- BBClist - maillist.psb.ugent.be

Open PhD and Postdocs positions in Vienna
by Anna.Santaella＠radboudumc.nl 07 Apr '17

07 Apr '17

Hi, A friend working in Vienna inform me about PhD and Postdoc positions in Bioinformatics in his lab. Please, forward these information to whom might be interested. Kind regards, Anna Santaella PhD student Radboud university medical center P.O. Box 9101, 6500 HB Nijmegen, The Netherlands Geert Grooteplein 10 (route 830) Anna.Santaella(a)radboudumc.nl Van: Serebreni,Leonid [mailto:leonid.serebreni@imp.ac.at] Verzonden: vrijdag 7 april 2017 10:19 Aan: Santaella Tortós-Sala, Anna Onderwerp: Fwd: bioinformatician ads Hi Anna, Our lab is looking for new PhD, Postdoc and staff bioinformaticians. Could you please circulate these ads in your institute? Many thanks! Leo > > 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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Bioinformatics postdoctoral position in Brussels -IB2
by Tom Lenaerts 07 Apr '17

07 Apr '17

Postdoctoral Bioinformatics position Interuniversity Institute for Bioinformatics in Brussels (IB2), ULB - VUB, Brussels, Belgium Position description The Brussels Universities (Université Libre de Bruxelles (ULB) and Vrije Universiteit Brussel (VUB)), are seeking candidates for a postdoctoral positions for the project BRIGHTanalysis, which targets the development of predictive methods and online tools for the study of oligogenic diseases. The successful candidates will participate in the Interuniversity Institute of Bioinformatics in Brussels, an institute that brings together the science, engineering and medical faculties of VUB and ULB in a collaborative and open atmosphere. The focus of the (IB)2 is on interdisciplinary research, with expertise in machine learning, big data, rare diseases, oligenic disorders, network analysis, genome analysis, metagenomics and structural bioinformatics. Located in heart of Brussels, both universities are known for quality research through their prestigious affiliate research centers and world-renowned faculty. Brussels, the capital of Belgium and the European Union, is a cosmopolitan city famous for its picturesque squares and buildings, serene parks and gardens and a very vibrant cultural life spiced up by many international languages. *Postdoctoral position in Data Science and Oligogenic diseases: The vacancy available (to be filled asap) offers a position of at least two years. The researcher is expected to carry out fundamental data science and bioinformatics research as well as service development, which is an essential part of the BRIGHTanalysis project that is funding the position. This project’s goal is to develop novel ICT tools for the analysis and identification of variant combinations in diseases related to cephalic, neurodevelopmental or cardiac disorders. Qualifications Applicants for the postdoctoral position should have a recent PhD on a subject related to data science, machine learning or computational statistics. Experience in the analysis of exome data and the prediction/ranking of genes and variants as well as the development of web services will be an asset. Applicants are expected to have strong programming skills, the ability to work independently, strong interpersonal skills, good writing, oral communication and project management skills. Upon offer of a position in IB2, the candidates who are non-EU citizens are required to obtain an appropriate long-term Schengen visa; further information is available from their nearest Belgian embassy. Deadline Applicants are encouraged to apply as soon as possible as the position will remain open until filled by a suitable candidate. Starting date of the contract no later than June 1., 2017. Contact Candidates are invited to send a motivation letter, the contact details for 2 references, CV (Europass format!)+ with the detailed list of publications and a research statement in .pdf format by email to tlenaert(a)ulb.ac.be. The subject field of your email must include IB2-JOB: BRIGHTanalysis position. Equal Opportunity Employer ULB is an equal opportunity employer and is committed to employing more handicapped individuals and especially encourages them to apply. ULB wishes to increase the proportion of women in areas in which they are underrepresented. Women are strongly encouraged to apply.

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Few places left on Introduction to Linux and Workflows for Biologists 24-28 April 2017, Edinburgh
by Bert Overduin 06 Apr '17

06 Apr '17

Dear all, We still have a few places left on our new Introduction to Linux and Workflows for Biologists workshop, which runs from 24-28 April 2017. Cheers, Bert ********** INTRODUCTION TO LINUX AND WORKFLOWS FOR BIOLOGISTS DATE: Monday 24 – Friday 28 April 2017 VENUE: The King's Buildings, The University of Edinburgh, Edinburgh, Scotland, UK REGISTRATION DEADLINE: Monday 10 April 2017 noon CANCELLATION DEADLINE: Monday 17 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-linux-and- workflows-biologists Most high-throughput bioinformatics work these days takes place on the Linux command line. The programs which do the majority of the computational heavy lifting — genome assemblers, read mappers, and annotation tools — are designed to work best when used with a command-line interface. Because the command line can be an intimidating environment, many biologists learn the bare minimum needed to get their analysis tools working. This means that they miss out on the power of Linux to customise their environment and automate many parts of the bioinformatics workflow. This course will introduce the Linux command line environment from scratch and teach students how to make the most of its tools to achieve a high level of productivity when working with biological data. INSTRUCTORS Dr. Martin Jones (Founder, Python for Biologists) Dr. Bert Overduin (Training and Outreach Bioinformatician, Edinburgh Genomics) WORKSHOP FORMAT The workshop is delivered over nine half-day sessions (see the detailed curriculum below). Each session consists of roughly a one hour lecture followed by two hours of practical exercises, with breaks at the organiser’s discretion. There will also be plenty of time for students to discuss their own problems and data. WHO SHOULD ATTEND This workshop is aimed at researchers and technical workers with a background in biology who want to learn to use the Linux operating system and the command line environment. REQUIREMENTS Students should have enough biological background to appreciate the examples and exercise problems, and have at least some interest in working with DNA sequence data. No previous computer skills are necessary, as we will introduce Linux starting with the very basics. Students need to bring a laptop with a Linux virtual machine installed (we will distribute instructions for downloading and installing the virtual machine before the course starts). SESSION CONTENT 1. The design of Linux In the first session we briefly cover the design of Linux: how is it different from Windows/OSX and how is it best used? We’ll then jump straight onto the command line and learn about the layout of the Linux filesystem and how to navigate it. We’ll describe Linux’s file permission system (which often trips up beginners), how paths work, and how we actually run programs on the command line. We’ll learn a few tricks for using the command line more efficiently, and how to deal with programs that are misbehaving. We’ll finish this session by looking at the built in help system and how to read and interpret manual pages. 2. System management We’ll first look at a few command line tools for monitoring the status of the system and keeping track of what’s happening to processor power, memory, and disk space. We’ll go over the process of installing new software from the built in repositories (which is easy) and from source code downloads (which is trickier). We’ll also introduce some tools for benchmarking software (measuring the time/memory requirements of processing large datasets). 3. Manipulating tabular data Many data types we want to work with in bioinformatics are stored as tabular plain text files, and here we learn all about manipulating tabular data on the command line. We’ll start with simple things like extracting columns, filtering and sorting, searching for text before moving on to more complex tasks like searching for duplicated values, summarizing large files, and combining simple tools into long commands. 4. Constructing pipelines In this session we will look at the various tools Linux has for constructing pipelines out of individual commands. Aliases, shell redirection, pipes, and shell scripting will all be introduced here. We’ll also look at a couple of specific tools to help with running tools on multiple processors, and for monitoring the progress of long running tasks. 5. EMBOSS EMBOSS is a suite of bioinformatics command-line tools explicitly designed to work in the Linux paradigm. We’ll get an overview of the different sequence data formats that we might expect to work with, and put what we learned about shell scripting to biological use by building a pipeline to compare codon usage across two collections of DNA sequences. 6. Using a Linux server Often in bioinformatics we’ll be working on a Linux server rather than our own computer— typically because we need access to more computing power, or to specialized tools and datasets. In this session we’ll learn how to connect to a Linux server and how to manage sessions. We’ll also consider the various ways of moving data to and from a server from your own computer, and finish with a discussion of the considerations we have to make when working on a shared computer. 7. Combining methods In the next two sessions — i.e. one full day — we’ll put everything we have learned together and implement a workflow for next-gen sequence analysis. In this first session we’ll carry out quality control on some paired-end Illumina data and map these reads to a reference genome. We’ll then look at various approaches to automating this pipeline, allowing us to quickly do the same for a second dataset. 8. Combining methods The second part of the next-gen workflow is to call variants to identify SNPs between our two samples and the reference genome. We’ll look at the VCF file format and figure out how to filter SNPs for read coverage and quality. By counting the number of SNPs between each sample and the reference we will try to figure out something about the biology of the two samples. We’ll attempt to automate this analysis in various ways so that we could easily repeat the pipeline for additional samples. 9. Customisation Part of the Linux design is that everything can be customised. This can be intimidating at first but, given that bioinformatics work is often fairly repetitive, can be used to good effect. Here we’ll learn about environment variables, custom prompts, soft links, and ssh configuration — a collection of tools with modest capabilities, but which together can make life on the command line much more pleasant. In this last session there will also be time to continue working on the next-gen sequencing pipeline. The last afternoon is reserved for finishing off the next-gen workflow exercise, working on your own datasets, or leaving early for travel. -- 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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Bioinformatician Vacancy & KeyGene N.V.
by Marcel van Verk 06 Apr '17

06 Apr '17

We have at Keygene N.V. a Bioinformatician vacancy in my team. Below and in the enclosed attachment you can find some more information about this position. Data, information and knowledge are among KeyGene's most important products. As a bioinformatician you will play an important role in our technical research to develop state-of-the-art bioinformatics products for the integration, visualization and extraction of genomic and genetic breeding data. These products serve as a customizable and interactive encyclopedia for our internal research but also for our customers to mine and understand the genomic and genetic background of the crops that they are working on. Besides research and development, you will therefore participate in the delivery of these products to our customers by collecting and adding crop-specific data to the system and by training customers to work with the system. Website: http://www.keygene.com/career/vacancies/ Best, Marcel van Verk p.s. we are also looking for Postdoctoral fellows to apply for a Marie Curie 2017 fellowship jointly with KeyGene. More information check our website! Keygene N.V. | P.O. Box 216 | 6700 AE Wageningen | The Netherlands T (+31) 317 46 68 66 | F (+31) 317 42 49 39 | CoC. 09066631 | http://www.keygene.com<http://www.keygene.com/> [http://www.keygene.com/images/170202.jpg]<http://www.keygene.com> Stay up-to-date! Subscribe to our bimonthly newsletter here<http://www.keygene.com/newsletter> [http://www.keygene.com/images/linkedin-grey.png]<https://www.linkedin.com/company/KeyGene> [http://www.keygene.com/images/twitter-grey.png] <https://twitter.com/KeyGeneInfo> [http://www.keygene.com/images/facebook-grey.png] <https://www.facebook.com/KeyGeneNV> The information contained in this message, and attachments if any, may be privileged and/or confidential and is intended to be received only by persons entitled to receive such information. Use of any part of this message and/or its attachments if any, in any other way than as explicitly stated by the sender is strictly prohibited. Should you receive this message unintentionally please notify the sender immediately, and delete it together with all attachments, if any. Thank you. The transmission of messages and/or information via the Internet is not secured and may be intercepted by third parties. KeyGene assumes no liability for any damage caused by any unintentional disclosure and/or use of the content of this message and attachments if any.

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Job opening VUmc Amsterdam: Genome biologist / Computational biologist
by Sie, Daud 05 Apr '17

05 Apr '17

Genome and proteome data integration to improve cancer patient treatment =========================================================== Your work environment ================== At the Cancer Center Amsterdam (CCA) of VU University Medical Center (VUmc) we perform internationally recognized research in genomics & proteomics. CCA houses state of the art genome technologies and IT-facilities for medical research. Your challenge =========== We are looking for an enthusiastic, communicative and pro-active bioinformatician / computational biologist. The work involves support of CCA researchers through training, and hands-on analysis of in house and public genomics and proteomics datasets. A focus will be on exploring tools for data mining, -visualization and -integration. One challenge is to adopt and adapt existing bioinformatics implementations to develop an in silico drug prescription strategy. Your profile ========= . University (PhD) education in Life Sciences, ie biology and/or biomedical informatics; . Proven computer programming proficiency and experience with integration of genomics and/ or proteomics data; . Proficient with scripting languages (Python, Perl); . Proficient with a statistical framework (R); . Experience in moving and handling large amounts of (scientific) data reliably and efficiently (UNIX); . Experience with a database framework (Postgress, MySQL); . Experience with programming language (C#/C++/C or Java); . Excellent communication skills and fluency in English (written & spoken); We offer ======= Salary Scale 10: 2618 to 4152 euro gross when employed full-time (depending on qualifications and experience). In addition to a good monthly salary we offer, among others, 8.3% extra allowance at the end of the year and 8% for holidays. For more information on our conditions, please visit www.werkenbijvumc.nl/arbeidsvoorwaarden (with link to English page). We offer a young and dynamic environment in health care, covering an active research group in genomics and data analysis. The project will last 2 years. Employment will initially be for a period of one year, after mutual agreement the contract will be extended till the end of the project. Additional information ================= The anticipated start date will be July 1, 2017. Your position is at the VU University Medical Center, within the Cancer Center Amsterdam. For more information you can visit www.vumc.nl/afdelingen/cca-site/ or the Tumor Genome Analysis Core website via www.tgac.nl. Interested? ========= If you're interested about this position, you can contact Prof. dr. Bauke Ylstra, Dept. Pathology, via telephone number +31(0)20-4442495. If you need more information about the application procedure, contact Faisca Stuiver, corporate recruiter at +31(0)20-4445635. Kind regards, Daoud Sie, PhD Coordinator Genomics Research Facility VU University Medical Center Amsterdam - department of Pathology E: d.sie(a)vumc.nl P: +31204442428 Present: Mon/Tue/Wed/Fri De Boelelaan CCA-1.22, 1081 HV Amsterdam Mailing adress: Postbus 7057, 1007 MB Amsterdam www.vumc.com www.vumc.com/directions --------------------------------------------------- Disclaimer This e-mail is confidential and may contain information that is not intended for you. If you are not the addressee or if this message was sent to you by mistake, you are requested to inform the sender and delete the message. VU University Medical Center accepts no liability for damage of any kind resulting from the risks inherent in the electronic transmission of messages. ---------------------------------------------------

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Open Position TUDelft: Assistant Professor Bioinformatics for Human Diseases
by Marcel Reinders - EWI 04 Apr '17

04 Apr '17

Assistant Professor Bioinformatics for Human Diseases at Delft University of Technology (NL) Delft Bioinformatics Lab The Delft Bioinformatics Lab<http://bioinformatics.tudelft.nl/> performs research and educates students in the field of bioinformatics with broad applications in human, micro- and plant biology. We distinguish ourselves by applying the latest developments in machine learning to design novel, state-of-the-art algorithms that allow the interpretation of biological datasets. We closely collaborate with biochemists, biologists and geneticists to answer complex biological questions and give direct societal relevance to our tailor-made algorithms. On human diseases we partner with major Dutch medical centres: NKI, LUMC and VUmc. Job description You will head the bioinformatics for human diseases research theme and its associated educational activities. Within this theme we aim to improve the understanding of human diseases, from biomarker discovery to mechanistic understanding of disease progression, with the ultimate aim of contributing to the design of precision medicine. Challenges relate to integrating genomics data (across difference levels of cellular regulation), deciphering heterogeneity in cells (in space and across time), exploiting physical properties of the cell (such as the 3D organisation of DNA), and rich, longitudinal phenotyping of patients (from medical records and imaging to wearable sensors). You will initiate your own research lines within this context, design the necessary pioneering bioinformatics methodologies, and apply these to impact the medical domain. You will do so as principal investigator, leading day-to-day research activities of your team, fostering creativity and scientific excellence, and initiating collaborations with internationally leading labs. In addition, you will contribute to courses at the BSc, MSc and PhD levels in the Computer Science, Life Science Technology and Nanobiology programmes of the TU Delft. In short, you will show leadership in bioinformatics for human diseases, be active in the relevant international communities, and set internationally recognised research directions. Requirements You have a PhD in bioinformatics or a related discipline, a strong track record demonstrated by well-cited publications in top journals, and affinities for machine learning/data science and human diseases. You are motivated, enthusiastic, and decisive, and you work effectively in a multidisciplinary team. You motivate peers and students to share your enthusiasm for your science. Your English is fluent with excellent writing skills. You are an inspiring teacher with a track record in undergraduate/graduate teaching programmes (teaching certificates are considered an advantage). Conditions of employment A tenure-track position at the Faculty of Electrical Engineering, Mathematics and Computer Science<http://www.ewi.tudelft.nl/en/> of the Delft University of Technology<http://www.tudelft.nl/> (the Netherlands) is offered for six years, which is a process leading up to a permanent appointment with the prospect of becoming an Associate or full Professor. This decision will be made by the fifth year based on performance indicators agreed upon at the start of the appointment. This includes acquiring (if necessary) teaching certificates. The TU Delft offers a structured career and personal development programme designed to offer individual academics as much support as possible, such as following internal or external courses to develop your competences further. The TU Delft offers a customisable compensation package, a discount for health insurance and sport memberships, and a monthly work costs contribution. Flexible work schedules can be arranged. An International Children’s Centre offers childcare and an international primary school. Dual Career Services offers support to accompanying partners. The salary scale is €3400 to €4654 per month gross. Salary and benefits are in accordance with the Collective Labour Agreement for Dutch Universities. Information and application For more information about this position, contact Prof. M.J.T. Reinders, phone: +31 (0)15-2786424, e-mail: m.j.t.reinders(a)tudelft.nl<mailto:m.j.t.reinders@tudelft.nl>. To apply, send a letter of application detailing your motivation for the position, a detailed CV, a research and an education statement, at least three references and five key publications. E-mail your application by 15 April 2017 to E.C.L.Turlings, Hr-eemcs(a)tudelft.nl<mailto:Hr-eemcs@tudelft.nl>. When applying for this position, refer to vacancy number EWI2016-35. For more information about the Tenure Track and the personal development programme, visit www.tudelft.nl/tenuretrack<http://www.tudelft.nl/tenuretrack> Employer Delft University of Technology is a multifaceted institution offering education and carrying out research in the technical sciences at an internationally recognised level. Education, research and design are strongly oriented towards applicability. The TU Delft develops technologies for future generations, focusing on sustainability, safety and economic vitality. At the TU Delft you will work in an environment where technical sciences and society converge. The TU Delft comprises eight faculties, unique laboratories, research institutes and schools. Delft University of Technology offers an internationally competitive academic environment. In the field of life sciences, it harbors renowned scientists in biotechnology, nanobiology, environmental biology, and bio-based technological innovations. The Faculty of Electrical Engineering, Mathematics and Computer Science (EEMCS) contributes to life sciences in the fields of microfabrication (organ-on-a-chip models), computational science (mathematical models of biological processes), high performance computing (accelerating bioinformatics algorithms), data visualisation and bioinformatics. The Delft Bioinformatics Lab is part of the EEMCS faculty.

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Fully funded PhD position Cichlid evolution
by Pooja Singh 04 Apr '17

04 Apr '17

Please find attached an advertisement for a open PhD position a the University of Graz in Austria on Cichlid fish transcriptomics and adaptation. Please forward to anyone who might be interested. Best regards, Pooja Singh -- *PhD student* *Institute of Zoology* *Universitätplatz 2* *University of Graz* *Graz 8010* *Austria* *Homepages: * https://homepage.uni-graz.at/de/pooja.singh/ http://www.evolutionsbiologie-uni-konstanz.com/pooja-singh.html

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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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