April 2017 - BBClist - maillist.psb.ugent.be

Vacancy: (Associate) Scientist Metabolic Engineering & Bioprocess Modeling
by Jellema, Renger 20 Apr '17

20 Apr '17

Dear all, We're looking for a scientist Metabolic Engineering & Bioprocess Modeling. See text below for more info and this link<http://tinyurl.com/lfapf45> for the full details: http://tinyurl.com/lfapf45 Career Opportunities: (Associate) Scientist Metabolic Engineering & Bioprocess Modeling The Position You will represent the Bioinformatics & Modeling discipline within multi-disciplinary DBC project teams. Your challenge will be to develop and apply computational technologies, including mathematical models, computer-aided-design, and DoE for microbial strain design, metabolic engineering and bioprocess optimization. You will work in close collaboration with molecular biology, analytics and fermentation. Responsibilities include for example: - Build mathematical models of enzyme kinetics, microbial metabolism and fermentation processes and apply these models to optimize strain/process performance in Design-Build-Test-Learn cycles - Analysis and design of metabolic pathways for the production of metabolites and enzymes - Optimal design of experiments to generate informative datasets for strain and process optimization - Analyze and visualize large amount of sophisticated phenotypic and omics data to generate strain and process improvement leads. The Ideal - Ph.D. in computer science, metabolic engineering, systems biology, fermentation technology, bioinformatics or a related discipline. - Experience in mathematical modeling / metabolic engineering / process modeling with applications to microbial strain development or fermentation processes. - Sound knowledge in cellular metabolism, physiology and fermentation processes. - Additional expertise in machine learning, big data, computational fluid dynamics or synthetic biology is considered an advantage - Good programming skills in Matlab, experience in R, Python, Spotfire or other mathematical software packages is a plus. - Preferably industrial experience. - Strong desire and proven ability to work in multidisciplinary project teams - Personal skills like problem analysis, creativity and being a strong communicator characterize your identity. Kind regards, Renger Jellema | Senior Scientist | DSM Biotechnology Center | Alexander Fleminglaan 1 | 2613 AX Delft | Netherlands | M +31 (0)6 15 53 54 60 | renger.jellema(a)dsm.com<mailto:renger.jellema@dsm.com> | DSM Biotechnology Center is part of DSM Food Specialties B.V., Trade Register Number 27235314 | Stay connected: [cid:image001.png@01D2B9C1.3B6A3AD0] <https://twitter.com/DSM> [cid:image002.png@01D2B9C1.3B6A3AD0] <https://www.linkedin.com/company/3108> [cid:image003.png@01D2B9C1.3B6A3AD0] <https://www.youtube.com/user/dsmcompany> [cid:image004.png@01D2B9C1.3B6A3AD0] <https://plus.google.com/117689312065000346895#117689312065000346895/posts> [cid:image005.png@01D2B9C1.3B6A3AD0] <http://www.facebook.com/DSMcompany> [cid:image006.jpg@01D2B9C1.3B6A3AD0] ________________________________ 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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Vacancy: data scientist
by Jellema, Renger 20 Apr '17

20 Apr '17

Dear all, We're looking for a data scientist. See text below for more info and this link<http://tinyurl.com/mnoah6p> for the full details: http://tinyurl.com/mnoah6p Career Opportunities: Data Scientist The Position As a data scientist, you will be located at the DBC in Delft. Your challenge will be to co-develop a big data platform for biotech and to support business-driven R&D projects with data processing, data standardization following FAIR data principles, data management and statistical analysis for applications in food, pharma and bio-based chemicals and fuels. As part of the job, you will participate in multidisciplinary project teams in which you will be the data scientist. At DBC, you will be part of a team consisting of data scientists, statisticians, genomics experts, metabolic & molecular modelers, and automation experts. You will also play a role in building and sharing knowledge around the topic of Big Data within the global DSM science community and participate in public private partnerships like DTL, ELIXIR and NMC. The Ideal - Ph.D. in mathematics, computer science, bioinformatics, physics, or a related discipline. - Additional experience or degree in biochemistry, molecular biology, food sciences, or biotechnology is an advantage. - 3+ year experience, preferably in data sciences and statistical data processing of biological data or fermentation data. - Experience with building statistical, mathematical, and predictive models or implementation of machine learning algorithms. - Experience with relational and non-relational databases. - Experience with programming in Python, Java, C or related languages - Experience with end-user analytical and visualization tools, e.g. Tableau, SAS, Spotfire, R, Matlab is a plus - Personal skills like problem analysis, creativity and being a strong communicator characterize your identity. Kind regards, Renger Jellema | Senior Scientist | DSM Biotechnology Center | Alexander Fleminglaan 1 | 2613 AX Delft | Netherlands | M +31 (0)6 15 53 54 60 | renger.jellema(a)dsm.com<mailto:renger.jellema@dsm.com> | DSM Biotechnology Center is part of DSM Food Specialties B.V., Trade Register Number 27235314 | Stay connected: [cid:image001.png@01D2B9B3.9E412640] <https://twitter.com/DSM> [cid:image002.png@01D2B9B3.9E412640] <https://www.linkedin.com/company/3108> [cid:image003.png@01D2B9B3.9E412640] <https://www.youtube.com/user/dsmcompany> [cid:image004.png@01D2B9B3.9E412640] <https://plus.google.com/117689312065000346895#117689312065000346895/posts> [cid:image005.png@01D2B9B3.9E412640] <http://www.facebook.com/DSMcompany> [cid:image006.jpg@01D2B9B3.9E412640] ________________________________ 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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Aphea.Bio is looking for a Microbiologist
by Jolien Van Impe 18 Apr '17

18 Apr '17

Aphea.Bio is looking for a Microbiologist. You can find the full description of the job advertisement here: http://www.vib.be/en/jobs/Pages/Aphea.Bio-Microbiome-Scientist---Microbiolo… 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)]

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[Gtpb] Subject: GTPB Entry Level Bioinformatics - applications are OPEN
by Pedro L. Fernandes 17 Apr '17

17 Apr '17

Announcement, We are pleased to inform that applications for the Entry Level Bioinformatics training course are open. http://gtpb.igc.gulbenkian.pt/bicourses/ELB17F with David P. Judge, Pedro Fernandes and Daniel Sobral IMPORTANT DATES for this Course Deadline for applications: May 1st 2017 <========= ! Course date: May 8th - May 12th 2017 This is our Entry Level course. It is the best way to start working with sequence data, gently introduced to participants with no experience. You just need to have minimal knowledge in Biochemistry and Molecular Biology and minimal computer usage skills. The course will take you to a level where you understand how to use NGS data as well. We aim at training the participants to gain independence in basic usage of bioinformatic tools and data resources. The course covers a very wide range of subjects. A successful participant will be able to do perform a great deal of bioinformatics tasks by him/herself. He/she will also to easily engage in most of our more specialised or advanced training courses. Above all, he/she will have a good understanding of how to work with data to support research activities, integrating wet lab research l research with data analytical tasks in a coherent framework. NOTE: 1) Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. 2) This course is often fully booked. Please do not delay your application if you are interested. Best wishes Pedro Fernandes -- Pedro Fernandes Bioinformatics Training Coordinator Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL 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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Bioinformatics postdoctoral position in Brussels -IB2
by tlenaert 15 Apr '17

15 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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Last call: BioSB HotTopics: ONT Nanopore sequencing, April 20th, Delft
by Thomas Abeel 12 Apr '17

12 Apr '17

Dear colleagues, April 20, 2017 we organize a BioSB HotTopics workshop on ONT Nanopore sequencing at TU Delft. You are cordially invited. Full program and registration: http://bit.do/biosb_nanopore Nanopore sequencing has been revolutionizing the sequencing arena for the last few years. The last decade, sequencing went from highly-specialized to a commodity product that can be readily purchased from a specialty provider. ONT has taken this again a step further and is now enabling anyone to get into 'do-it-yourself' sequencing. Sequencing now requires no capital investment, very little in lab setup and anybody with a steady hand can start to generate data. While the technology has tremendous potential, there are still a few teething problems and sharing expert knowledge is critical to realize its full potential. The goal of this meeting is to bring the 'local' ONT community together and strengthen information sharing and collaboration within the Netherlands and beyond. The program is aimed at novice and expert users alike. This is the last call for participation and registration. Registration closes April 14, 9am. kind regards, Thomas

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vacancy statistician
by Veronique Storme 12 Apr '17

12 Apr '17

Dear all, The VIB-UGent Center for Plant Systems Biology (PSB) in Ghent, Belgium, is currently looking for a full-time statistician in support of the research activities in the Center. [ http://www.vib.be/en/jobs/Pages/Statistician.aspx | Read more ] kind regards, Veronique Véronique Storme - Biostatistician Applied Bioinformatics And Biostatistics VIB-UGent Center for Plant Systems Biology Ghent University Technologiepark 927 - 9052 Ghent - Belgium Tel. +32(0)9 331 39 50 [ http://www.psb.ugent.be/ | www.psb.ugent.be ]

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Science Manager and Software Engineer positions at ELIXIR-Luxembourg Node
by Venkata Satagopam (TeC) 12 Apr '17

12 Apr '17

Dear all ELIXIR Luxembourg is hiring Software Engineer<http://recruitment.uni.lu/en/details.html?id=QMUFK026203F3VBQB7V7VV4S8&nPos…> to work on web-based knowledge management tools, bioinformatics analysis algorithms and GUI design and implementation. Another opening is for Science Manager<http://recruitment.uni.lu/en/details.html?id=QMUFK026203F3VBQB7V7VV4S8&nPos…> to support the establishment and operation of the Node and manage its strategy development. Best regards Venkata -- Venkata Satagopam Technical Coordinator ELIXIR-Luxembourg Node Bioinformatics Core Luxembourg Centre For Systems Biomedicine (LCSB) University of Luxembourg Campus Belval, House of Biomedicine II 6, avenue du Swing L-4367 Belvaux T +352-466-644-6421 F +352-466-644-6949 venkata.satagopam(a)elixir-luxembourg.org<mailto:venkata.satagopam@elixir-luxembourg.org> https://www.elixir-europe.org/about/elixir-luxembourg ----- This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies. -----

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Workshop GATK Best Practices for Variant Discovery, 17-19 July 2017 - Registration open
by Bert Overduin 12 Apr '17

12 Apr '17

Dear all, I am happy to announce that for the third year in a row we have been able to get three members of the GATK team of the Broad Institute ( https://software.broadinstitute.org/gatk/) over to Edinburgh for a few days to teach a workshop on GATK Best Practices for Variant Discovery. Details of the workshop can be found below. With kind regards, Bert ********** GATK BEST PRACTICES FOR VARIANT DISCOVERY DATE: Monday 17 - Wednesday 19 July 2017 VENUE: The King's Buildings,The University of Edinburgh, Edinburgh, Scotland, UK REGISTRATION DEADLINE: Monday 3 July 2017 CANCELLATION DEADLINE: Monday 10 July 2017 PLACES: 85 (lectures), 30 (hands-on sessions) (first come, first served) REGISTRATION FEE: £70 for the lectures, £35 for each half-day hands-on session (includes coffee/tea, but no lunch) INFORMATION: Bert Overduin (bert.overduin(a)ed.ac.uk) TO REGISTER: http://genomics.ed.ac.uk/services/gatk-best-practices-variant-discovery This workshop will focus on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. You will learn why each step is essential to the variant discovery process, what are the operations performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of your dataset. In the course of this workshop, we highlight key functionalities such as the GVCF workflow for joint variant discovery in cohorts, RNAseq-specific processing, and somatic variant discovery using MuTect2. We also preview capabilities of the upcoming GATK version 4, including a new workflow for CNV discovery, and we demonstrate the use of pipelining tools to assemble and execute GATK workflows. "Excellent opportunity to learn from world-renowned experts!" (April 2016) INSTRUCTORS GATK staff (The Broad Institute, Cambridge, MA, United States) WORKSHOP FORMAT The workshop is composed of one day of lectures (including many opportunities for Q&A) and two optional days of hands-on training, structured as follows: Lectures (day 1): Rationale, theory and application of the GATK Best Practices for Variant Discovery in high-throughput sequencing data. Hands-on 1 (day 2 am): Germline variant discovery (SNPs + Indels) Hands-on 2 (day 2 pm): Germline variant filtering (SNPs + Indels) Hands-on 3 (day 3 am): Somatic variant discovery (SNPs + Indels + CNV) Hands-on 4 (day 3 pm): Pipelining on the cloud with WDL Please note that the lectures part is mandatory. It is not possible to attend any of the hands-on sessions without attending the lectures. In the three optional hands-on sessions focused on analysis, we walk attendees through exercises that teach them how to manipulate the standard data formats involved in variant discovery and how to apply GATK tools appropriately to common use cases and data types. In the course of these exercises, we demonstrate useful tips and tricks for interacting with GATK and Picard tools, dealing with problems, and using third-party tools such as Samtools, IGV, RStudio and RTG Tools. In the optional hands-on session on pipelining, we walk attendees through exercises that teach them to write workflow scripts using WDL, the Broad's new Workflow Description Language, and to execute these workflows locally as well as through publicly available cloud-based services. Please note that this workshop is focused on human data analysis. The majority of the materials presented applies equally to non-human data, and we will address some questions regarding adaptations that are needed for analysis of non-human data, but we will not go into much detail on those points. WHO SHOULD ATTEND The lecture-based component of the workshop is aimed at a mixed audience of people who are new to the topic of variant discovery or to GATK, seeking an introductory course into the tools, or who are already GATK users seeking to improve their understanding of and proficiency with the tools. Attendees should already be familiar with the basic terms and concepts of genetics and genomics. The hands-on component is aimed at novice to intermediate users who are seeking detailed guidance with GATK and related tools. Basic familiarity with the command line environment is required. Please note that for the hands-on sessions attendees will be expected to bring their own laptops with software preinstalled (detailed instructions will be posted two weeks before the workshop). Supported systems are Mac and Unix/Linux systems. MS Windows is not supported. COVERED TOPICS Lectures Introduction to variant discovery analysis and GATK Best Practices Marking Duplicates Indel Realignment Base Recalibration Variant Calling and Joint Genotyping Filtering variants with VQSR Genotype Refinement Workflow Callset Evaluation Somatic variant discovery with MuTect2 Preview of CNV discovery with GATK4 Hands-on 1 Germline variant discovery (SNPs + Indels) Hands-on 2 Germline variant filtering (SNPs + Indels) Hands-on 3 Somatic variant discovery (SNPs + Indels + CNV) Hands-on 4 Pipelining on the cloud with WDL -- 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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Postdoc Computational Biology
by Stein Aerts 11 Apr '17

11 Apr '17

http://www.vib.be/en/jobs/Pages/Postdoc-Computational-Biology.aspx [cid:19996CE1-1D0D-4916-914E-D785735EA06A@home]

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