November 2017 - BBClist - maillist.psb.ugent.be

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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Vacancy: Computational Immunologist
by Nicola Bonzanni 15 Nov '17

15 Nov '17

Dear All, We are currently looking for a computational immunologist to join our team. More information below or at https://www.enpicom.com/careers/computational-immunologist. Kind Regards, Nicola Bonzanni, CSO ENPICOM | Science Park 402 | 1098 XH Amsterdam www.enpicom.com<http://www.enpicom.com/> +31 (0)20 895 0964 +31 (0)648 913793 WORKING AT ENPICOM ENPICOM is a young, dynamic and expanding biomedical software development company. We use computational biology to build solutions that truly matter and improve people's lives and health. Originally setup in 2015 to create tailored computational solutions for life science, but since 2017 also on a mission to bring innovative products to the market to support the development, guidance and monitoring of immunotherapies. Our first product under development is a T-cell receptor and B-cell receptor repertoire analysis platform. ENPICOM has a strong focus on developing bleeding edge technology, combined with a passion for the well-being of people. Quality, creativity and self-development are our top priorities. We believe in a good work-life balance. We offer flexible working hours, flexibility in organizing your work and an employee stock ownership plan. WE AIM HIGH You are a best-in-class computational immunologist, have a getting the job done mentality, stand for quality and continuous improvement. You don't mind a good discussion on the best solution and are continuously looking for the latest technology and features, all in the interest of the best results. You are a true team player and want to share your knowledge and learn from others, yet you are also perfectly capable of working independently. YOUR ROLE As computational immunologist in our team, you will have a leading role in the development of statistical methods and algorithms for our immune genomics products, but also be involved in our customer projects and academic collaborations. You run the internal validation studies, develop new methods, provide content support to the commercial team, write (white) papers, present at conferences. YOUR PROFILE Required Qualifications: * A PhD in Bioinformatics, Computational Biology or related discipline * Experience in the field of immunology (preferably oncoimmunology) * Experience in the development of statistical methods and algorithms * Hands-on experience with Next-Generation Sequencing data analysis * Proficiency in R and/or Python * An excellent scientific track-record, backed by publications and recommendations * Fluent in English (speaking Dutch is an advantage) Desirable experience: * Experience with projects involving the use of genomics and immune profiling data to identifying candidate targets and biomarkers * Experience with machine learning * Experience in handling multiple projects in parallel * Excellent communication skills LOCATION 's-Hertogenbosch, The Netherlands JUST CONTACT US If you need more information about this job opportunity or are already excited to get on board, mail Dr. Nicola Bonzanni (Chief Scientific Officer) at n.bonzanni(a)enpicom.com<mailto:n.bonzanni@enpicom.com>. We look forward to hearing from you.

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Invitation to CTLS 2018 conference
by Alexander Botzki 13 Nov '17

13 Nov '17

Dear all, On behalf of the organising committee please see the invitation to CTLS 2018 (Core Technologies for Life Sciences 2018) below. After two successful editions of the CTLS conference, VIB is honoured to organize the 2018 conference in the beautiful and historic city of Ghent. CTLS2018@VIB aims to offer core facility staff and those interested in careers as expert scientists an opportunity to learn, network and forge alliances to strengthen core facility science throughout Europe. Over the 4 days of the conference there will be plenary and parallel sessions focusing on all facets of core facility operations, management and specific technologies of interest to core facility staff. Keynote talks will be given by 2001 Nobel laureate Paul Nurse, Frances Weis-Garcia (Past-President of ABRF) and Kurt Vandenberghe Director of Policy Development and Coordination, European Commission. Poster sessions will be held to allow core scientists to present new developments in their technologies and a core facility marketplace area will also be available for facilities to promote their expertise and services. A Belgian beer tasting, guided boat trip through the city’s canals and conference dinner in the old fish market will highlight the social program. The conference is open to all and details can be found on the website, https://vibconferences.be/event/ctls2018vib. A substantial discount (€120) on the registration fees will be given to members of CTLS. See http://www.ctls-org.eu/membership/apply-for-membership/ to join us. Looking forward to welcoming some of you in Ghent. 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/> [MAIL SIGNATURE - ABLS2] [signatureFooter (002)]

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PhD project @ University of Edinburgh
by Francisco Azuaje 10 Nov '17

10 Nov '17

Dear colleague, We are seeking applicants for a PhD project to be jointly supervised by S. Luz at the University of Edinburgh and me at the Luxembourg Institute of Health (LIH). www.jobs.ac.uk/job/BFO059/3-year-funded-phd-in-biomedical-informatics<http://www.jobs.ac.uk/job/BFO059/3-year-funded-phd-in-biomedical-informatics> Cordially, Francisco. _________________________________ Francisco Azuaje, PhD Principal Investigator, Proteome and Genome Research Unit Luxembourg Institute of Health Department of Oncology 1A-B, rue Thomas Edison, L-1445 Strassen Luxembourg Tel: +352 26970-875 Fax: +352 26970-719 Email: francisco.azuaje(a)lih.lu<mailto:francisco.azuaje@lih.lu> Website: https://www.lih.lu/ [http://files.lih.lu/outlookSignature/lih.jpg] Join us on Facebook and follow our activities on Twitter: https://www.facebook.com/Luxembourg.Institute.of.Health http://twitter.com/LIH_Luxembourg This message (including any attachments) is intended for the addressee only and may contain confidential and/or privileged information and/or information protected by intellectual property rights. If you have received this message by mistake, please notify the sender by return e-mail and delete this message from your system. You should not use, alter, copy or distribute this message or disclose its contents to anyone. E-mail transmission can not be guaranteed to be secure or error free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. Luxembourg Institute of Health shall not be responsible nor liable for the proper and complete transmission of the information contained in this communication nor for any delay in its receipt or damage to your system.

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Journée Scientifique Bilille : Working with networks and pathways in molecular biology
by Eva-Maria Krammer 09 Nov '17

09 Nov '17

The Bilille bioinformatics platform organizes, on November 20th, 2017, an afternoon workshop entitled "*Working with networks and pathways in **molecular biology*". This half-day workshop will take place on the campus of the *Institut Pasteur de Lille* (Amphi IBL, 1 rue du professeur Calmette, Metro line 2, station "Lille Grand Palais") from 1.00pm to 6.00pm. Invited speakers: * Marie Beurton Aimar (LaBRI - Equipe Image et Son - Université de Bordeaux). /Visual Exploration of Feasible Pathways through Metabolic Network/ * Guillaume Brysbaert (UGSF - UMR 8576 CNRS - Université de Lille). /An overview of Cytoscape for network biology with a focus on residue interaction networks/ * Martina Summer-Kutmon (BiGCaT, Maastricht University). /From Pathways to Networks: the WikiPathways app for Cytoscape/ * Florence Pinet (Unité d'Epidémiologie et de Santé Publique - Inserm-U1167 - Institut Pasteur Lille). /Integrative network analysis with Cytoscape reveals time-dependent molecular events underlying left ventricular remodeling in post-myocardial infarction patients/ * Aura Ileana Moreno-Vega (Institut Curie - UMR Compartimentation et Dynamique Cellulaire). /Identification of the regulatory network of the tyrosine kinase receptor FGFR3 in bladder cancer/ * Inna Kuperstein (Institut Curie - Department of Bioinformatics and Computational Systems Biology of Cancer). /Atlas of cancer signaling network and navicell: systems biology resources for studying cancer biology/ The program and form for registration are available on the website of the platform: https://wikis.univ-lille1.fr/bilille/networks_2017 Deadline to register: 13th November 2017 (registration is free but mandatory). -- -------------------------------------------- Eva-Maria Krammer Structure et Fonction des Membranes Biologiques CP 206/02 Université Libre de Bruxelles Bld du Triomphe B-1050 Bruxelles Belgium Phone : 32-2-650 2049 Fax : 32-2-650 5382 E-mail: ekrammer(a)ulb.ac.be --------------------------------------------

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BBC 2017 - call for abstract
by Daniele Parisi 09 Nov '17

09 Nov '17

Dear all, the DEADLINE for submitting your work as poster or oral talk at the Benelux Bioinformatics Conference is approaching soon (SUNDAY 5TH NOVEMBER), be sure you won't miss it! Information and free registration on the website https://bbc2017blog.wordpress.com/ Are you interested on the workshop "HANDLE YOUR DATA THE TIDY WAY: DATA SCIENCE USING R AND THE TIDYVERSE"? Find more and register https://bbc2017blog.wordpress.com/workshops/ -- DANIELE PARISI PhD student at ESAT - STADIUS, Yves Moreau's group President of RSG Belgium Board member of PhD Leuven society Kasteelpark Arenberg 10 - box 2446 3001 Leuven, Belgium Tel: +32488794394

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two-year post-doctoral position in computer sciences at INRA
by Karoline Faust 09 Nov '17

09 Nov '17

A two-year post-doctoral position in computer sciences is now opened at INRA-Dijon (France). The post-doctoral scientist will develop logic-based machine-learning algorithms for the reconstruction of microbial networks from metabarcoding datasets. We envision that these algorithms will be very useful to the biocontrol of plant pathogens in the near future, by allowing us to automatically identify candidate biocontrol agents. Plants are associated with a huge diversity of microorganisms that interact. Deciphering these microbial interactions is crucial since they underpin the regulation of plant diseases. These microbial interactions are usually identified using co-culture experiments. This is a tedious and time-consuming process that cannot easily be extended to the whole microbial community with which a pathogen interacts. A current challenge is to reconstruct microbial interaction networks directly from environmental DNA. The purpose of the project will be (1) to develop generic methods for learning microbial interaction networks from metabarcoding data and (2) to demonstrate that these new methods inform biological control of pathogens because they reveal antagonistic interactions between pathogen species and other microorganisms. This proof-of-concept study will be performed using both simulated datasets and real metabarcoding datasets on some major foliar pathogens of grapevine and wheat. The post-doctoral position is part of the BCMicrobiome project funded by the public-private Biocontrol Consortium*. Regular reporting to the Consortium will be requested and there will be an exclusivity period on the results obtained on the real metabarcoding datasets. The post-doctoral researcher will be based in Dave Bohan's lab at INRA-Dijon. He will work in close collaboration with the project's PI (Corinne Vacher, INRA-Bordeaux) and with other ecologists and plant pathologists involved in the project. A three-month stay in the Department of Computing at the University of Surrey will allow the post-doctoral researcher to gain new skills in machine-learning by working in collaboration with Alireza Tamaddoni-Nezhad. Close collaboration with the group of Stéphane Robin (AgroParisTech, Paris), who develops statistical methods of network inference, is also expected. The candidate should ideally have a background in machine-learning and/or statistics, good communication skills, and some interest in ecology and agriculture. Candidates having some experience in the analysis of ecological networks are also welcome to apply. Starting date: between January 2018 and April 2018 Gross salary: 3892 euros per month Contact: David Bohan (david.bohan(a)inra.fr) and Corinne Vacher (corinne.vacher(a)inra.fr<mailto:corinne.vacher@inra.fr>) * http://institut.inra.fr/Partenaires/Entreprises-et-filieres/Tous-les-magazi…

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