March 2017 - 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

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Aphea.Bio is recruiting
by Jolien Van Impe 31 Mar '17

31 Mar '17

Dear Aphea.Bio is a new start-up company from VIB. Aphea.Bio is now recruiting: * Database/IT Manager<http://www.vib.be/en/jobs/Pages/Aphea.Bio---Database-IT-Manager.aspx> * Field Trial Manager - Agronomist<http://www.vib.be/en/jobs/Pages/Aphea.Bio---Field-Trial-Manager---Agronomis…> * Plant Pathologist - Physiologist<http://www.vib.be/en/jobs/Pages/Aphea.Bio---Plant-Pathologist---Physiologis…> Best regards, Jolien Van Impe - HR Officer VIB Rijvisschestraat 120 - 9052 Ghent - Belgium Tel. +32 9 244 66 11 www.vib.be<http://www.vib.be/> [signatureFooter (002)] [KotK]<http://www.1000km.be/team/vibikers>

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HPC / cloud Linux sysopsdevops met interesse in big data DNA en RNA analyses
by Patrick Deelen 31 Mar '17

31 Mar '17

Werkomgeving We zoeken een ervaren Linux system administrator voor in het Genomics Coordination Center (GCC), de ‘big data’ research & service hub van het Universitair Medisch Centrum Groningen, afdeling Genetica. Het zijn spannende tijden met biotechnologie die terabytes aan Biobank, DNA-, gen-, mutatie-, eiwit- moleculaire- en fenotype profielen oplevert. Dit biedt ongekende mogelijkheden voor het voorspellen van ziekte en gezondheid, maar ook grote uitdagingen in het delen, (her)gebruiken en analyseren van al deze nieuwe, maar vaak gevoelige data. Wij werken daarom met 25 collega’s in diverse lokale, nationale en EU projecten aan slimme software om mensgebonden onderzoek te versnellen en zorg te verbeteren met open source web applicaties (zie http://github.com/molgenis) (HPC) analyse pipelines en grootschalige e-infrastructuur (cluster, storage, cloud). Op deze manier draagt GCC in belangrijke mate bij aan het FAIR maken van research data en wetenschappelijk onderzoek. Hierbij hanteren we een agile aanpak. Functiebeschrijving Wij zoeken een ervaren Linux sysops of devops voor het functioneel beheer van onze vier HPC rekenclusters (30 nodes, 1000+ cpu, 1 petabyte) en onze 8 OpenStack ‘cloud’ servers (100 VMs met onze MOLGENIS software), inclusief geautomatiseerd configuratie management, autorisatie systemen, monitoring, verbetervoorstellen en ontwerpen en inrichten van nieuwe systemen en nieuwe technologieen. Je werkt tussen een team van 6 bioinformatici met als missie geautomatiseerde pipelines voor grootschalige DNA en RNA data analyse ten behoeve van onderzoek en diagnostiek, en 6 software engineers die webapplicaties maken voor analyse van wetenschappelijke en zorgdata. Verder werk je in nauwe samenwerking met het Centrum voor Informatie Technologie (CIT) van de Rijksuniversiteit Groningen die al onze IT faciliteiten technisch beheren en collega systeem beheerders bij UMCG en onze nationale en Europese samenwerkingspartners en heb je veel multidisciplinair contact met toponderzoekers, (bio)statistici, diagnostici en artsen. Wat vragen wij De ideale kandidaat is professioneel Linux beheerder: - met aantoonbare ervaring in cloudomgeving en/of HPC computer clusters - is communicatief vaardig, klantvriendelijk en werkt nauwkeurig - heeft goede mondelinge en schriftelijke uitdrukkingsvaardigheden - kan zowel zelfstandig als in teamverband werken - is initiatiefrijk en heeft een proactieve houding - heeft een goede beheersing van de Nederlandse en Engelse taal in woord en geschrift. We verwachten HBO of WO achtergrond. Ervaring met wetenschappelijk onderzoek of het werken in een academische omgeving is een pre. Kennis van SLURM, PBS, postgresql, R, python, virtualisatie/cloud technologie, microservice infrastructuur, configuratie management tools (ansible, puppet, easybuild, etc), container technologie (Docker), firewalls, continuous delivery, etc, is een pre. Ook achtergrond in Windows wordt gewaardeerd voor kleine hulp in onze ziekenhuisomgeving. Het UMCG voert een preventief Hepatitis B beleid. Dit kan betekenen dat u voldoende bescherming tegen Hepatitis B moet hebben opgebouwd voordat u kunt worden aangesteld. Indien nodig verzorgt het UMCG de vaccinatie. Wat bieden wij Een aanstelling voor 0.8 fte als Linux systeembeheerder in een boeiende omgeving en met ruimte om veel nieuwe kennis op te doen, voor één jaar, met een mogelijke verlenging. Uw salaris bedraagt minimaal € 2.178,- tot maximaal € 3.339,- bruto per maand (schaal 7 of 8) afhankelijk van kwalificaties en op basis van een fulltime aanstelling. Daarnaast biedt het UMCG 8% vakantietoeslag, 8,3% eindejaarsuitkering en een budget voor ontwikkeling. Arbeidsvoorwaarden conform de CAO Universitair Medische Centra (CAO-UMC). *Meer informatie* Neem voor meer informatie contact op met: dr. Pieter Neerincx, coördinator e-infrastructuur, of dr. Elisa Hoekstra, hoofd analyse team, of prof.dr. Morris Swertz, hoofd Genomics Coordination Center, via telefoon +31 (0) 50 361 7100 of e-mail: pieter.neerincx(a)gmail.com (e-mailadres niet gebruiken voor sollicitaties). SolliciterenU kunt uitsluitend reageren via het digitale sollicitatieformulier onderaan deze pagina. Solliciteren kan tot en met *11 april 2017*. Meteen na het verzenden van het digitale sollicitatieformulier wordt een ontvangstbevestiging gemaild met nadere informatie. http://www.umcg.nl/NL/UMCG/Werken_in_het_UMCG/Vacatures/Externe_vacatures/ Managementondersteuning/Paginas/HPC__cloud_Linux_ sysopsdevops_met_interesse_in_big_data_DNA_en_RNA_analyses.aspx

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Few places left on Introduction to Python for Biologists 10-14 April 2017, Edinburgh
by Bert Overduin 29 Mar '17

29 Mar '17

Dear all, We still have a few places left on our Introduction to Python for Biologists workshop, which runs from 10-14 April 2017. Cheers, Bert ********** INTRODUCTION TO PYTHON FOR BIOLOGISTS DATE: Monday 10 – Friday 14 April 2017 VENUE: The King's Buildings, The University of Edinburgh, Edinburgh, Scotland, UK CANCELLATION DEADLINE: Monday 3 April 2017 noon PLACES: 20 (first come, first served) REGISTRATION FEE: £525 (includes coffee/tea, but no lunch) INFORMATION: Bert Overduin (bert.overduin(a)ed.ac.uk) Martin Jones ( martin(a)pythonforbiologists.com) TO REGISTER: http://genomics.ed.ac.uk/services/introduction-python- biologists Python is a dynamic, readable language that is a popular platform for all types of bioinformatics work, from simple one-off scripts to large, complex software projects. This workshop is aimed at complete beginners and assumes no prior programming experience. It gives an overview of the language with an emphasis on practical problem-solving, using examples and exercises drawn from various aspects of bioinformatics work. The workshop is structured so that the parts of the language most useful for bioinformatics are introduced as early as possible, and that students can start writing plausibly-useful programs after the first few sessions. After completing the workshop, students should be in a position to (1) apply the skills they have learned to tackling problems in their own research and (2) continue their Python education in a self-directed way. "Great learning from someone with a biology background rather than computer science - meant we were on the same wavelength." (February 2016) "Brilliantly well-run. From the book; to the USB stick with all the files we need; to the topics covered; to the system of helping us one-on-one, I cannot fault this course." (February 2016) INSTRUCTORS Dr. Martin Jones (Founder, Python for Biologists) Dr. Bert Overduin (Training and Outreach Bioinformatician, Edinburgh Genomics) WORKSHOP FORMAT The workshop is delivered over ten half-day sessions. Each session consists of roughly a one hour lecture followed by two hours of practical exercises, with breaks at the organiser’s discretion. Each session uses examples and exercises that build on material from the previous one, so it’s important that students attend all sessions. A description of the sessions can be found at the bottom of this page. WHO SHOULD ATTEND This workshop is aimed at researchers and technical workers with a background in biology who want to learn programming. The syllabus has been planned with complete beginners in mind; people with previous programming experience are welcome to attend as a refresher but may find the pace a bit slow. If in doubt, take a look at the detailed session content below or drop Martin Jones or Bert Overduin an email. REQUIREMENTS Students should have enough biological/bioinformatics background to appreciate the examples and exercise problems (i.e. they should know what a protein accession number, BLAST report, and FASTA sequence is). No previous programming experience or computer skills (beyond the ability to use a text editor) are necessary. During the workshop students will use their own laptops. Instructions for any software to be installed will be sent out prior to the course. SESSION CONTENT 1. Introduction In this session I introduce the students to Python and explain what we expect them to get out of it and how learning to program can benefit their research. I explain the format of the course and take care of any housekeeping details (like coffee breaks and catering arrangements). I outline the edit-run-fix cycle of software development and talk about how to avoid common text editing errors. In this session, we also check that the computing infrastructure for the rest of the course is in place (e.g. making sure that everybody has an appropriate version of Python installed). Core concepts introduced: source code, text editors, whitespace, syntax and syntax errors, Python versions 2. Manipulating text In this session students learn to write very simple programs that produce output to the terminal, and in doing so become comfortable with editing and running Python code. This session also introduces many of the technical terms that we’ll rely on in future sessions. I run through some examples of tools for working with text and show how they work in the context of biological sequence manipulation. We also cover different types of errors and error messages, and learn how to go about fixing them methodically. Core concepts introduced: terminals, standard output, variables and naming, strings and characters, special characters, output formatting, statements, functions, methods, arguments, comments. 3. Working with files I introduce this session by talking about the importance of files in bioinformatics pipelines and workflows, and we then explore the Python interfaces for reading from and writing to files. This involves introducing the idea of types and objects, and a bit of discussion about how Python interacts with the operating system. The practical session is spent combining the techniques from session 2 with the file IO tools to create basic file- processing scripts. Core concepts introduced: objects and classes, paths and folders, relationships between variables and values, text and binary files, newlines. 4. Lists and loops A discussion of the limitations of the techniques learned in session 3 quickly reveals that flow control is required to write more sophisticated file-processing programs, and I introduce the concept of loops. We look at the way in which Python loops work, and how they can be used in a variety of contexts. We explore the use of loops and lists together to tackle some more difficult problems. Core concepts introduced: lists and arrays, blocks and indentation, variable scoping, iteration and the iteration interface, ranges. 5. Conditions I use the idea of decision-making as a way to introduce conditional tests, and outline the different building-blocks of conditions before showing how conditions can be combined in an expressive way. We look at the different ways that we can use conditions to control program flow, and how we can structure conditions to keep programs readable. Core concepts introduced: Truth and falsehood, Boolean logic, identity and equality, evaluation of statements, branching. 6. Writing functions We discuss functions that we’d like to see in Python before considering how we can add to our computational toolbox by creating our own. We examine the nuts and bolts of writing functions before looking at best-practice ways of making them usable. We also look at a couple of advanced features of Python - named arguments and defaults. Core concepts introduced: argument passing, encapsulation, data flow through a program. 7. Regular expressions I show how a range of common problems in bioinformatics can be described in terms of pattern matching, and give an overview of Pythons regex tools. We look at the building blocks of regular expressions themselves, and learn how they are a general solution to the problem of describing patterns in strings, before practising writing some specific examples of regular expressions. Core concepts introduced: domain-specific languages, modules and namespaces. 8. Dictionaries We discuss a few examples of key-value data and see how the problem of storing them is a common one across bioinformatics and programming in general. We learn about the syntax for dictionary creation and manipulation before talking about the situations in which dictionaries are a better fit that the data structures we have learned about thus far. Core concepts introduced: paired data types, hashing, key uniqueness, argument unpacking and tuples. 9. Working with the filesystem We discuss the role of Python in the context of a bioinformatics workflow, and how it is often used as a language to “glue” various other components together. We then look at the Python tools for carrying out file and directory manipulation, and for running external programs - two tasks that are often necessary in order to integrate our own programs with existing ones. Core concepts introduced: processes and subprocesses, the shell and shell utilities, program return values. 10. Final day The schedule for the final day will be set based on the progress of the course and the interests of the students. We will have time set aside for attendees to finish exercises, work on their own data, or get one-on-one help with real-world problems arising from their research. We may also use some of the time to cover more advanced topics of interest to the attendees, including BioPython, data visualisation, packaging and distributing code, and using alternative interfaces such as iPython. -- 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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Introduction to RNA-seq Data Analysis workshop 29-30 May 2017 now open for applications
by Bert Overduin 27 Mar '17

27 Mar '17

Dear all, Our first upcoming Introduction to RNA-seq Data Analysis workshop is now open for applications: http://genomics.ed.ac.uk/services/introduction-rna-seq-data-analysis A few notes: - There will be many more RNA-seq workshop this year. The first one after the 29-30 May one will be on 29-30 June 2017. Application for this one will open once application for the May one has closed. - IMPORTANT: Starting with this workshop a basic working knowledge of Linux (at the level of our "Linux for Genomics" workshop) will be a pre-requirement for the workshop, as our experience is that teaching a short intro into Linux during the workshop was often not really enough for those who had never used the command line before. - If you have applied for this workshop before but haven't been selected, please add this information to your application. With kind regards, Bert -- 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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[bioinfo] 3rd BeNeLuxFra Student Symposium : First abstracts call
by Alexander Botzki 26 Mar '17

26 Mar '17

On behalf of the Organising committee: The 3rd BeNeLuxFra Student Symposium will be held in Lille on July 6 and 7, directly following the french bioinformatics conference (JOBIM 2017). This symposium is coorganized by RSGs France, Belgium, Netherlands and Luxembourg. The program of this symposium includes contributed talk from early career scientists (Master students, PhD students, Postdoctoral researcher and engineer). We particularly encourage master students and early stage PhD students to submit an abstract. Submissions are now open. Details about the symposium and submissions are available on our website : https://jebif.fr/en/evenements/jebif-workshop/lille-jobim-2017-3eme-symposi… See you in Lille, The organizing committee -- RSG France - JeBiF Association des Jeunes Bioinformaticiens de France contact(a)jebif.fr | https://jebif.fr Twitter @JeBiF Facebook JeBiF.RSG.France

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Postdoc bioinformatics/data science - FAIR data and reproducible science
by Patrick Deelen 25 Mar '17

25 Mar '17

Working environment The postdoc will be part of the Genomics Coordination Centre (GCC), the ‘big data’ research & service hub of the University Medical Centre Groningen (UMCG), and the Franke-Swertz Lab research group ( http://systemsgenetics.nl) situated in the Genetics department of the UMCG. These are exciting times in biotechnology that are producing terabytes of Biobank, DNA, mutation, protein, molecular and phenotype profile data. This wealth of data offers unprecedented possibilities for new ways of predicting both disease and health status, but also presents big challenges in how to share, (re)use and analyse all this new, and sensitive, information. Our 25-member team is working together on diverse local, national and EU projects to produce clever software that expedites medical research and improves healthcare using open source web applications (see http://github.com/molgenis <https://github.com/molgenis>), (HPC) analysis pipelines and large-scale e-infrastructure (cluster, storage, cloud). Through these efforts the GCC contributes to the goal of making scientific research data meet FAIR (Find Able, Accessible, Interoperable, Reusable) principles. Job description We are looking for a postdoc data scientist to develop models, techniques and tools for promoting the re-use and reproducibility of scientific research in accordance with FAIR principles. In recent years, the GCC has been heavily invested in developing smart tools to integrate data using ontologies and semantic search methods (Biobank Connect, SORTA, MOLGENIS/connect) and in developing data models and data structures that promote re-use (Observ-OM, MIABIS, FAIR) and sharing of data (Beacons, CafeVariome). Our work has produced many top-quality MOLGENIS open source software applications, and writing the publications about these tools is part of this postdoc. We expect that this research line will develop further through our (inter)national collaborations with institutes in the BBMRI, CORBEL, ELIXIR, DTL and RD-connect networks, and in cooperation with the six-person MOLGENIS open source team and 20-person Franke-Swertz Lab to produce widely-applicable reusable e-infrastructure, particularly for the life sciences and personalized medicine. What do we need The ideal candidate is a PhD in (Bio)informatics or Data Science who: - Has a passion for data modelling/ontologies/integration/re-use - Communicates easily with colleagues and collaborators, primarily in English - Can write publications about our methods, software and applications - Can implement methods in Java services with Javascript user interfaces - Can test these in practice in the context of large-scale ‘top-level’ biomedical research - Collaborates well in international consortia and with researchers from other disciplines - Is prepared to travel Experience in large-scale biomedical studies involving Biobanks, NGS, molecular experiments and phenotype data and with the resulting bioinformatic data integration and (HPC) analysis pipelines, as well as knowledge of, for example, semantic web/linked data, REST/JSON-LD, linked data fragments, standards in biosharing.org, machine learning and biomedical ontologies is a plus. The UMCG has a preventive Hepatitis B policy. You may be required to build up sufficient protection against Hepatitis B before you can be appointed. Vaccination is provided by the UMCG if necessary. What do we offer An appointment of 0.8-1.0 FTE as a postdoctoral fellow for two years (with a possible extension), embedding in a dynamic department of top genetic researchers (including a Spinoza prize winner), a large group of programmers to publish with, a service desk that assists a wide range of researchers, and the opportunity to work both in Europe and internationally. Your salary will be a maximum of € 4.152,- gross per month (scale 10), depending on your qualifications and relevant experience, based on a full-time appointment. In addition, the UMCG will offer you 8% holiday pay, an 8.3% end-of-year bonus and a development budget. The terms of employment comply with the Collective Labour Agreement for Medical Centers (CAO-UMC). *For more information please contact:* Prof. Morris Swertz, Head of the Genomics Coordination Centre, by telephone +31 (0) 50 361 7100 or email: m.a.swertz(a)rug.nl (please do not use for applications) S. Scholtens, manager, telephone +31 (0)50 361 1087 op email: s.scholtens(a)umcg.nl (please do not use for applications) Applying for a job http://www.umcg.nl/NL/UMCG/Werken_in_het_UMCG/Vacatures/Externe_vacatures/M…

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The Idea DREAM Challenge is entering its collaborative phase
by Alexander Botzki 24 Mar '17

24 Mar '17

From: Chloe-Agathe Azencott [mailto:chloe-agathe.azencott@mines-paristech.fr] Sent: 24 March 2017 15:39 Subject: The Idea DREAM Challenge is entering its collaborative phase Dear colleagues, The Idea DREAM Challenge has entered its public discussion stage. To date, researchers from the DREAM Community have proposed exciting biological or medical questions, together with appropriate models to serve as strong baselines for new DREAM challenges, and the data they would need to drive their project all the way to an important scientific discovery. We have selected seven most promising of these ideas, and they are now up for discussion! We invite you to help create the next DREAM Challenge by joining us on https://www.synapse.org/#!Synapse:syn5659209/wiki/414654 to learn more about these ideas and debate them on their respective discussion threads. Your input is the key to the success of this innovative process of doing computational research. Please spread the word! The public discussion phase will close on *April 30th, 2017*. Sincerely, Anna Goldenberg and Chloe Azencott, on behalf of the Idea DREAM Challenge Organizers

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PhD position: Amsterdam and Delft, The Netherlands
by Lodewyk Wessels 24 Mar '17

24 Mar '17

PhD position: ‘TRANSFER LEARNING FOR PERSONALISED CANCER TREATMENT’ COLLABORATING INSTITUTES Technical University of Delft (TUDelft), Delft VU University Medical Center, VUMC, Amsterdam and The Netherlands Cancer Institute (NKI), Amsterdam. PROJECT DESCRIPTION How can we find better diagnostic markers for early stages of cancer? How can we better predict which therapy is best for which patient? The aim of the ‘COMPUTE CANCER’ project is to develop a novel methodological and computational framework that improves the selection of diagnostic and predictive biomarkers from cancer genomics data. Our strategy is to adapt known prediction methods (e.g. penalized regression, random forests) to allow for the inclusion of ‘co-data’: auxiliary information on the genomic variables derived from other data sources. Examples include p-values from related external studies or genomic and drug response data from cancer cell lines. INTERDISCIPLINARY COLLABORATION The group of Mark van de Wiel (Biostatistics, VUMC) will focus on developing ‘weighted learners’, where the challenge is to determine weights from co-data in an automatic and objective way. The groups of Marco Loog, Marcel Reinders and Lodewyk Wessels (TUDelft and NKI) will develop transfer learning approaches that exploit large cell line response data sets to predict therapy response in tumors. We will focus on response to chemotherapy in neo-adjuvant breast cancer and metastatic colorectal cancer. The project is embedded within broad oncological collaborations within the VUMC as well as the NKI. The successful candidate will be employed at the TUDelft and will spend at least two days per week at the NKI. Regular meetings between project partners and oncologists will be held to generate sufficient cohesion and momentum. CANDIDATE PROFILE We are seeking a highly motivated PhD candidate with: • A degree in bioinformatics, computer science or a related discipline • Experience in statistics, machine learning and/or pattern recognition • Proficiency in bioinformatics programming languages (e.g. R, Python) • Good cross-disciplinary collaborative and communication skills • Experience in analysing high-throughput molecular data is a plus • Experience in cancer biology and clinical applications is a plus INTERESTED? Please send CV and motivation letter to Magali Michaut (m.michaut(a)nki.nl <mailto:m.michaut@nki.nl>) & Lodewyk Wessels (l.wessels(a)nki.nl <mailto:l.wessels@nki.nl>). Please include the names and contact information of at least two references. DEADLINE 24 April 2017

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SCS2017 Prague announcement
by Julien Fumey 23 Mar '17

23 Mar '17

The ISCB Student Council is excited to announce the 13th Student Council Symposium (SCS) which will be hosted, preceding ISMB/ECCB 2017, at the Prague Convention Centre in Czech Republic on July 21, 2017. The SCS is an annual student-organised event, with a goal to highlight latest research from a wide variety of subfields of bioinformatics and computational biology. This year, SCS 2017 will bring an exciting program that includes keynote talks, contributed talks, poster session, and a social event in the evening. The symposium is a great opportunity to present your research to an international audience, learn about latest advances, and build a worldwide scientific network. We are pleased to announce our first keynote speaker, Professor Christine Orengo from University College London (UCL). Prof. Orengo is an expert in bioinformatics and research group, at UCL, focuses on understanding how protein domains are conserved over evolutionary time and developing methods to predict protein function. Please visit our website http://scs2017.iscbsc.org/scs2017-keynotes to read more. Abstract submission for SCS 2017 is currently open! We encourage you to visit symposium.iscbsc.org to submit your research today! All abstracts will be subjected to peer-review. Travel fellowship call will open soon for all presenting authors (oral and poster). Important Dates: Abstract submission deadline: April 17, 2017 Abstract notification of acceptance: May 22, 2017 Late Poster Submission Deadline: April 30, 2017 You can help us spread the word by using the hashtag #SCS17 on social media. We look forward to welcome you in Prague this summer! Julien Fumey (Chair) and Mehedi Hassan (Co-chair)

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