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[Gtpb] IB16F - Introductory Bioinformatics - with a soft introduction to NGS Data Analysis - Announcement
by Pedro Fernandes 21 Mar '16

21 Mar '16

Dear all, The Applications for the bioinformatics training course IB16F - Introductory Bioinformatics - which is our ENTRY LEVEL training course, with a soft introduction to NGS Data Analysis - are now *OPEN* IMPORTANT DATES for this Course Deadline for applications: April 9th 2016 <======= !!! Course date: April 18th - April 22nd 2016 Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. *WARNING* this is one of our most popular training courses. It usually gets fully booked quite rapidly. Details, including application instructions, are available here: http://gtpb.igc.gulbenkian.pt/bicourses/IB16F This is an ENTRY LEVEL course, not because it is too simple, but because the level of the pre-requisites is very low. It is designed for participants with no a-priori knowledge about Bioinformatics. A variety of reasons, technical and economical, have led to a situation where affordable nucleotide sequencing data comes exclusively from Next Generation Sequencing machinery. This creates extra needs in knowing how to handle such data. Our course will cover this subject in a soft way. As usual in our courses we have two aims: to transfer a lot of skills by hands-on experience, and to maximise usage independence. All of this is achieved in highly interactive sessions, using teamwork and feedback techniques quite extensively. Best wishes, Pedro Fernandes -- Pedro Fernandes GTPB Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt _______________________________________________ GTPB mailing list GTPB(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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Fwd: Vacancy at SAMS, Scotland: Computing and Informatics Technician
by Lieven Sterck 17 Mar '16

17 Mar '16

apologies for cross-posting. wkr, lieven > From: "Claire Gachon" <Claire.Gachon(a)sams.ac.uk> > Sent: Thursday, 17 March, 2016 19:31:08 > Subject: Vacancy at SAMS, Scotland: Computing and Informatics Technician > Dear all, > We are currently looking for a new IT person at SAMS, to support a variety of > scientific projects across marine sciences. Though not necessary, expertise in > bioinformatics would be a key advantage. I would be for ever grateful if you > could spread the word and pass on the following advert to potential candidates. > Thanks so much in advance, > Claire > _________________ > Computing and Informatics Technician > Salary: £28,143 to £30,738 per annum > Fixed Term Appointment – 2 years > SAMS is seeking an enthusiastic person with skills in scientific computing and > data management. Duties will be to support a broad range of scientific projects > in all areas of marine science covering high performance computing, databases, > bioinformatics and application development. Linux Administration, database\SQL > and strong scripting skills are essential; experience with bioinformatics > software and application development would be of major benefit. > Initially for 2 years, this post has potential to be extended as new scientific > projects are awarded. > SAMS offers an employee benefits package as well as generous pension scheme. > Situated at Dunstaffnage on the beautiful west coast of Scotland, the area > offers a range of activities for those who enjoy the outdoors. There is a > nursery adjacent to SAMS as well as a visitor centre and café. > Further information is available on line at www.sams.ac.uk and > https://sams.ciphrro.com/ . Alternatively, please write to: Human Resources, > Computing & Informatics Technician, Job Ref D08/15.SG, The Scottish Association > for Marine Science, Scottish Marine Institute, Oban, Argyll PA37 1QA or e-mail > recruitment(a)sams.ac.uk > The closing date for receipt of applications is 15th April 2016 > SAMS is a registered Scottish charity (SC 009206), has an equal opportunities > policy and welcomes applications from all sections of the community. > ++++++++++++++++++++ > Dr Claire GACHON > Senior Lecturer in Molecular Phycology > Scottish Association for Marine Science > Scottish Marine Institute > PA37 1QA Oban > United Kingdom > claire.gachon(a)sams.ac.uk > Skype contact : claire.gachon > Tel: 0044 16 31 559 318 > Fax 0044 16 31 559 001 > http://www.sams.ac.uk/claire-gachon > ++++++++++++++++++++ > The Scottish Association for Marine Science (SAMS) is registered in Scotland as > a Company Limited by Guarantee (SC009292) and is a registered charity (9206). > SAMS has two actively trading wholly owned subsidiary companies: SAMS Research > Services Ltd (SC224404) and SAMS Ltd (SC306912). All Companies in the group are > registered in Scotland and share a registered office at Scottish Marine > Institute, Oban Argyll PA37 1QA. The content of this message may contain > personal views which are not the views of SAMS unless specifically stated. > Please note that all email traffic is monitored for purposes of security and > spam filtering. As such individual emails may be examined in more detail.

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Research position in Data science at VITO
by Valkenborg Dirk 17 Mar '16

17 Mar '16

Job opening for an associate researcher in data science at VITO Dear Colleagues, We have a job opening at VITO for a data scientists: R&D PROFESSIONAL DATASCIENCE HEALTH The unit Sustainable Health of VITO is looking for a data scientist to join their R&D team which is active in the domain of genomics, proteomics and mobile health. Data science, in its broadest definition, has become an essential pillar to translate health-related research into solutions for the industry and the medical world. As a member of the ABS (Applied Bio&molecular Systems) team, you translate research results into algorithms, operational tools and software packages based on the needs of clients and the market. The developed tools, algorithms and IP may, in the future, lead to new patents. Typically, statistical techniques, data science algorithms and bioinformatics-methods, beyond the state of the art, are applied and developed. This is inseparably tied with knowledge of the measuring platform and the application in the health sector. The added value created by this combined approach is then translated into solutions and products. You will work closely together with the project manager, your colleagues of the ABS team and the client, to identify needs en define client-centered solutions within the agreed time and budget limits. Our customers include (inter)governmental organizations, companies and hospitals. You will contribute to the acquisition of projects and writing of proposals and project proposals. You will ensure the cooperations within national and European consortia en you will expand your network with industrial partners and governments. In the future, you will have the opportunity to acquire projects independently and the possibility to grow towards business development or launch a spin-off initiative. Qualifications You have a Master's degree or PhD in bio-informatics, computer sciences, computational physics/biology or a similar domain. You combine a strong quantitative, mathematical background with a business-oriented spirit. You have experience with programming languages such as Python, Java, C++, ... and with statistical/mathematical software such as R, Matlab, ... You enjoy working in an interdisciplinary environment (bio-informatics, computer sciences, physico-chemistry, molecular biology, mobile health applications, business development, ...) You are interested in the inspiring context of sustainable health. You are solutions-oriented en you enjoy communicating with external partners and clients. You have a customer-oriented attitude and an eye for opportunities. Enthusiasm and entrepreneurship are qualities that characterize you. You like to take initiative, you work flexibly as a team player and you adapt easily to changing circumstances. You have strong communication skills and able to express yourself clearly in English, both orally and in writing. Offer A position in an eminent client-oriented organization, in the area of innovative technology research and science-backed consulting. The opportunity to contribute to putting Flanders on the international map as active knowledge region and thus contribute to sustainable development. An interesting salary package complete with extralegal benefits. Contact Candidates are invited to apply online: https://vito.taleo.net/careersection/vito_careersection_external/jobdetail.… For more information on this vacancy please contact: dirk.valkenborg(a)vito.be<mailto:dirk.valkenborg@vito.be> jef.hooyberghs(a)vito.be<mailto:jef.hooyberghs@vito.be> VITO Disclaimer: http://www.vito.be/e-maildisclaimer

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New job NGS Bioinformatician in LUMC, Leiden, NL
by H.Mei＠lumc.nl 14 Mar '16

14 Mar '16

Dear all, We have one open position for a new bioinformatician working on NGS data analysis and building pipelines in Linux here in Leiden. https://www.lumc.nl/over-het-lumc/werken-bij/vacatures-solliciteren/researc… Please feel free to forward this vacancy to people who might be interested in it. Best regards, Leon -- Hailiang (Leon) Mei Sequencing Analysis Support Core Leiden University Medical Center - http://sasc.lumc.nl Office: LUMC T6-48 Phone: +31 (0)71 5269836 Skype: leon_mei

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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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