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

Bioinformatics position available at the Erasmus MC Cancer Computational Biology Center
by Harmen van de Werken 04 Oct '19

04 Oct '19

A bioinformatics position is currently available at the Erasmus MC Cancer Computational Biology Center. http://www.erasmusmc.nl/vacature/?num=21578 Please apply, if you are enthusiastic and eager to improve our knowledge on cancer biology. Harmen van de Werken

2 1

COMPUTATIONAL BIOLOGIST - TUMOR IMMUNOLOGY
by Lodewyk Wessels 25 Jul '19

25 Jul '19

VACANCY COMPUTATIONAL BIOLOGIST - TUMOR IMMUNOLOGY YOUR ROLE WITHIN THE INSTITUTE The research groups of Dr Karin de Visser, dr Marleen Kok and Prof dr Lodewyk Wessels, are looking for a motivated and talented Computational Biologist to join their teams at the Netherlands Cancer Institute (NKI). The Inflammation and Cancer group of dr. Karin de Visser is studying the impact of the immune system on metastatic breast cancer utilizing sophisticated mouse tumor models and state-of-the art ex vivo and in vitro immunological and molecular assays. The lab of de Visser closely collaborates with the translational research group of medical oncologist dr Marleen Kok. The mission of this team is to discover novel mechanisms underlying the crosstalk between breast cancer and the immune system, to optimize immunotherapy for breast cancer patients using novel combination treatments in clinical trials and the discovery of predictive biomarkers. The Computational cancer biology group of Prof dr Lodewyk Wessels is focused on quantifying and understanding treatment response in model systems and patients. To this end we develop bespoke and novel computational methods focusing on data integration and tailored to new technologies. We actively collaborate with many research groups in the NKI and strongly believe in the power of 'team science'. PROJECTS You will be involved in the following projects: 1. MOUSE MODELS FOR METASTATIC ESCAPE FROM IMMUNE CONTROL. To study the causal relationship between immune cells and metastatic breast cancer, we utilize state-of-the art genetically engineered mouse tumor models. We have extensive RNA-sequencing datasets of isolated immune cell populations, as well as RNA-sequencing and exome sequencing data of primary breast tumors and organ-specific metastases from these mouse models. You will be responsible for the computational analyses of the data, and to extract candidate pathways/genes from these datasets that can subsequently be tested in follow up experiments in the lab. Moreover, you will link these pre-clinical data to human datasets. 2. SYSTEMIC AND INTRA-TUMORAL IMMUNOMONITORING FOR PRECISION IMMUNE-MODULATION. We are performing extensive immunomonitoring studies in human breast cancer patients treated with immune checkpoint blockade, with the ultimate aim to validate hypotheses derived from our preclinical research in human cancer patients, and to stratify breast cancer patients for immunomodulatory therapies. We are setting-up multiplex immunohistochemistry with antibody panels that audit intratumoral lymphoid and myeloid cell populations and their functional state. In parallel, we have established an extensive multiplex flow cytometry pipeline to monitor the systemic immune landscape of breast cancer patients and healthy controls. These analyses generate a substantial amount of data which require thorough computational analyses. 3. MAPPING IMMUNO-GENOMIC INTERACTIONS. We are interested in dissecting the impact of the genetic make-up of breast tumors on the intra-tumoral and systemic immune landscape. You will be responsible for the identification and validation of genotype-immunophenotype associations by connecting DNA exome sequencing data, RNA sequencing data and immune profiles derived from our mouse tumor models and cancer patients. You will use both publicly available datasets and newly generated datasets. You will be embedded in the collaborative and enthusiastic international research groups of dr. Karin de Visser, dr Marleen Kok and Prof. dr. Lodewyk Wessels, providing a unique environment that combines computational cancer biology with pre-clinical and translational research into immune-oncology. YOUR PROFILE We seek to recruit an ambitious postdoc, capable of independent thinking, with a strong commitment to translational research. Candidates should hold a degree in bioinformatics, computer science or a related discipline, have experience in statistics and/or machine learning and be proficient in bioinformatics programming languages (e.g. R, Python). We expect candidates to be highly self-motivated, creative, and a team-player with strong communication skills. General background knowledge in biology and immunology is essential, and experience with projects involving the use of genomics and immune profiling data to identifying candidate targets and biomarkers is a plus. WANT MORE INFORMATION? Please visit our home pages https://www.nki.nl/divisions/tumor-biology-immunology/de-visser-k-group/ https://ccb.nki.nl or contact Karin de Visser: k.d.visser(a)nki.nl Marleen Kok: m.kok(a)nki.nl Lodewyk Wessels: l.wessels(a)nki.nl

1 2

ECCB'18 workshop on "Logical Modelling of Cellular Networks", Athens, September 9th, 2018
by Denis Thieffry 27 Apr '18

27 Apr '18

Dear all, We are pleased to announce the forthcoming ECCB'18 workshop on "Logical Modelling of Cellular Networks", which will take place on Saturday, September 8th, 2018, in Athens, Greece. This workshop is coupled with a tutorial entitled "Logical Modelling", on the following day (September 9th, 2018), thereby forming a SIG meeting devoted to logical modelling of cellular networks over two full days. The workshop day (Sept 8th, 2018) will be split in two sessions: the first session will be dedicated to recent methodological developments, the second session to biological case studies. Each speaker will be attributed 20 to 30’ (including questions and answers), depending on the final number of contributions. At this point, we are welcoming one-page long abstracts (max 4,000 characters, including title, authors, affiliations and spaces), which will be considered for oral presentations by the scientific committee. Abstracts should be sent to thieffry(a)ens.fr <mailto:thieffry@ens.fr> and anna.niaraki(a)univ-evry.fr <mailto:anna.niaraki@univ-evry.fr> by June 15th, 2018. More information about the workshop, the scientific committee and the confirmed speakers can be found at the url: http://eccb18.org/workshop-6/ <http://eccb18.org/workshop-6/> We are looking forward to hearing from you, please do not hesitate to contact us if you have further questions. Best regards, Anna Niarakis & Denis Thieffry -------------------------------------------------- Prof. Denis THIEFFRY Ecole Normale Supérieure - Département de Biologie IBENS - UMR ENS - CNRS 8197 - INSERM 1024 46 rue d'Ulm, 75230 Paris Cedex 05, FRANCE

1 0

Opening at EBI
by Frederik Coppens 27 Apr '18

27 Apr '18

FYI, an Infrastructure Team Leader position at EBI opened > Begin forwarded message: > > From: Helen Parkinson <parkinso(a)ebi.ac.uk> > Subject: [Interoperability] OPening at EBI > Date: 27 April 2018 at 13:05:21 GMT+2 > Reply-To: parkinson(a)ebi.ac.uk > > Dear ELIXIR interoperability colleagues, > > please could you circulate the following opening EBI faculty post in your respective organisations: > > New Infrastructure Team Leader post at EBI in the Molecular Archives cluster, > > https://www.embl.de/jobs/searchjobs/index.php?ref=EBI_01196&newlang=1&loc%5… > > I am happy to speak to any prospective applicants, > > thanks > > Helen > > -- > Helen Parkinson, PhD > Team Leader - Samples, Phenotypes and Ontologies > Head of Molecular Archives > European Bioinformatics Institute (EMBL-EBI) > European Molecular Biology Laboratory > Wellcome Trust Genome Campus > Hinxton > Cambridge CB10 1SD > United Kingdom > > EBI (0) +44 1223 494672 > For scheduling assistance please contact Marta Teran - mag-admin(a)ebi.ac.uk +44 (0) 1223 494112 > Skype: helen.parkinson.ebi > http://www.ebi.ac.uk/about/people/helen-parkinson > > _______________________________________________ > Interoperability mailing list > Interoperability(a)elixir-europe.org > Frederik Coppens - Project leader & IT manager Applied Bioinformatics And Biostatistics I.T. Support VIB-UGent Center for Plant Systems Biology Ghent University Technologiepark 927 - 9052 Ghent - Belgium Tel. +32(0)9 331 38 12 www.psb.ugent.be <http://www.psb.ugent.be/>

1 0

PhD position in modelling human microbiota at LUMC/RIVM
by Karoline Faust 27 Apr '18

27 Apr '18

We have a position available for a PhD student in modelling human microbiota at the Leiden University Medical Center (LUMC) . The project is a collaboration between LUMC and the Dutch Institute for Public Health (RIVM). This is the link to the vacancy: https://www.academictransfer.com/nl/47098/phd-student-modelling-of-human-mi… Could you please spread it in your network? Many thanks in advance, Elisa and Hans ---------------------------------------------------------------------------- Elisa Benincà, PhD Centre for Zoonoses and Environmental Microbiology National Institute for Public Health and the Environment (RIVM) Room V.250, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven PO Box 1, 3720BA Bilthoven, The Netherlands tel +31 30 274 8532 elisa.beninca(a)rivm.nl<mailto:elisa.beninca@rivm.nl> ----------------------------------------------------------------------------

1 0

Fwd: CORBEL train-the-trainer and course development hackathon 4-5-6 July Amsterdam
by Celia van Gelder 26 Apr '18

26 Apr '18

Fyi Verstuurd vanaf mijn iPhone Begin doorgestuurd bericht: > Van: Vera Matser <matser(a)ebi.ac.uk> > Datum: 25 april 2018 om 17:37:46 CEST > Aan: Celia van Gelder <celia.van.gelder(a)dtls.nl> > Onderwerp: CORBEL train-the-trainer and course development hackathon > > Dear Celia, > > As part of the CORBEL project (http://www.corbel-project.eu) we are organising a train-the-trainer course (TtT) and course development hackathon event on the 4-6th July in Amsterdam. > > This workshop is for you if you work within a research infrastructure; you may be a trainer, educator, training coordinator or project manager with training falling under your remit. > > The aim of the workshop is to provide participants with new ideas and tools to make their training events or workshops even better and easier to run and prepare. The course development event allows you to put these new ideas into practice and work on your own training concepts with input from colleagues. > > Date: 4-5th July (TtT) 6th July (course hackathon) > Location: Lloyd Hotel & Cultural Embassy, Amsterdam, Netherlands > Registration deadline: 2nd May 2018 > Cost: Free > > This event combines two separate events, a 2-day train-the-trainer workshop and a 1-day course development hackathon. You can choose to attend one or both events. > > For registration and more details see the announcement pdf (attached) and the CORBEL webpage: > http://www.corbel-project.eu/news-events/event-articles/train-the-trainer-w… > > Any question please don't hesitate to get in touch! > > Kind regards > > Vera > > -- > Vera Matser PhD > Training Liaison Officer, EMBL-EBI > ORCID: 0000-0002-2010-6844 > > Tel: +44 (0)1223 49 4149 > Skype: vera_matser > e-mail: matser(a)ebi.ac.uk > Twitter: @VeraMatser > URL: www.ebi.ac.uk/training > Find us in on-course®: www.on-course.eu > > European Bioinformatics Institute (EMBL-EBI) > European Molecular Biology Laboratory > Wellcome Genome Campus > Hinxton > Cambridge > CB10 1SD > UK

1 0

BioSB 2018 - detailed scientific programme online!
by Femke Francissen 25 Apr '18

25 Apr '18

4th Dutch Bioinformatics & Systems Biology Conference - BioSB 2018 May 15-16, 2018 Congrescentrum De Werelt, Lunteren Conference website: www.aanmelder.nl/biosb2018 The detailed scientific programme of our annual conference in Lunteren is now online. The quality of submitted abstracts and the profiles of the keynotes make us look forward to a very exciting meeting! Take a look at the conference programme <https://www.aanmelder.nl/biosb2018/part_program> The 2-day programme features: Four international keynote speakers: Chiarra Dalla Man (University of Padova), Martin Kircher (Berlin Institute of Health), Jason Locasale (Duke University) and Alexander van Oudenaarden (Hubrecht Institute). Two plenary HotTopics sessions: Single Molecule Sequencing & Single Cell Omics Topical parallel sessions on: Genomics, Personalized medicine, Metabolomics, Tools & resources, Network biology, Metabolic modelling, Microbiome & Ecosystems, Regulation & signalling, Integration of (omics) data sets, Genetic variants & population studies, RNA & protein diversity. Featuring both invited (senior) as selected presentations. An ELIXIR-NL parallel track with sessions focussing on FAIR Data and Agrifood Data concepts and applications. Poster & demo sessions Five breakout sessions on May 16. Conference dinner and social event in the evening of May 15. Join us now & register! More about the conference fees & registration can be found here <https://www.aanmelder.nl/biosb2018/wiki/267520/registration>. We look forward to meeting you all in Lunteren! On behalf of the organizing & programme committee Femke Francissen Community manager BioSB Research School Visiting address (as of 1 July 2017): Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht Postal address (as of 1 July 2017): Postbus 8500 | 3503 RM Utrecht E-mail: femke.francissen(a)biosb.nl <mailto:femke.francissen@biosb.nl>

1 0

Announcement: Conference Systems Epigenetics: Towards Precision Cancer Medicine, Amsterdam, 27-30 Nov 2018
by P.D. Moerland 20 Apr '18

20 Apr '18

1 0

Advanced bachelor programme of bioinformatics via distance learning
by Howest 20 Apr '18

20 Apr '18

If you are not able to see this mail, click http://mrbe.r.a.d.sendibm1.com/2d8puzbwqx0jf.html Please feel free to forward to anyone who might be interested Dear colleague, We would like to inform you about the start of our advanced bachelor programme of bioinformatics via distance learning (@home). The programme is intended for every technician (bachelor), master and PhD with a profound knowledge of molecular biology and an interest in (bio)informatics who is currently working in the biological or biomedical work field. During the two years programme (30 ECTS/year) we focus on new and emerging technologies within the work field and the application of computer science techniques for “wet lab” problems. We divide the course units in three categories: informatics, bioinformatics and programming. Within the field of informatics, you learn to work on a Unix system, to store biological data in databases and to analyse large datasets using data mining techniques. Second, you become familiar with comparative genomics, structural bioinformatics, systems biology and the analysis of high-throughput experimental data. In the last important topic, programming skills are introduced to create web applications (HTML, PHP, CSS), to script bioinformatics pipelines in Python and to perform statistical and exploratory analysis in R. The programme is organized at the request of the labour market and several courses are given by experts in the field. After two years the transformation from wet-lab to dry-lab scientist is complete, future proof to work within a constantly changing working field and a perfect blend between the ICT expert and the molecular biologist. Per module three contact moments of two hours are organized. The contact moments take place every two weeks on the campus in Bruges from 6 PM to 8 PM, but can also be followed via live stream on YouTube. The subject matter is mainly processed via self-study, in combination with coaching/exercises/questions or a crash course during the contact moments. During the first year, it is possible to apply for educational leave to follow the programme. If you are interested to follow the advanced bachelor programme of bioinformatics, please come and visit us at one of the [ information sessions on the campus ]( http://mrbe.r.a.d.sendibm1.com/track/click/9gyvfxbh8qx0jd ). You can also have a look on the [ website ]( http://mrbe.r.a.d.sendibm1.com/track/click/9gyvfxc9oqx0jd ) for more information or contact us at [ bit(a)howest.be ]( mailto:bit@howest.be ). Best regards, Advanced Bachelor of Bioinformatics Biomedical Laboratory Science Howest University of Applied Sciences Howest University of Applied Sciences Campus Rijselstraat Rijselstraat 5 - 8200 Brugge Tel.: +32 50 38 12 77 [ ]( http://mrbe.r.a.d.sendibm1.com/track/click/9gyvfxd24qx0jd ) Please feel free to forward to anyone who might be interested [ Unsubscribe here ]( http://mrbe.r.a.d.sendibm1.com/2d8puzbwqx0jg.html ) © 2018 Howest

1 0

Job openings at The Hyve: System Administrator and more
by Ward Weistra 18 Apr '18

18 Apr '18

Dear all, At our bioinformatics company The Hyve we are looking for multiple new colleagues to complement the team. The System Administrator job description is listed below, but please find all our open positions at https://thehyve.nl/the-hyve/working-at-the-hyve/. Thank you for sharing! Best regards, Ward Weistra System Administrator *Job description* The Hyve is a young, innovative and fast growing company employing software engineers, bioinformaticians and data scientists. We are dedicated to developing software and data management tools to support scientists in life sciences and healthcare R&D with open source software, open data and open standards. We maintain a growing farm of Cloud servers as part of our professional open source software hosting and service contracts. Our clients include top universities, hospitals, and a number of international pharma and food companies. If you are an experienced system administrator looking for a varied role, then this is an excellent opportunity to join The Hyve. As system administrator you are responsible for keeping the infrastructure operational. You are trustworthy and reliable. A service oriented problem solver. A team player and excellent communicator with developers, managers and clients. *Tasks:* - Set up and configure new servers - Maintain servers - Security, availability and vitals monitoring - Backup management - Application deployment automation - Application support: problem diagnosis, configuration changes, assist with code changes (i.e. bug fixes) - Network infrastructure configuration - Cloud infrastructure configuration / scripting - Performance monitoring and optimization *Required are:* - Linux System administration (Ubuntu, RedHat, main focus: command line tools) - Deployment automation / configuration management tools (Puppet, Ansible, Vagrant) - Networks (TCP/IP, VPN, SSH tunnels, etc.) - Website hosting (Apache, SSL certificates, etc.) - Database configuration (PostgreSQL, MySQL, Oracle) - Personality and ability to learn new technologies - Fluency in English (oral and written) - Based in the Netherlands (or willing to relocate) - Proven experience with system and/or application security *Desired are:* - Puppet configuration management - Experience in scaling applications (Java/Scala backends) and databases (PostgresDB, MySQL, MongoDB) - Hadoop stack experience (especially Spark, Parquet, HDFS) - Technical support for Mac and Windows computers - Remote access tooling (Citrix, RDP, etc.) - Git and Github (see https://github.com/thehyve) - Hypervisors (OpenStack APIs, especially Nova, VMware, etc.) - Knowledge of ISO27001 or similar information security management standards - Fluency in Dutch *We offer:* We offer a 32-40 hours workweek, a competitive salary and a pleasant working environment with young and bright colleagues. *More information?* Marinel Cavelaars, Manager Services Jojanneke Blaak, HR Officer +31 30 7009713 or hr(a)thehyve.nl -- Ward Weistra | Team Lead Data Warehousing *Out of office on Friday* E. ward(a)thehyve.nl T. +31 30 700 9713 W. www.thehyve.nl Skype. wardweistra | M. +1 347 979 2731 | Twitter <https://twitter.com/WardWeistra>. | LinkedIn <https://www.linkedin.com/in/wardweistra/>.

1 0