- BBClist - maillist.psb.ugent.be

FW: available position at the NARILIS institute, search for candidates with bioinformatic knowledge
by Vanneste, Kevin 27 Nov '17

27 Nov '17

Dear all, A position requiring strong bioinformatics affinity is available at the lab of Nicolas Gillet in the university of Namur, focusing on the involvement of viral infections in oncogenesis. Please see attachment for more details. Best regards, Kevin [Description: logo ISP-WIV] Kevin Vanneste Bioinformatician Platform Biotechnology and Molecular Biology Expertise, Service Provision and Customer Relations Rue Juliette Wytsmanstraat 14 | 1050 Brussels | Belgium T +32 (0)2 642 50 65 | F +32 (0)2 642 52 92 Email: kevin.vanneste(a)wiv-isp.be<mailto:kevin.vanneste@wiv-isp.be> | Skype: wiv-isp.kevin.vanneste Scientific Institute of Public Health | www.wiv-isp.be<http://www.wiv-isp.be/> ########################################################### Checked as being free of known viruses. Scientific Institute of Public Health, Brussels, Belgium Wetenschappelijk Instituut Volksgezondheid, Brussel, Belgi� Institut scientifique de Sant� publique, Bruxelles, Belgique Visit our website: http://www.wiv-isp.be ############################################################# DISCLAIMER: Please see https://www.wiv-isp.be/EmailDisclaimer #############################################################

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PhD position: meiotic control of recombination in crops
by Ridder, Dick de 27 Nov '17

27 Nov '17

Dear all, We are looking for an enthusiastic bionformatics PhD candidate on a Marie Curie ITN project titled "Meiotic control of recombination in crops". The goal is to analyse crossover formation in crop genomes using novel combinations of high-throughput sequencing (Illumina, PacBio, Oxford Nanopore, 10X Genomics) and optical mapping (BioNano Genomics) data, to learn about crossover frequency in haplotypes, genome structure and structural variation in parental lines and offspring of crops such as tomato, potato, melon, and lettuce. Sequence and genome structural data will be mined using machine learning techniques to find features influencing recombination. Candidates should hold an MSc degree in bioinformatics, computer science (with a demonstrable affinity for biology) or related area. We are specifically seeking a candidate with a strong background in algorithm development, preferably related to machine learning, and demonstrable skills in mathematics and statistics. You will be based in Wageningen, and collaborate with other PhD candidates in this EU-wide project and with researchers at Wageningen University and in industry. Note that under the Marie Curie ITN rules, applicants cannot have resided in The Netherlands for more than 12 months over the past three years. Additional information about the position can be found at https://www.wur.nl/nl/vacature/PhD-position-Meiotic-control-of-recombinatio…. Interested candidates can apply up to January 15, 2018 through this website. Best regards, prof. Dick de Ridder Bioinformatics Group, Wageningen University, The Netherlands

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Bioinformatician: GENMAB - NKI collaboration
by Lodewyk Wessels 26 Nov '17

26 Nov '17

Bioinformatician position: ‘Biomarker discovery for HexaBody-DR5/DR5 therapy’ Partners: Genmab BV, Utrecht, The Netherlands The Netherlands Cancer Institute (NKI), Amsterdam. Project description. How can we find better treatment strategies for solid cancers? How can we select the patient population or individual patients that will show exquisite response to these treatments? Genmab, an international biotechnology company. is currently developing HexaBody®-DR5/DR5, a therapeutic antibody product targeting the DR5 death receptor protein in solid cancers. This agonistic antibody product mimics ligand-induced apoptosis by clustering of DR5. The general aim of this research collaboration is two-fold. First to find molecular biomarkers to identify HexaBody®-DR5/DR5-responsive patients. Second, to understand the mechanism of action of HexaBody®-DR5/DR5. Our strategy is to employ large panels of tumor cell lines and patient-derived xenograft (PDX) tumor models that have been molecularly profiled and screened for response to HexaBody®-DR5/DR5. Specifically, we have whole exome and RNA sequencing data as well as HexaBody®-DR5/DR5 response measurements across tumor cell lines spanning 14 tumor indications and PDX models covering 2 tumor types. To provide more mechanistic insight we also have access to data from functional genetic screens aimed at identifying modulators of HexaBody®-DR5/DR5 response. Public-private collaboration. Genmab is an international biotechnology company specializing in the generation and development of differentiated antibody therapeutics for the treatment of cancer. DARZALEX® and Arzerra® are two approved drugs that were developed by Genmab. Genmab has a strong commitment to research and innovation with numerous external research collaborations akin to this one. The Computational Cancer Biology (CCB) group led by Lodewyk Wessels, has a strong track record in developing predictors of drug response from cell line panels, especially in collaboration with the Wellcome Trust Sanger Institute culminating in the second release of the Genomics of Drug Sensitivity on Cancer (GDSC1000) cell line panel (Iorio et al, Cell, 2016). Together with Genmab, the successful candidate will develop machine learning approaches to integrate the molecular data from the cell lines and PDX models in order to find effective HexaBody®-DR5/DR5 biomarkers and shed light on the mechanisms of response and resistance. The successful candidate will be employed at the NKI but regular visits to and meetings with Genmab will ensure sufficient cohesion and momentum. Candidate profile. We are seeking a highly motivated bioinformatician with: - A degree in bioinformatics, computer science or a related discipline - Experience with high-throughput data analysis, especially sequencing data - Proficiency in bioinformatics programming languages (e.g. R, Python) - Good cross-disciplinary collaborative and communication skills - Experience in statistics, machine learning and/or pattern recognition is a plus - Experience in cancer biology and clinical applications is a plus Interested? Please send CV and motivation letter to Lodewyk Wessels (l.wessels(a)nki.nl) and Jan-Hermen Dannenberg (jhd(a)genmab.com) Please include the names and contact information of at least two references. Deadline: 15 December 2017

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PhD position Plant.ID training Network on hardwood identification in string instruments
by Fons Verbeek 24 Nov '17

24 Nov '17

In a collaborative project between Naturalis Biodiversity Centre and Leiden University (Leiden Institute of Advanced Computer Science) we are looking for a computer scientist with an interest in biology or a bioinformatician with knowledge in pattern recognition and image analysis. Experience with state-of-the-art techniques such as CNN’s are considered valuable. If you are interested you are very much invited to apply for the position. Read about the project in the short project description: Acoustic string instruments are made of several hardwood species including ebony (Diospyros). Many species of ebony are nowadays over-exploited in the wild. The Convention on International Trade in Endangered Species (CITES) placed all species of ebony from Madagascar on Appendix II in 2014 but other species are not legally protected. Computational microscopic phenotyping based on wood anatomical sections, chemical profiling and DNA barcoding are increasingly used to recognize wood traded under Forest Stewardschip Council (FSC) labels. Therefore, anatomy data, DNA barcodes and DART-TOF MS will be collected from reference specimens. Metabarcodes will be generated from ebony wood used in (parts of) instruments supplied by violon and bow builders and compared with microscopy, DART-TOF MS and bomb peak calibrated C14-dates to distinguish antique wood from wood harvested after 2013. Objective:Species-level identification of ebony wood for control of trade in legally protected species. Supervisors: Barbara Gravendeel and Frederic Lens from Naturalis Biodiversity Center, and promotor Fons Verbeek, Leiden University, Leiden Institute of Advanced Computer Science (LIACS). Planned secondments to Leiden University and Copenhagen University and short visits to the Dutch association of violin and bow makers and World Justice Commission. ——— Further information and instructions for application can be found on: https://science.naturalis.nl/en/about-us/jobs-and-fellowships/plantid-phd-f… <https://science.naturalis.nl/en/about-us/jobs-and-fellowships/plantid-phd-f…> http://www.plantid.uio.no/jobs/ <http://www.plantid.uio.no/jobs/> Prof Dr Ir Fons J. Verbeek, Imaging & BioInformatics LIACS, Leiden University The Netherlands f.j.verbeek(a)liacs.leidenuniv.nl

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Edinburgh Genomics Python workshops 2018
by Bert Overduin 22 Nov '17

22 Nov '17

Dear all, Edinburgh Genomics is happy to again offer a range of Python workshops in the first half of 2018. All workshops are taught by Dr. Martin Jones, founder of Python for Biologists (https://pythonforbiologists.com) writer of several books on Python (https://pythonforbiologists.com/python-books/) and most likely the best Python instructor you will ever come across. Details of the workshops can be found below. With kind regards, Bert ************************* *5-day Introduction to Python for Biologists* Date: Mon 19 - Fri 23 February 2018 Registration deadline: Mon 5 February 2018 Places: 20 (first come, first served) Fee: £525 Instructor: Dr. Martin Jones (Python for Biologists) More info and registration: http://genomics.ed.ac.uk/services/introduction- python-biologists *5-day Data Manipulation and Visualisation with Python* Date: Mon 9 - Fri 13 April 2018 Registration deadline: Mon 26 March 2018 Places: 15 (first come, first served) Fee: £525 Instructor: Dr. Martin Jones (Python for Biologists) More info and registration: http://genomics.ed.ac.uk /services/data-manipulation-and-visualisation-python *5-day Advanced Python for Biologists* Date: Mon 9 - Fri 13 July 2018 Registration deadline: Mon 25 June 2018 Places: 15 (first come, first served) Fee: £525 Instructor: Dr. Martin Jones (Python for Biologists) More info and registration: http://genomics.ed.ac.uk/services/advanced- python-biologists <https://genomics.ed.ac.uk/services/advanced-python-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 http://genomics.ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Vacancy Scientist Bioinformatics (MEC335) - Galapagos - Mechelen, BE
by Mate Ongenaert 22 Nov '17

22 Nov '17

Galapagos is a clinical-stage biotechnology company, specialized in the discovery and development of small molecule medicines with novel modes of action. Our ambition is to become a leading global biotechnology company, focused on the development and commercialization of novel medicines that will improve people's lives. For our site in Mechelen, we are looking for a Scientist Bioinformatics (MEC335) All info and applications: http://careers.glpg.com/o/scientist-bioinformatics-mechelen Job description Ref: MEC335 As a member of the bioinformatics team you will participate in bioinformatics efforts supporting the drug discovery projects at Galapagos. By carrying out functional analyses, data integration, and implementing and executing data analysis methodologies, you work with the multidisciplinary disease biology and drug discovery teams in acquiring scientific insights to direct the research strategy. You will play a key role in implementing bioinformatics tools and methods supporting a wide range of activities, from research projects to proof-of-concept studies. In collaboration with the Information Systems (IS) team, these tools will be incorporated into Galapagos' informatics infrastructure. This position offers an exciting opportunity to develop and deploy bioinformatics-driven solutions to the scientific community at Galapagos. Requirements * Scientific Master Degree with at least 3 years of relevant work experience or PhD with a demonstrated track record in bioinformatics, preferably in a pharma/biotech setting; * Knowledge of expression data analysis, micro-arrays and/or sequencing-based, and experience in developing analysis strategies and workflows in transcriptomics; * Experience in data-science techniques (regression, machine learning); experience with data structures and data-interchange formats (e.g. JSON) and experience with document databases (such as MongoDB or Cassandra) and/or relational databases; * Working knowledge of Linux and programming expertise (e.g., C#, Java, Perl or Python) * Strong problem-solving ability, and the aptitude and zeal to acquire new skills necessary for the job * Rigorous and well organized; good verbal and written English communication skills; * Team player able to work and communicate effectively in a multidisciplinary environment with people with different professional backgrounds (biology, chemistry, molecular modelling, IS, IT); Desirable skills * Good knowledge of R (and the BioConductor libraries) and experience with reporting in R (sweave/knitr) and interactive web-interfaces (R/shiny); * Demonstrated experience in working out proof of concept workflows, analysis tools or visualizations; * Broadly applicable general bioinformatics skills (pathway analysis, data and text mining, querying databases and repositories in the public domain); * Knowledge of disease-related pathways and systems biology approaches in relation to drug target discovery; [cid:image001.jpg@01D16D66.BD487830]<http://www.glpg.com/> Maté Ongenaert, PhD Senior Scientist Bioinformatics T: +32 15 342 927 Galapagos NV Generaal De Wittelaan L11 A3 2800 Mechelen * Belgium -- This e-mail and its attachment(s) (if any) may contain confidential and/or proprietary information and is intended for its addressee(s) only. Any unauthorized use of the information contained herein (including, but not limited to, alteration, reproduction, communication, distribution or any other form of dissemination) is strictly prohibited. If you are not the intended addressee, please notify the originator promptly and delete this e-mail and its attachment(s) (if any) subsequently. Neither Galapagos nor any of its affiliates shall be liable for direct, special, indirect or consequential damages arising from alteration of the contents of this message (by a third party) or as a result of a virus being passed on.

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Bioinformatics postdoc in the Blanpain lab
by Stein Aerts 21 Nov '17

21 Nov '17

Dear all, Please find an interesting bioinformatics position in Cedric Blanpain’s lab. Best regards, Stein

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FW: [Training-coordinators] Training Course on Linux shell scripting for high-throughput biological data processing on supercomputers
by Alexander Botzki 20 Nov '17

20 Nov '17

COURSE ANNOUNCEMENT Please circulate this email to those who might be interested. ELIXIR-IIB, in collaboration with CINECA, is pleased to announce the upcoming training course on “Linux shell scripting for high-throughput biological data processing on supercomputers”. IMPORTANT DATES: Deadline for applications: 20 Dec 2017 Course date: 16-17 Jan 2018 A maximum of 20 candidates will be selected based on their need for the course as emerging from the application form. Notifications of acceptance will be sent shortly after the application until we reach 20 participants. Priority will be given to candidates from ELIXIR-IIB member institutions and ELIXIR nodes. The course does not include any fee, but the participants are expected to pay their own travel, meals and hotel costs. VENUE: CINECA, Via dei Tizii, 6B, 00185 Rome, Italy. Full details at: https://elixir-iib-training.github.io/website/2018/01/16/Linux-Shell-Roma.h… COURSE DESCRIPTION: Biological big data increasingly require supercomputers for their processing and analysis. Running high-throughput (HTP) bioinformatics data pipelines on supercomputing machines requires advanced Linux shell command line and scripting skills. In this two-day course, we will introduce the Linux shell and, on day one, we will show how to navigate and work with files and directories, how to combine commands to do new things, how to perform the same actions on many different files, how to filter and selectively extract data from tables, and how to find objects in files. Moreover, we will show how to connect to a remote supercomputer and how to utilise a supercomputing environment to analyse big amount of biological data, run simple shell scripts and bioinformatics pipelines. Day 2 will be wholly practical. Should you have any question, do not hesitate to contact the ELIXIR-IIB Training Team (elixir.ita.training(a)gmail.com<mailto:elixir.ita.training@gmail.com>). Thank you for your interest, the Organisers Tiziana Castrignanò (CINECA, Rome, Italy) Allegra Via (ELIXIR-IIB Training Coordinator) Loredana Le Pera (ELIXIR-IIB Training Coordinator Deputy) [Image removed by sender. logo_iib.png] -- ELIXIR-IIB Training https://elixir-iib-training.github.io/website/

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5 Early Stage Researcher positions in Finland
by Lasse SINKKONEN 20 Nov '17

20 Nov '17

Dear All, Prof Minna Kaikkonen-Määttä, and her colleagues at the University of Eastern Finland, are currently looking for 5 Early Stage Researchers (PhD students) as part of the Marie Curie Actions funded GenomMed program (http://www.uef.fi/en/web/genommed) In particular applications from candidates with bioinformatics skills and interest in integrative omics analysis are encouraged (but not limited to). Please see the attached flyer and the description below for more information. Thank you for distributing the information. Best Regards, Lasse Sinkkonen -- Dr. Lasse SINKKONEN Research Scientist Head of the Epigenetics Team Systems Biology Group Life Sciences Research Unit UNIVERSITY OF LUXEMBOURG Biotech II 6, avenue du Swing L-4367 Belvaux LUXEMBOURG Tel. +352-4666446839 E-mail: lasse.sinkkonen(a)uni.lu<mailto:lasse.sinkkonen@uni.lu> Web: http://wwwen.uni.lu/research/fstc/life_sciences_research_unit/research_area… 2nd Call: Early stage researcher positions, GenomMed Cofund Doctoral Programme The University of Eastern Finland, UEF, is one of the largest multidisciplinary universities in Finland. We offer education in nearly one hundred major subjects, and are home to approximately 15,000 students and 2,500 members of staff. We operate on three campuses in Joensuu, Kuopio and Savonlinna. In international rankings, we are ranked among the leading universities in the world. The Faculty of Health Sciences operates at the Kuopio Campus of the University of Eastern Finland. The Faculty offers education in medicine, dentistry and pharmacy, as well as in some other central fields of the health care sector. The Faculty is research-intensive, and its internationally recognised research activities are closely linked to the strategic research areas of the University. There are approximately 2 500 degree students and about 450 PhD students in the Faculty. The faculty has 680 staff members.http://www.uef.fi/en/ttdk/etusivu 5 Doctoral Student (Early Stage Researcher) Positions in GenomMed Doctoral programme (Marie Skłodowska Curie Actions (MSCA) Cofund programme) at University of Eastern Finland, Faculty of Health sciences, Kuopio campus The Faculty of Health Sciences offers doctoral training in a new EU co-funded Doctoral programme Genomics and mechanisms in translational medicine (GenomMed, http://www.uef.fi/genommed) in which 5 early stage researcher (ESR) positions are now open for application. This is a second call for GenomMed programme. GenomMed programme will provide the selected ESRs with multidisciplinary research skills introduced in more detail at the programme web site: http://www.uef.fi/en/web/genommed/how-to-apply A person to be appointed as an early stage researcher shall be qualified to pursue postgraduate studies, i.e. he or she is required to have completed a suitable higher university degree (MSc or equivalent in a relevant field). Early stage researcher positions are always filled for a fixed term (UEF Administrative Regulations, Section 30). Persons finalizing their higher university degree may also apply (degree must be finished by 3 December), but are required to submit their degree certificate and transcript of records by 15 December 2017. The ESR positions may be applied for by persons fulfilling the mobility requirement of the MSCA actions. Detailed eligibility criteria can be found at: http://www.uef.fi/en/web/genommed/eligibility A fluent English language proficiency is required of applicants performing their research in English. The doctoral student positions will be filled as from January-March 2018 for four years. The persons selected to the doctoral student positions will be hired as early stage researchers by the UEF academic departments and schools. The main duty of the doctoral students is to complete their doctoral dissertation in accordance with their approved research proposal. The salary of the early stage researcher is based on levels 2–4 of the job requirement level chart for teaching and research staff in the Salary System for Finnish Universities (i.e. the job requirement component amounts to €1,985.85–€2,475.31/ month). In addition to the job requirement component, the salary includes a personal performance component, which may be up to 46.3% of the job requirement component. The salary is determined on the basis of the phase of the doctoral dissertation and the person’s personal performance. The following evaluation criteria will be considered in the selection of the doctoral students: excellence of the applicant (motivation and commitment, academic qualifications, research, practical, and international experience), scientific quality of the research proposal (excellence, innovativeness, feasibility, interdisciplinary approaches, relevance and acknowledgement of ethical aspects), and quality of research environment (infrastructure, training and supervision, and career development means). Full instructions on eligibility criteria, application evaluation criteria and description of required documents can be found on the GenomMed web- site at: http://www.uef.fi/genommed<https://www.uef.fi/en/web/genommed> For further information on the application procedure, please contact: genommed(a)uef.fi<mailto:genommed@uef.fi> A probationary period will be applied to new members of the university staff. The application should contain the following appendices: * research proposal, max. two A4 pages including ethics statement where relevant * certified copy of MSc degree diploma and transcript of records in English * curriculum vitae (CV) * motivation letter describing applicant’s motivation to pursue PhD studies in GenomMed programme in the selected research field Applications will be evaluated by evaluation panels external to UEF. Based on the evaluation, most qualified applicants will be invited to an interview. Applications are submitted in the electronic recruitment system Saima. The application deadline is Sunday 3 December 2017 (by 24.00 hours Finnish time).

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European Galaxy Administrator Workshop, 8-12 January 2018, Oslo. FREE
by Dave Clements 17 Nov '17

17 Nov '17

*We are pleased to announce that registration <https://skjema.uio.no/galaxy-admin-workshop-2018> is now open for the European Galaxy Administrator Workshop <https://www.elixir-europe.org/events/european-galaxy-administrator-workshop>* . - Mon 8 January 2018 to Fri 12 January 2018 CET - Python room, Blindern, UiO campus, Ole Johan Dahls hus <https://www.uio.no/english/about/getting-around/areas/gaustad/ga06/>, Gaustadalléen 23B, Oslo, 0373, Norway Participants will learn how to install, configure, customize, and extend their own Galaxy <https://galaxyproject.org/> servers. Topics include tool configuration, authentication and user management, using heterogeneous storage and compute services, and many other topics that will enable you to get your own Galaxy server up and running, performing well, and used by your community. Have a look at the programme <https://github.com/elixir-no-nels/dagobah-training/blob/2018-oslo/README.md> to see more details on the planned content of the workshop. *Maximum number of participants is limited to 30, and we will manage registrations to allow for geographical distribution and proritize participants with responsibility of administrating galaxy servers.* After registering you will get a second confirmation if/when a slot has been allocated to you. Although located in Europe, and named to reflect this, the workshop is definitely *open to a world-wide audience.* The workshop is a result of the collaboration between the Elixir Galaxy WG <https://www.elixir-europe.org/about/groups/galaxy-wg> and the Galaxy Project, and so far known, this is the only Galaxy Admin workshop planned for 2018. *Participants are to cover their own travel and accomodation, while the workshop participation is free of charge.* Instructors - Björn Grüning <https://github.com/bgruening> (Elixir Galaxy WG <https://www.elixir-europe.org/about/groups/galaxy-wg>, Elixir Germany <https://www.elixir-europe.org/about-us/who-we-are/nodes/germany>, University of Freiburg <https://www.uni-freiburg.de/?set_language=en>) - Marius van den Beek <https://github.com/mvdbeek> (Elixir Galaxy WG <https://www.elixir-europe.org/about/groups/galaxy-wg>, Institute Curie <https://science.institut-curie.org/>, France) - Nicola Soranzo <http://www.earlham.ac.uk/nicola-soranzo> (Elixir Galaxy WG <https://www.elixir-europe.org/about/groups/galaxy-wg>, Earlham Institute <http://www.earlham.ac.uk/>, UK) - Enis Afgan <https://galaxyproject.org/people/enis-afgan/> (Galaxy Project <https://galaxyproject.org/>, Johns Hopkins University <https://jhu.edu/>, USA) - Abdulrahman Azab <http://www.usit.uio.no/om/organisasjon/itf/ft/ansatte/azab/index.html> (Elixir Norway <https://www.elixir-europe.org/about-us/who-we-are/nodes/norway>, USIT <http://www.usit.uio.no/>, University of Oslo <http://www.uio.no/>, Norway) *About Galaxy* Galaxy <https://galaxyproject.org/> is an open, web-based platform for data-intensive biomedical analysis used by tens of thousands of researchers around the world. It supports ad hoc exploration and analysis through scalable and repeatable data analysis pipelines for large research studies. Galaxy is available in over 90 free and publicly accessible web servers, on commercial and national cloud infrastructures, and is locally installed at hundreds, if not thousands, of research organisations around the world. -- https://galaxyproject.org/ https://usegalaxy.org/

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