinformatics: Gene regulatory network inference of RNA binding proteins The goal of the project is to discover new regulatory mechanisms that control the repertoire of RNA binding proteins (RBPs). This is a collaborative project between professors Erik Sonnhammer and Claudia Kutter, both at SciLifeLab in Stockholm, Sweden. SciLifeLab is a national center for large-scale life science research with an advanced technological infrastructure. At SciLifeLab, multidisciplinary research is conducted based on DNA sequencing, gene expression analysis, proteomics, bioinformatics, biostatistics and systems biology. Bioinformatics and systems biology are central activities within the center. The Sonnhammer group has extensive experience in inferring gene regulatory networks (GRNs) and has developed several new algorithms to improve the reliability of the GRNs inferred from perturbations. The Kutter lab has a research focus on RNA binding proteins and their bound RNAs, especially lncRNAs. The project aims to infer a reliable GRN from shRNARNAseq perturbation data from ENCODE data and in-house data from the Kutter lab. The GRN will be analyzed for regulatory links in relation to known functions and lncRNA binding and subjected to experimental validation of the scientifically most valuable links. The project involves programming, data analysis, benchmarking, and modelling, as well as application of the developed methods to experimental data generated by the project. The successful candidate should be highly motivated and have a Ph.D. in bioinformatics or related field, and good knowledge of molecular biology. Alternatively, a Ph.D. in molecular biology or related field and 2 years of postdoctoral experience in bioinformatics research and programming, documented by scientific publications. Demonstrable familiarity with sequence and molecular data analysis techniques is essential. Excellent skills in computer programming (primarily Matlab, Python, R), UNIX, and knowledge of biological database systems are necessary merits. To apply, send your CV, a cover letter, and the email address of 2 references to Erik.Sonnhammer(a)scilifelab.se. The position is fully funded for 2 years of full-time study and offers a competitive salary and excellent computational resources. For further information about the research project, contact Erik.Sonnhammer(a)scilifelab.se or Claudia.Kutter(a)scilifelab.se. See http://sonnhammer.org and https://ki.se/en/mtc/claudiakutter-group

1 0

FW: Vacancy Bioinformatics position
by I. van der Pluijm 24 Oct '19

24 Oct '19

I received an email that the attachment was too big, therefore I deleted the flyer. Please see my email below. Kind regards, Ingrid van der Pluijm From: I. van der Pluijm Sent: donderdag 24 oktober 2019 10:37 To: 'bbclist(a)psb.ugent.be' <bbclist(a)psb.ugent.be> Cc: N. Taneja <n.taneja(a)erasmusmc.nl> Subject: Vacancy Bioinformatics position Dear sir/madam, We are planning to appoint a Bioinformatician at the Molecular Genetics department (headed by Roland Kanaar) at the Erasmus University Medical Center in Rotterdam. Via this route I would like to ask if you would be willing to send attached vacancy via the BeNeLux bioinformaticians forum. To attract people, we have also made a flyer; please see attached. We would be very grateful if you could forward this vacancy! Kind regards, Ingrid van der Pluijm Nitika Taneja

1 0

VIB: Staff Scientist Integrative Bioinformatics
by Alexander Botzki 23 Oct '19

23 Oct '19

Dear BBC list members, Currently, we have an opening of a Staff Scientist position in Integrative Bioinformatics at the central VIB Bioinformatics Core facility. More information and the application information is available at this web site: https://vibvzw.jobsoid.com/jobs/35bba14f-79b7-4388-b015-a4fb9d97ee41/23329/… Kind regards Alexander Botzki 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)]

1 0

PhD position
by Vanessa Vermeirssen 23 Oct '19

23 Oct '19

Dear colleagues There is a position for a PhD researcher in computational biology in my group. It would be great if you could spread this information to potential candidates. https://www.ugent.be/en/work/vacancies/scientific/phd-student-4ketl Kind regards Vanessa Vermeirssen Vanessa Vermeirssen, PhD ---------------------------------------------------------- Ghent University Department of Biomedical Molecular Biology Department of Biomolecular Medicine Cancer Research Institute Ghent (CRIG) C. Heymanslaan 10, ingang 34 (2MRB1) 9000 Ghent Belgium Email: vanessa.vermeirssen(a)ugent.be Phone: +32 (0) 9 332 3945

1 0

Registration open for ELIXIR-NL Training: Technical Data Stewardship, 2-4 December 2019, Amsterdam, the Netherlands
by Celia van Gelder 22 Oct '19

22 Oct '19

Dear colleague, Please find below the information for our ELIXIR-NL Training on technical aspects of Data Stewardship. Course: Technical Data Stewardship Date: 2-4 December 2019 Location: Amsterdam Science Park Congress Centre, Science Park 123, 1098 XG Amsterdam. Course fee: Registration is free of charge Registration page: <https://www.eventbrite.co.uk/e/elixir-nl-training-technical-data-stewardshi p-registration-77268192243> https://www.eventbrite.co.uk/e/elixir-nl-training-technical-data-stewardship -registration-77268192243 Course description We will explore the ELIXIR Data stewardship wizard and see how one can employ and adopt it towards a community or research project. We will set the first steps on the path to FAIRify metadata by means of linked data. And finally we will see how FAIR data can be used in computational workflows and how to gather provenance data while working with data assets. The training is organised by ELIXIR-NL and will be given by DTL, ELIXIR CZ, SURF and Wageningen University. Target audience The training is targeted at data stewards, data scientists and research software engineers who would like to deepen their knowledge on concepts and practical implementations of data management/stewardship tools. We assume that you are familiar with programming in a language like Python, R or Matlab. Learning outcomes Participants will gain insight into the Data Stewardship Wizard how to employ and adjust the tool towards a special use case. They will learn about the principles of data modeling and making data FAIR by means of linked data. During the course we will apply these technologies to a real world data set. Participants will know afterwards how to approach their own data and can set first steps on the FAIRification process. Finally participants will know how to manage data and metadata in iRODS and how to employ data and metadata stored in iRODS in calculations on a remote compute cluster. Technologies ELIXIR Data stewardship wizard; Linked data; iRODS; python; SURF compute clusters Prerequisites Own laptop; Bash-shell, login to VM by ssh; Elementary knowledge of python Draft programme Monday December 2, 2019 - 12:00-17:00 (onsite & remote training) Trainers: Rob Hooft (ELIXIR-NL, DTL), Robert Pergl (ELIXIR-CZ, CCMI-FIT), Jan Slifka (ELIXIR-CZ, CCMI-FIT) * 12:00 - arrival with lunch * Introduction to Data management plan * Introduction and practical demonstration of the features of DSW: user-view and Data-steward view * Hands-on session Tuesday December 3, 2019 - 09:00 - 17:00 Trainers: Ben Schaap (Agrosystems Research, WUR), Erik van den Berg (WDCC, WUR), Jasper Koehorst (Systems and Synthetic Biology, WUR), Anand Gavai (WFSR, WUR) * Linked data training * Introduction to Linked Open Data * Exercise 1: pencil & paper exercise * Presentation on SPARQL and wikidata * Hands on real data, putting everything into practice Wednesday December 4, 2019 - 09:00 - 17:00 Trainer: Arthur Newton (SURFsara) * iRODS and compute You can find all the information and registration possibilities here: <https://www.eventbrite.co.uk/e/elixir-nl-training-technical-data-stewardshi p-registration-77268192243> https://www.eventbrite.co.uk/e/elixir-nl-training-technical-data-stewardship -registration-77268192243 Please spread this announcement in your organisation as you see fit. Best regards, Celia van Gelder 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: <https://www.dtls.nl/> https://www.dtls.nl/, <https://www.elixir-europe.org/platforms/training> https://www.elixir-europe.org/platforms/training 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.

1 0

PhD and Researcher / Software Developer positions available
by Anthony Mathelier 21 Oct '19

21 Oct '19

Dear colleagues, We have two open positions in my group. It would be great if you could spread the ads to potential candidates. A funded 3-year PhD candidate position is available to study the binding of TFs to DNA and how aberrant DNA methylation can alter gene regulation in cancers. More info and applications at https://www.jobbnorge.no/en/available-jobs/job/176997/phd-candidate-positio… A funded 2-year Research Scientist / Software Developer position is available to help us develop, maintain, fix, and upgrade our bioinformatics pipelines, tools, and resources. More info and applications at https://www.jobbnorge.no/en/available-jobs/job/177163/researcher-software-d… Thanks for sharing with whoever would be interested. Best AM -- Anthony Mathelier, PhD Group Leader - Computational Biology & Gene Regulation Group Centre for Molecular Medicine Norway (NCMM) Adjunct Researcher - Dept. of Cancer Genetics, Oslo University Hospital http://mathelierlab.com anthony.mathelier(a)ncmm.uio.no (+47) 22840561

1 0