- BBClist - maillist.psb.ugent.be

FW: Bioinformatician job offer
by Alexander Botzki 09 Feb '16

09 Feb '16

From: Bioinformatics Interest Group (BIG) [mailto:BIG@LS.KULEUVEN.BE] On Behalf Of Vimac Nolla Ardevol Sent: 09 February 2016 18:40 To: BIG(a)LS.KULEUVEN.BE Subject: Bioinformatician job offer Dear all, A colleague of mine has just forwarded me this opening for a bioinformatician in Mind the byte, a start-up bioinformatics company specializing in computational drug discovery using a pay-peruse SaaS platform (software as a service) located in Barcelona. Feel free to distribute the offer. Cheers, Vimac --------------------------------- Dr Vímac Nolla Ardèvol Division of Soil and Water Management KU Leuven Kasteelpark Arenberg 20 - box 2459 3001 Leuven room: 02.214 tel. +32 16 37 47 47<tel:+32+16+37+47+47> fax +32 16 3 21997<tel:+32+16+3+21997> e-mail: vimac.nollaardevol(a)ees.kuleuven.be<mailto:vimac.nollaardevol@ees.kuleuven.be> vimacnolla(a)gmail.com<mailto:vimacnolla@gmail.com>

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Job opening - PhD Candidate 'Metabolomics data evaluation for Systems Biology'
by Egon Willighagen 06 Feb '16

06 Feb '16

Dear colleagues, our group at Maastricht University is looking for a PhD candidate to work on metabolomics data analysis. Full information can be found at: https://www.academictransfer.com/employer/UM/vacancy/31818/lang/en/ Please forward this information to anyone who might be interested. Best regards, -- E.L. Willighagen Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ORCID: 0000-0001-7542-0286 ImpactStory: https://impactstory.org/EgonWillighagen

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Position at Unit of Animal Genomics (Liège, Belgium)
by Tom Druet 05 Feb '16

05 Feb '16

The Unit of Animal Genomics (Liège, Belgium) and the Walloon Breeders Association invite applications for a position to implement genomic selection in Belgian Blue Beef cattle. The Unit of Animal Genomics (http://www.giga.ulg.ac.be/cms/c_20639/fr/unit-of-animal-genomics-home) under the supervision of Prof Michel Georges, focuses on the forward genetic dissection of Mendelian and complex traits in domestic animals and humans. One of the key projects of the group is the development of approaches for the utilization of molecular information in livestock breeding, including genomic selection and transgenics. The lab is based in the Interdisciplinary Cluster of Applied Genoproteomics (GIGA-Research) at the University of Liège in Belgium (http://www.giga.ulg.ac.be <http://www.giga.ulg.ac.be/>). The researcher will join our team to implement a genomic selection program in the Belgian Blue Beef cattle breed, whose animals are famous for their exceptional muscular development referred to as « double-muscling ». The main responsibility will be the development of a new evaluation model for all traits recorded on farm. In addition, he will explore solutions to improve the accuracy of genome-enabled predictions through the development of statistical models or through integration of information obtained through whole-genome sequencing (causative or functional variants). The successful candidate will have access to high-density genotyping and whole-genome sequencing data in addition to phenotypes for a large serie of traits. The candidates should have good skills and strong interest in statistical modeling and programming. A background in quantitative genetics is an asset. Experience in genetic and genomic evaluation and in animal breeding would be desirable. The work will be performed in an international environment with communication in English. Applications, including a C.V., a letter of interest in the position and a list of three referees (with contact information) should be adressed per e-mail to : tom.druet(a)ulg.ac.be Dr Tom Druet Unit of Animal Genomics GIGA-Research and Faculty of Veterinary Medicine University of Liège Belgium The position remains open until a good candidate is identified.

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INSTRUCT practical course on advanced methods for the integration of diverse structural data with NMR data
by Alexandre Bonvin 04 Feb '16

04 Feb '16

INSTRUCT practical course Advanced methods for the integration of diverse structural data with NMR data – 2nd Edition See the online course page at: http://www.bonvinlab.org/education/INSTRUCT-practical-course/ Aims of the course The course aims at training young researchers in the combined use of NMR data with other structural biology techniques, such as SAXS, X-ray diffraction or Cryo-EM in order to understand and rationalize the structural and dynamical properties of macromolecular systems. In addition, this course will introduce and make extensive use of user-friendly e-science portals to facilitate the adoption of the methods and techniques by the students in their everyday work. This INSTRUCT <http://www.structuralbiology.eu/> course will provide lectures describing the basics of the methods applied and hands-on training with the intuitive, web-based services of the WeNMR <http://www.wenmr.eu/> infrastructure, in collaboration with the MoBrain <http://mobrain.egi.eu/> Competence Center, the West-Life <http://www.west-life.eu/> VRE and the BioExcel <http://www.bioexcel.eu/> center of excellence H2020 EU projects, with the support of SURFSara <https://www.surf.nl/en/about-surf/subsidiaries/surfsara/>, which is part of the MoBrain CC and is supporting us in the organisation of this course. The hands-on sessions will allow the students to try the methods on either pre-packaged or their own research data. The course will address state-of-the-art tools and facilities. Participants will be selected among all applicants taking into account the following criteria: previous experience in the field of biomolecular NMR and structure biology; experience in computational aspects of structural biology; gender balance; relevance of current research to the course contents. Location and dates Event Date: 11th Apr 2016 to 15th Apr 2016 Location: SURF Offices Hoog Overborch (Hoog Catharijne), Moreelsepark 48, 3511 EP Utrecht, The NetherlandsPadualaan 8 Directions <https://www.google.nl/maps/place/SURF/@52.0891266,5.1113904,17z/data=!3m1!4…> Plan you travel within NL <http://9292.nl/en> The course will start on Monday afternoon April 11th and run until lunch time on Friday April 15th, allowing for arrival and departure in the morning/afternoon of the first and last days. Utrecht can easily be reached from various airports: Several low-cost companies fly into Amsterdam Schiphol <http://www.schiphol.nl/>, Rotterdam <http://www.rotterdamthehagueairport.nl/en/> or Eindhoven <http://www.eindhovenairport.com/en/> airports, which are all connected by direct and fast trains <http://www.ns.nl/en> to Utrecht (between half an hour to one hour travel time). The SURF location <https://www.google.nl/maps/place/SURF/@52.0891266,5.1113904,17z/data=!3m1!4…> is very close to Utrecht central station. Application procedure: Applicants should send to the lead contact (see below) by email a short CV and letter of motivation explaining how they will benefit from attending this course. The deadline for applying is set to February 15th, 2016. Accepted applicants will be notified by March 1st, 2016. Lead contact Prof. Dr. Alexandre M.J.J. Bonvin – a.m.j.j.bonvin(a)uu.nl Number of participants: 20 Course programme The course will start in the afternoon of April 11th at 13:00 and end at 12:00 on April 15th. Lunch will be provided for all days except the Monday. A detailed programme will be provided at a later stage. April 11 (room 3.1): MS and solution NMR Morning: arrival 13:00-13:10 Welcome + intro (Bonvin) 13:10-13:30 Short intro to HPC/HTC infrastructure and services (SURFSara) 13:30-15:00 Heck: Characterization of large assemblies by mass spectrometry 15:00-15:30 coffee break 15:30-17:00 Boelens: Characterization of macromolecular assemblies by solution NMR April 12 (room 3.3): NMR-based protein structure refinement + integration with SAXS 9:00-10:45: Parigi: Paramagnetic NMR data and integration of SAXS and NMR data for the analysis of protein structure/dynamics 10:45-11:15: coffee break 11:15:13:00: Rosato: Molecular dynamics for NMR-based protein structure refinement 13:00:13:45: Lunch 13:45-17:00: AMPS-NMR + FANTEN + MAXOCC computer practicals (Rosato / Parigi) April 13 (room 3.3): Cryo-EM / Xray 9:00-10:45: Gros: Characterization of macromolecular complexes by X-Ray crystallography and cryo-EM 10:45-11:15: coffee break 11:15-13:00: Carazo: Cryo-EM analysis of biomolecular assemblies 13:00:13:45: Lunch 13:45:17:00: Cyro-EM computer practical (Jose Miguel de la Rosa) Evening: workshop dinner April 14 (room 4.1): Integrative modelling 9:00-10:45: Bonvin: Integrative modelling of biomolecular complexes by docking 10:45-11:15: coffee break 11:15-13:00: Bonvin: Integrative modelling of biomolecular complexes by docking 13:00:13:45: Lunch 13:45:17:00: HADDOCK computer practical (Bonvin + local assistant) April 15 (room 3.3): Solid state NMR lecture + open discussion / question and answers 9:00-10:45: Baldus: Characterization of macromolecular assemblies by solid-state NM 10:45-11:15: coffee break 11:15-12:15: Open discussion / question and answers 12:15:13:00: Lunch Departure Note that participants are required to bring their own laptop for the practicals, ideally with applications allowing remote ssh access and also VirtualBox installed to allow for running Virtual Machines that will be provided to the participants so that the students can take them back with them for further analysis/use back home. We will also make use of SURFSara cloud resources for the practicals. Case studies will be provided via the web for re-examination also at the home lab. Lecturers: Alexandre Bonvin <http://www.uu.nl/staff/amjjbonvin> (Bijvoet/Instruct-NL) Albert Heck <http://www.uu.nl/staff/AJRHeck> (Bijvoet/Instruct-NL) Piet Gros <http://www.uu.nl/staff/PGros> (Bijvoet/Instruct-NL) Rolf Boelens <http://www.uu.nl/staff/RBoelens> (Bijvoet/Instruct-NL) Marc Baldus <http://www.uu.nl/staff/MBaldus> (Bijvoet/Instruct-NL) Antonio Rosato <http://www.cerm.unifi.it/people/antonio-rosato> (CERM/INSTRUCT-IT) Giacomo Parigi <http://www.cerm.unifi.it/people/giacomo-parigi> (CERM/INSTRUCT-IT) José Maria Carazo <http://biocomp.cnb.csic.es/carazo> (I2PC) Costs: 100 euros for participants from Instruct countries (check here <https://www.structuralbiology.eu/resources/countries>), 300 euros for others. The registration fee covers lunches and coffee breaks and the course dinner. Travel and lodging are not included. Housing information: A list of hotels, hostels and bed and breakfast possibilities in Utrecht can be downloaded here <http://www.bonvinlab.org/docs/Hotels-Utrecht-Nov2015.pdf>. Participants are responsible for arranging their own housing. --------------------------------------------------------------------------------------------------------------------------- Dr. Alexandre M.J.J Bonvin | Professor of Computational Structural Biology Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands Phone: +31-30-2533859 / 2652 | Fax: +31-30-2537623 Email: a.m.j.j.bonvin(a)uu.nl http://www.uu.nl/staff/AMJJBonvin | http://www.bonvinlab.org ---------------------------------------------------------------------------------------------------------------------------

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BioSB 2016 - Call for abstracts & registration open!
by Femke Francissen 04 Feb '16

04 Feb '16

*Dutch Bioinformatics & Systems Biology Conference 2016 (BioSB 2016)* Date: April 19 / 20, 2016 Venue: Congrescentrum De Werelt, Lunteren, NL Conference website: http://www.aanmelder.nl/biosb2016 *Call for abstracts* Abstract submission for the BioSB 2016 conference is now open. You can submit an abstract for the following topics/sessions: - Gene regulation - Genotype/phenotype & disease - Industrial applications & synthetic biology - Metabolomics - Modeling - Networks & data integration - NGS data analysis - Proteomics - Statistics - Systems medicine - Infrastructure (ELIXIR-ISBE track) - Metagenomics - Structural bioinformatics (NSBM) You can submit an abstract for a lecture in one of the sessions, a poster presentation or a poster/demo. Find out here how to submit your abstract <https://www.aanmelder.nl/biosb2016/wiki/154972/abstract%20submission>. *Keydates* - Abstract submission deadline for oral presentations: March 1, 2016 - Notification date oral presentations: March 22, 2016 - Abstract submission deadline for posters: April 14, 2016 *Our keynote speakers* Our confirmed keynote speakers for the conference are: - *Mick Watson*, Director of ARK-Genomics, The Roslin Institute, R(D)SVS, University of Edinburgh. - *Jasmin Fisher*, Senior Researcher in the Programming Principles and Tools group at Microsoft Research Cambridge - *Jonathan Karr*, Fellow, Institute and Department for Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai, New York - *Sander Tans*, Groupleader, FOM-Institute for Atomic and Molecular Physics (AMOLF), Amsterdam - *Adriano Henney *(After Dinner Keynote Speaker), Executive director of the VHP Institute (Virtual Physiological Human Institute for Integrative Biomedical Research), Leuven, Belgium *Call for nominations: BioSB Young Investigator Award 2016 * During the BioSB 2016 on April 19, we will present the BioSB Young Investigator Award 2016. The winner will receive a prize of 500 Euros sponsored by the BioSB research school and will present an honorary lecture. Read more about the criteria and how to nominate a candidate <https://www.aanmelder.nl/biosb2016/wiki/164489/biosb%20young%20investigator…>. Submission deadline: March 15, 2016. *BioSB PhD retreat* The Young Computational Biologists are pleased to invite you to the BioSB PhD retreat 2016 on April 18. Like previous years the retreat will be hosted in Lunteren, directly preceding the BioSB conference. The retreat provides you with the opportunity to present your research to fellow students and young professionals. In the evening there will be a dinner in Lunteren, followed by a social activity, which allows you to network with fellow young systems biologists and bioinformaticians. Read more <https://www.aanmelder.nl/biosb2016/wiki/154925/biosb%20phd%20retreat> *Our sponsors* - DSM - Utrecht Bioinformatics Center (UBC) - Keygene NV - Wageningen UR *Conference updates* More information about the conference programme will follow soon! You can find the latest conference updates at the conference website. Regular updates will also be sent via the BioSB mailing list. Contact: Femke Francissen, community manager BioSB, email: femke.francissen(a)biosb.nl ** **

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Job opening - Bioinformatician at CHU Liège
by Stephane Wenric 01 Feb '16

01 Feb '16

Dear colleagues, The genetics department at the university hospital of Liège is looking for a full-time bioinformatician. More details can be found in the attached document. Please forward this information to anyone who might be interested. Best regards, Stephane Wenric -- Stephane Wenric, Ir PhD candidate Human Genetics GIGA +2, CHU, Sart Tilman Liège Belgium 04 366 47 20

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Job opening - Programmer/Bioinformatician for SILVA
by Katrijn Vannerum 28 Jan '16

28 Jan '16

-------- Doorgestuurd bericht -------- Onderwerp: [straininfo] Job opening - Programmer/Bioinformatician for SILVA wanted! Datum: Thu, 28 Jan 2016 08:59:24 +0100 Van: Frank Oliver Glöckner <f.gloeckner(a)jacobs-university.de><mailto:f.gloeckner@jacobs-university.de> Antwoord-naar: straininfo(a)lists.ugent.be<mailto:straininfo@lists.ugent.be>, Frank Oliver Glöckner <f.gloeckner(a)jacobs-university.de><mailto:f.gloeckner@jacobs-university.de> Organisatie: Jacobs University Bremen gGmbH Dear Colleagues, the SILVA Team is searching for a full time Programmer/Bioinformatician for 3 years funded by the DFG. More information can be found at www.arb-silva.de/jobs/<http://www.arb-silva.de/jobs/> Please forward this information to anyone who might be interested. Many thanks Frank Oliver Glöckner -- Prof. Dr. Frank Oliver Glöckner Head of the Microbial Genomics and Bioinformatics Research Group Max Planck Institute for Marine Microbiology Jacobs University Bremen gGmbH E-mail: fog(a)mpi-bremen.de<mailto:fog@mpi-bremen.de> Address: MPI for Marine Microbiology Celsiusstrasse 1 28359 Bremen MPI: +49 (0) 421 2028 970 Jacobs: +49 (0) 421 200 3167 Fax: +49 (0) 421 2028 580 Mobile: +49 (0) 172 82 70 191 WWW: http://www.microbial-genomics.de http://www.ribocon.com http://www.microb3.eu Submit your next paper to: http://www.journals.elsevier.com/marine-genomics/

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EMBO courses on computational biology and biological interactions
by Roland KRAUSE 26 Jan '16

26 Jan '16

There are two EMBO courses nteresting to early stage bioinformaticians. EMBO Practical Course on computational analysis of protein-protein interactions: sequences, networks and diseases 30 May-4th June 2016<http://airmail.calendar/2016-05-30%2012:00:00%20GMT+2> in Budapest, Hungary organized by Zsuzsanna Dosztányi with a strong support from the EMBL as well. http://events.embo.org/16-protein-protein/ EMBO Practical Course on Computational Biology, ran at the EMBL by in Heidelberg by a group around Peer Bork (EMBL) 19 - 23 Jun 2016 http://www.embl.de/training/events/2016/COM16-01/ (I am an organizer of the second course) Best regards, Roland -- Roland Krause Luxembourg Centre for Systems Biomedicine University of Luxembourg Campus Belval 7, avenue des Hauts-Fourneaux L-4362 Esch-sur-Alzette roland.krause(a)uni.lu<mailto:roland.krause@uni.lu> +352 466644<tel://+352%20466644> 6267

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postdoc in Computational structure based drug design
by Martijn.Huijnen＠radboudumc.nl 26 Jan '16

26 Jan '16

Postdoctoral position in Computational structure based drug design at the CMBI, Radboud University Medical Centre Job description Project title: 3D-e-Chem: Integrated eScience workflow to translate biological and chemical data into structure-based protein-ligand polypharmacology prediction. Efficient exploitation of the massive amount of modern-day life science data requires a integrative approach that only eScience technologies can provide. The 3D-e-Chem project<https://www.esciencecenter.nl/project/3d-e-chem> will design a KNIME-based workflow for the integration of chemical and biological data for the prediction of polypharmacological action of drug molecules (ligands) on multiple proteins.This project will combine the strengths of the CMBI<http://www.cmbi.ru.nl> on protein structures together with the knowledge on ligand screening data and its interpretation from the department of Division of Medicinal Chemistry at VU University<http://www.chem.vu.nl/en/research/division-of-medicinal-chemistry/index.aspx> to develop novel chem- and bioinformatic workflows together with the Netherlands eScience Center in Amsterdam<https://www.esciencecenter.nl/> that improve the interpretation and prediction of polypharmacological effects. Key words: Chem- and Bioinformatics, protein structures, polypharmacology, workflow development. Postdoc 'Computational structure based drug design' * Center for Molecular and Biomolecular Informatics * Scale 10.4: max. € 43570 gross income per year at full employment (incl. vacation bonus and end of year payments) * 36 - 36 hours per week * Published: 26-01-2016 * Closing date: 08-02-2016 * Contract: Temporary, 1 year with possible extension Profile candidate * PhD in Molecular Sciences, Bioinformatics, Computer Science, Pharmacy or equivalent * Experience in Linux, Python, Java * Expertise in computational structure based drug design * Experience with KNIME or Pipeline pilot are a plus * Affinity with fundamental research related to human disease * Good communication skills * Ambition * Ability to work in an interdisciplinary team Organization The Computational Discovery and Design group is part of the Center for Molecular and Biomolecular Informatics (www.cmbi.ru.nl) and located within the Radboud Institute for Molecular Life Sciences<http://www.rimls.nl/>. Working at Radboudumc Radboudumc aims to be at the forefront of the development of innovative, sustainable and affordable healthcare. Our mission is 'to have a significant impact on healthcare'. We believe we can achieve that by providing excellent quality, participatory and personalized healthcare, operational excellence and by working together in sustainable networks. The starting point for this is patients and their quality of life. Throughout all this, patient care, research and education go hand in hand. To realize our mission, we are searching for colleagues who want to take on this challenge with us; employees who are excellent in their field of expertise and give it their all by pushing boundaries and providing 'that little bit more'. At Radboudumc, you gain the confidence, receive and take responsibility to successfully make these changes. For the best patient care and the best future of healthcare. Comments and contact information Conditions of employment * Employment will initially be for one year, with possible extension * Salary starts in scale 10.4: € 3122 gross per month, up to a maximum of € 4111 gross per year, depending on experience. You will also receive an additional vacation bonus (8% per year) and end of year payments (8.3% per year). Application Include your curriculum vitae, description of research experience and names and addresses of 2 references in your application. Information Additional information about the vacancy can be obtained from dr. Tina Ritschel, Tina.Ritschel(a)radboudumc.nl<mailto:Tina.Ritschel@radboudumc.nl>. (This e-mail address is to be used for information purposes only. Use the ‘Apply’ button to apply for the position.) Please apply before February 9, 2016. Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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Cytomine open-source software for collaborative analysis of multi-gigapixel bioimages
by Raphael.Maree. 26 Jan '16

26 Jan '16

Dear colleagues, After five years of research and development at the University of Liège, Belgium, I would like to draw your attention to the release under an open source licence of our Cytomine software (http://www.cytomine.be/) for collaborative analysis of multi-gigapixel imaging data. Although our initial focus was on biomedical research with cytology and histology whole-slide images, this is a generic software that might be useful for other types of imaging data from various fields (e.g. botany, geology, astronomy, environmental biology, ...). Based on modern web, database, and machine learning algorithms, it has been designed to foster active and distributed collaboration between computer vision/machine learning researchers and other scientists dealing with very large images. Among other functionalities, it implements: - a web user interface to explore (à la Google Maps) very large images using pyramidal formats; - web user interfaces to efficiently and collaboratively build large semantic ground-truth datasets from multi-gigapixel images; - a multi-thread implementation of our tree-based learning recognition algorithms (for content-based image retrieval [MIR2010], object classification [PatternRecognitionLetters2016], image segmentation [VISAPP2009], and landmark detection; - web proofreading tools to edit (ours or yours) algorithm predictions; - a RESTful API and software templating mechanisms to easily import/export data with your own software and extend it to your own purposes; - Python and Java clients to easily access and extend the system. Our paper in Bioinformatics (open access): http://bioinformatics.oxfordjournals.org/content/early/2016/01/09/bioinform… Other related papers: http://www.cytomine.be/#publications Read more (documentation, source code, etc.) on: http://www.cytomine.be/ Best regards, Raphaël. -- Raphaël Marée (PhD) http://www.montefiore.ulg.ac.be/~maree/ http://www.cytomine.be/ Tél.: +32 4 366 26 44 | Fax: +32 4 366 29 84

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