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Two positions for research data management in AMC.
by A.H.C. van Kampen 14 Mar '16

14 Mar '16

Dear colleague, I would appreciate if you could distribute/advertise the attached positions for data management (see below for text version) Antoine van Kampen | Prof dr Antoine H.C. van Kampen | (1) Bioinformatics Laboratory | Clinical Epidemiology, Biostatistics and Bioinformatics (KEBB) | Academic Medical Center (AMC) | Visiting address: Meibergdreef 9, J1B-208 (J-building, floor 1B) | Postal address: PO Box 22700, 1100 DE Amsterdam, the Netherlands | www.bioinformaticslaboratory.nl<http://www.bioinformaticslaboratory.nl/> | (2) Biosystems Data Analysis | Swammerdam Institute for Life Sciences (SILS) | University of Amsterdam | Visiting address: Science Park 904, C2-206 | 1098 XH Amsterdam, The Netherlands | www.bdagroup.nl<http://www.bdagroup.nl/> |phone: ++31-20-5667096 (AMC) |Mobile: 06-41768067 | a.h.vankampen(a)amc.uva.nl<mailto:a.h.vankampen@amc.uva.nl> | Skype:antoine.van.kampen | Vacancies for Data Steward and Scientific Programmer ============================================== Dept. of Epidemiology, Biostatistics and Bionformatics (KEBB) Academic Medical Center of the University of Amsterdam Recently the AMC has funded a project to implement Research Data Management (RDM) for biomedical research. The project aims to setup an infrastructure for RDM and involves interactions with a large number of local, national and international initiatives and stakeholders in the active field of RDM. For this project we are looking for a data steward and a scientific programmer who will work in a multidisciplinary research team at the Academic Medical Center (AMC) of the University of Amsterdam (UvA) to design, develop, validate and disseminate the application of data research management practices into biomedical research. Position 1: Data Steward -------------------------------- The data steward is responsible for the management and usability of data and metadata. You will have a specialist role that incorporates (AMC) processes, policies, guidelines, and (data)standards for data management in compliance with regulatory obligations (e.g., security and privacy of information). You will be responsible for defining and implementing new guidelines and data standards to safeguard the integrity and quality of the (meta)data. You contribute to the organization of existing and new (meta)data using available tools, data repositories, and infrastructures. This will involve the development of software for, for example, data conversion, data import, and use of data standards. It also involves the support of end-users with data management to ensure broad adoption of RDM in the AMC. The data steward contributes to the development of RDM solutions. This includes the design, development and deployment of science gateways using the Rosemary platform . The data steward also participates in (inter)national RDM initiatives, project meetings, and training events for the stakeholders. The data steward will report (written and oral) about the project to the project leaders. He/she will also contribute to system management. Function Requirements • Education in bioinformatics or related field. • Large experience in programming and scripting, including Java and Python. • Experience with data management tools (e.g., relational databases). • Experience with the use of metadata and data standards (e.g., vocabularies, ontologies) • Experience with management of linux system • Experience with software project management (usage of tools such as redmine, git) • Experience with document-based databases (experience with MongoDB is an advantage) • Knowledge about data management and data standards in biomedical research • Interest in distributed infrastructures (knowledge about iRODS is a pre) Position 2: Scientific Programmer -------------------------------------------- The scientific programmer will lead the design and development of research data management solutions for broad adoption at the AMC. This will include design, development and deployment of science gateways using the Rosemary platform . Daily tasks will involve design of new solutions, integration with existing (external) data infrastructures, deployment and assessment with users, participation in national and international RDM initiatives, reporting, participation in writing of scientific papers and organization of project meetings, dissemination and training for stakeholders. The scientific programmer will also report orally and in written to project leaders and project stakeholders. Function Requirements • Education in computer science, engineering or related field. • Large experience in programming and scripting, including Java and Python. • Experience with software project management (usage of tools such as redmine, git) • Experience with document-based databases (experience with MongoDB is highly appreciated) • Knowledge about data management, including search engines and semantic web technologies (experience with Lucene is highly appreciated) • Acquaintance with management of linux system. • Acquaintance with virtualization (KVM, Docker) • Acquaintance with Scala programming (experience is highly appreciated) • Acquaintance with distributed e-infrastructures (knowledge about iRODS is highly appreciated) For both positions we are looking for candidates that have good analytical and writing skills and are strong in taking initiative, communication, and organization. The candidates should be excellent team players but also be able to function autonomously. They should be experienced in working in multi-disciplinary teams and preferably also acquainted with a biomedical research or hospital environment. Information about appointment • Full-time appointment (36h/week). Minimum of 26h/week is required. • Contract for 1 year. Can be extended with another year depending on results and performance. • Salary max € 3.250 gross per month for full-time appointment depending of level of education and experience. • Location at the Department of Clinical Epidemiology, Biostatistics and Bioinformatics (KEBB) of the AMC. Appointment at AMC Medical Research . • Benefits include: End of year bonus (8.3%), holiday payment (8%) and public transport costs. • Start as soon as possible Information and application Candidates for the Data Steward position are invited to send inquiries about this vacancy to prof. dr. A.H.C. van Kampen (a.h.vankampen(a)amc.uva.nl) To apply, please send a motivation letter and CV (both as pdf document). Include names of references in CV. Candidates for the Scientific Programmer position are invited to send inquiries about this vacancy to Dr. S.D. Olabarriaga (s.d.olabarriaga(a)amc.nl) To apply, please send a motivation letter, CV and names of potential references. ________________________________ AMC Disclaimer : https://www.amc.nl/disclaimer ________________________________

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COURSE: Introduction to R (19-21 September, 2016) at Maastricht University
by Viechtbauer Wolfgang (STAT) 14 Mar '16

14 Mar '16

COURSE: Introduction to R (19-21 September, 2016) at Maastricht University Three-day course on R, the free and open-source software environment for statistical computing and graphics, covering the following topics: * history and introduction to R * data structures, functions, basic arithmetic, data manipulation * working with data and command files * data inspection and summary statistics * graphs, plots, and tabulations * statistical methods: continuous data * statistical methods: categorical and time-to-event data * finding, installing, and loading additional packages * programming structures and flow control * generating random data and Monte Carlo simulations * generic, method, and user-written functions * advanced and miscellaneous topics The course is aimed at researchers, (Master and PhD level) students, data analysts/scientists, and essentially anybody interested in learning how to work with R. A mixture of lectures and hands-on exercises is used that provide ample opportunities for practicing the concepts taught. Course Dates: 19-21 September, 2016 Course Location: Maastricht, the Netherlands Registration Deadline: 12 September, 2016 Course Fee: 600 Euros Please see the course website (http://www.wvbauer.com/doku.php/course_r) for more details on the course contents, location, instructors, schedule, and registration information.

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Job opening at Bejo Zaden
by Jurgen Nijkamp 14 Mar '16

14 Mar '16

Dear all, We are looking for assistant scientist in Bioinformatics who will work in the Marker Technology & Genomics department of Bejo Zaden. Please follow the link below for more information (in Dutch). The closing date is March 31. https://www.werkenbijbejo.nl/pg-29173-7-102071/pagina/vacature_-_assistent_… Kind regards, Jurgen Nijkamp Jurgen Nijkamp, PhD | Scientist Bioinformatics | Marker Technology & Genomics | Bejo Zaden B.V. | * + 31 226 397 422 | j.nijkamp(a)bejo.nl<mailto:j.nijkamp@bejo.nl> | www.bejo.nl<http://www.bejo.nl/>

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announcement of course UAngers
by Alexander Botzki 12 Mar '16

12 Mar '16

Hi, FYI - a summerschool in bioinformatics at U Angers. http://summerschools.univ-angers.fr/en/index/about-schools/schools/bioinfor… Best regards, Alex

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BioSB Course: In silico life: constraint-based modelling at genome scale, May 9-11 2016, Amsterdam
by Femke Francissen 11 Mar '16

11 Mar '16

*BioSB Course: In silico life: constraint-based modelling at genome scale* *Date:* May 9-11, 2016 *Location:* Amsterdam *Course Coordinator:* Bas Teusink and Brett Olivier, Vrije Universiteit Amsterdam *Website:* http://biosb.nl/education/course-portfolio-2/course-constraint-based-modell… *Registration:* http://biosb.nl/education/course-portfolio-2/course-constraint-based-modell… Constraint-based modelling is a powerful modelling methodology that is being used to model a diverse range of biological phenomena. These include both fundamental and applied questions relevant to biotechnology, microbiology and medicine. Central to constraint-based modelling is the use of a genome-scale reconstructions (GSR’s) that maps out the metabolism of a cell as a biochemical reaction network. In this course you will be introduced to: - techniques for the construction of a working GSR: tools, tricks and pitfalls - the underlying mathematical definition and description of a constraint-based model - methods for interrogating models and interpreting results, such as Flux Balance Analysis and Flux Variability Analysis - software and standards The preliminary course structure will be to divide each day into both lectures and practical sessions so that learned theory can immediately be applied in silico. *Target Audience* Constraint-based modelling is a rapidly growing field that is being use in both fundamental and applied research and biotechnology. It sits at the intersection between quantitative metabolic modelling, bioinformatics and cellular physiology and, as such, is an example of systems biology at work. While participants would benefit from some knowledge of either quantitative modelling, bioinformatics or microbial physiology this is not required. This includes, for example, scientists working in a laboratory and wanting to learn more about building or using genome-scale models, as well as, those who have used basic FBA, but want to know how else it can be applied to their research. The course is part of the Education Programme of BioSB, the Netherlands Bioinformatics and Systems Biology Research School, which offers training and education for in bioinformatics and systems biology. More information about BioSB can be found at www.biosb.nl. Kind regards, ** ** *Femke Francissen* Community manager BioSB BioSB Research School Visiting address: Geert Grooteplein 28, route 260, 6525 GA Nijmegen Postal address: P.O. box 9101, route 260, 6500 HB Nijmegen E-mail: femke.francissen(a)biosb.nl Tel: +31 24 36 19 500 Mobile: +31 6 17 90 4888 Skype: femke.francissen Website: www.biosb.nl LinkedIn link <http://nl.linkedin.com/in/femkefrancissen>

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Fwd: [SocBiN] Post-doc and PhD student positions in Bergen, Norway
by Tom Venken 11 Mar '16

11 Mar '16

Dear all, Please find below vacancies for Post-doc and PhD student positions at the University of Bergen, Norway. The background of the candidates needs to be informatics or mathematics (in the broad sense); candidates with MSc or PhD in bioinformatics will be qualified as long as they have a strong informatics or math background (with courses and experience in for example programming, statistics, etc…) Kind regards, Tom Venken --- Tom Venken Postdoctoral researcher Computational Biology Unit Molecular Biology Institute University of Bergen Thormøhlensgate 55 Bergen, Norway http://www.uib.no/en/rg/reuter > Begin forwarded message: > > From: Inge Jonassen <Inge.Jonassen(a)ii.uib.no> > Subject: [SocBiN] Post-doc and PhD student positions in Bergen, Norway > Date: 11 March 2016 at 08:54:51 GMT+1 > To: socbin(a)socbin.org > > > Dear all, > > at the Department of Informatics at the University of Bergen we have one post-doc > and two PhD student openings. > > Applicants interested in working with us at the Computational Biology Unit are very > welcome to contact us and to apply for these positions!! > > We can offer challenging and interesting projects, a highly stimulating and friendly > work environment, in the center of a very nice city. > > The PhD students will be affiliated with the new national PhD school in bioinformatics > and biostatistics ( www.norbis.no ) - lead from the CBU. Please contact us to discuss > possible projects etc. > > More about the positions: > > https://www.jobbnorge.no/en/available-jobs/job/122667/research-fellows-phd-… > > https://www.jobbnorge.no/en/available-jobs/job/123227/postdoctoral-fellow-i… > > > Inge > > Inge Jonassen, Prof PhD > Head of Node, Elixir Norway > Computational Biology Unit > Department of Informatics > University of Bergen > HiB > N5020 Bergen > Norway > > Inge.Jonassen(a)uib.no > > _______________________________________________ > SocBiN mailing list > SocBiN(a)lists.su.se > https://lists.su.se/mailman/listinfo/socbin-at-sbc.su.se >

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Job opening for an (Associate) Scientist Bioinformatics & Modeling at DSM
by Roubos, Hans 10 Mar '16

10 Mar '16

Job opening for an (Associate) Scientist Bioinformatics & Modeling at DSM Dear friends. Currently we have a job opening for an (Associate) Scientist Bioinformatics & Modeling at the DSM Biotechnology R&D Center located in The Netherlands. https://www.linkedin.com/jobs2/view/107086720?trk=vsrp_jobs_res_name&trkInf…<https://www.linkedin.com/jobs2/view/107086720?trk=vsrp_jobs_res_name&trkInf…> Kind regards, Hans Roubos Hans Roubos | Principal Scientist Bioinformatics & Modeling | DSM Food Specialties B.V. | Alexander Fleminglaan 1 | 2613 AX Delft | Netherlands | T +31 (0)15 2792147 | Trade Register Number 27235314 | Stay connected: [http://static.dsm.com/content/dam/dsm/images/twitter.png] <https://twitter.com/DSM> [http://static.dsm.com/content/dam/dsm/images/linkedin.png] <https://www.linkedin.com/company/3108> [http://static.dsm.com/content/dam/dsm/images/youtube.png] <https://www.youtube.com/user/dsmcompany> [http://static.dsm.com/content/dam/dsm/images/googleplus.png] <https://plus.google.com/117689312065000346895#117689312065000346895/posts> [http://static.dsm.com/content/dam/dsm/images/facebook.png] <https://www.facebook.com/DSMcompany> [http://static.dsm.com/content/dam/dsm/images/DSM_Email_EN.jpg] ________________________________ DISCLAIMER: This e-mail is for the intended recipient only. If you have received it by mistake please let us know by reply and then delete it from your system; access, disclosure, copying, distribution or reliance on any of it by anyone else is prohibited. If you as intended recipient have received this e-mail incorrectly, please notify the sender (via e-mail) immediately.

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Edinburgh Genomics Bioinformatics workshops - GATK, Linux, RNA-seq, MinION, Python
by Bert Overduin 10 Mar '16

10 Mar '16

Dear all, We have currently a large variety of bioinformatics workshops open for registration, ranging from general entry level workshops, like "Linux for Genomics", which is targeted towards those who have never used the command line before, to more specialised and advanced ones, like "Oxford Nanopore MinION Sequencing - Data Handling, Analysis and Applications". Note that we are offering now three(!) different weeklong Python courses, an introductory one, an advanced one, as well as one focused on data manipulation and visualisation. All three are taught by dr Martin Jones, founder of Python for Biologists (http://pythonforbiologists.com) and author of several books on Python ( http://pythonforbiologists.com/index.php/books/) Registration for all workshops can be done through the workshop pages indicated below, on which you can also find much more detailed information about each workshop. I hope to see you at one (or more) of our workshops! With kind regards, Bert Overduin *2-day GATK Best Practices for Variant Discovery* Date: Thu 14 & Fri 15 April 2016 Price: £50 (day 1) / £100 (day 1 + day 2) Registration: first come first serve Deadline: Thu 30 March 2016 noon Details: https://genomics.ed.ac.uk/gatk-best-practices-variant-discovery *1-day Linux for Genomics* Date: Fri 13 May 2016 Price: £155 Registration: first come first serve Deadline: Fri 29 April 2016 noon Details: https://genomics.ed.ac.uk/linux-genomics *2-day Introduction to RNA-seq Data Analysis* Date: Thu 19 & Fri 20 May 2016 Price: £310 Registration: participant selection Deadline: Thu 21 April 2016 noon Details: https://genomics.ed.ac.uk/introduction-rna-seq-data-analysis *1-day Oxford Nanopore MinION Sequencing - Data Handling, Analysis and Applications* Date: Mon 13 June 2016 Price: £155 Registration: participant selection Deadline: Mon 16 May 2016 noon Details: https://genomics.ed.ac.uk/oxford-nanopore-minion-sequencing-data-handling-a… *5-day Introduction to Python for Biologists* Date: Mon 11- Fri 15 July 2016 Price: £500 Registration: first come first serve Deadline: Mon 13 June 2016 noon Details: https://genomics.ed.ac.uk/introduction-python-biologists-july-2016 *5-day Advanced Python for Biologists* Date: Mon 25 - Fri 29 July 2016 Price: £500 Registration: first come first serve Deadline: Mon 27 June 2016 noon Details: https://genomics.ed.ac.uk/advanced-python-biologists-july-2016 *5-day Data Manipulation and Visualisation with Python* Date: Mon 5 - Fri 9 September 2016 Price: £500 Registration: first come first serve Deadline: Mon 8 August 2016 noon Details: https://genomics.ed.ac.uk/data-manipulation-and-visualization-python -- Bert Overduin, PhD TRAINING AND OUTREACH BIOINFORMATICIAN Bert.Overduin(a)ed.ac.uk 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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BioSB Course Kick start R (4th edition), April 25, 2016, Amsterdam
by Femke Francissen 10 Mar '16

10 Mar '16

*BioSB Course Kick start R (4th edition) * *Date: April 25, 2016* *Location: Amsterdam* *Course Coordinator: Douwe Molenaar (VU)* *Website*, including course programme: http://biosb.nl/education/course-portfolio/course-kick-start-r/ *Registration: * http://biosb.nl/education/course-portfolio/course-kick-start-r/enrollment-k… On April 25, 2015, BioSB organises the fourth edition of the Kick Start R course in Amsterdam. The goal of this kick-start course is to: 1. Introduce the structure and philosophy behind the R-language. 2. Introduce a number of tools specific to the R-language. This is an introductory course to speed up the study of R. *Target audience* Primarily targeting researchers from academia, but participants from the private sector are also welcome. The course is part of the Education Programme of BioSB, the Netherlands Bioinformatics and Systems Biology Research School, which offers training and education for in bioinformatics and systems biology. More information about BioSB can be found at www.biosb.nl. Best regards, ** ** *Femke Francissen* Community manager BioSB BioSB Research School Visiting address: Geert Grooteplein 28, route 260, 6525 GA Nijmegen Postal address: P.O. box 9101, route 260, 6500 HB Nijmegen E-mail: femke.francissen(a)biosb.nl Tel: +31 24 36 19 500 Mobile: +31 6 17 90 4888 Skype: femke.francissen Website: www.biosb.nl LinkedIn link <http://nl.linkedin.com/in/femkefrancissen>

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GATK Best Practices for Variant Discovery workshop 14-15 April 2016 (third announcement)
by Bert Overduin 08 Mar '16

08 Mar '16

Dear all, We still have places available for the first day of our GATK Best Practices for Variant Discovery workshop (the lectures part). This workshop will focus on the core steps involved in calling variants with the Broad Institute’s Genome Analysis Toolkit ( https://www.broadinstitute.org/gatk/) which is one of the most, if not the most, commonly used tool for variant calling. We are very lucky to have this workshop delivered by three members of the GATK team, which means you will receive training by the most expert instructors imaginable. As they have to come all the way from the United States, we cannot promise we will organise this workshop again soon, so if you're interested in variant calling / GATK, this really is an opportunity not to be missed! The workshop will be as interactive as possible, and offer plenty of opportunity for questions and answers. For more information and to register, please visit https://genomics.ed.ac.uk/gatk-best-practices-variant- <https://genomics.ed.ac.uk/gatk-best-practices-variant-discovery>discovery <https://genomics.ed.ac.uk/gatk-best-practices-variant-discovery>. Note that the second day of the workshop (the hands-on part) is currently fully booked, but it is still possible to be placed on the waiting list, in case any places become available closer to the workshop date. Please feel free to forward this mail to anyone else potentially interested and/or to print out the attached flyer for further distribution. Hope to see many of you in April! With kind regards, Bert -- Bert Overduin, PhD TRAINING AND OUTREACH BIOINFORMATICIAN Bert.Overduin(a)ed.ac.uk 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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