April 2016 - BBClist - maillist.psb.ugent.be

Vacancy: PhD position on copy number variation detection in experimental evolution
by Ridder, Dick de 19 Apr '16

19 Apr '16

Dear all, We are looking for an enthusiastic bionformatics PhD candidate on a project titled "Exploiting copy number variation for rapid improvement of abiotic stress tolerance in crops", a collaboration with the Laboratory of Genetics at Wageningen University. Our goal is to experimentally evolve plants in the laboratory under severe stress conditions – high salt or zinc exposure – and study the resulting genomic changes, which we expect to mainly be copy number variation. This will help us understand the role of copy number variation in plant genome evolution and allow us to find ways of use it in crop plant breeding, to improve stress tolerance. We are looking for an ambitious PhD candidate with an MSc degree in bioinformatics or computer science (with a demonstrable affinity for biology). We are specifically seeking a candidate with a strong background in algorithm development, preferably in NGS data analysis, and demonstrable skills in mathematics and statistics. You will be based in Wageningen, and work in close cooperation with the other PhD candidate in this project and with researchers at Wageningen University and in industry. Additional information about the position can be found at http://tinyurl.com/h2gfvcx. Interested candidates can apply up to May 21, 2016 through this website. Best regards, prof. Dick de Ridder Bioinformatics Group, Wageningen University, The Netherlands

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Vacancy for ELIXIR Technical Lead (Data and Interoperability)
by Mascha Jansen 18 Apr '16

18 Apr '16

Dear all, The ELIXIR-HUb is recruiting a technical officer to support data and interoperability platforms at the ELIXIR Hub: https://www.elixir-europe.org/about/vacancies/elixir-technical-lead <https://www.elixir-europe.org/about/vacancies/elixir-technical-lead> Could you please help to spread this in your networks? The opening closes on April 25. Thanks! Mascha Jansen Coordination FAIR Data projects Dutch Techcentre for Life Sciences Visiting address: Catharijnesingel 54 | 3511 GC Utrecht Postal address: Postbus 19245 | 3501 DE Utrecht E-mail: mascha.jansen(a)dtls.nl Tel: +31 612119993 Website: <>w <http://www.dtls.nl/> <>ww.dtls.nl <http://www.dtls.nl/>

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BioSB Course: In silico life: constraint-based modelling at genome scale, May 9-11 2016, Amsterdam
by Celia.vanGelder＠radboudumc.nl 15 Apr '16

15 Apr '16

Dear colleague, The BioSB course In silico life: constraint-based modelling at genome scale (first edition), is open for registration. Please spread this message to other researchers in your network that might be interested. Date: May 9-11, 2016 Location: Amsterdam Course Coordinators: Bas Teusink (VU), Brett Olivier (VU), Vrije Universiteit Amsterdam, Celia van Gelder (BioSB) Speakers & tutors: Dr. Filipe Branco dos Santos (UVA), Prof. Frank Bruggeman (VU), Dr. Richard Notebaard (RUMC), Dr. Peter Schaap (WUR), Prof. Bas Teusink (VU), Dr. Katy Wolstencroft (LIACS), Dr. Ahmad Zeidan (Chr. Hansen), Dr. Zheng Zhao (DSM), Jasper Koehorst (WUR), Dr. Brett Olivier (VU) Website: http://biosb.nl/education/course-portfolio-2/course-constraint-based-modell… Registration: http://biosb.nl/education/course-portfolio-2/course-constraint-based-modell… 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. Course description 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. Full Course Programme Monday (09/05/2016) Tuesday (10/05/2016) Wednesday (11/05/2016) FALW, WN-F654 O2 Building 01W08 O2 Building 01W08 9:30 -11:00 Bas Teusink (VU) b.teusink(a)vu.nl<mailto:b.teusink@vu.nl> Frank Bruggeman (VU) f.j.bruggeman(a)vu.nl<mailto:f.j.bruggeman@vu.nl> Filipe Branco dos Santos (UVA) f.brancodossantos(a)uva.nl<mailto:f.brancodossantos@uva.nl> 11:00 - 11:30 Coffee Coffee Coffee 11:30 - 12:45 Peter Schaap (WUR) peter.schaap(a)wur.nl<mailto:peter.schaap@wur.nl> Bas Teusink (VU) b.teusink(a)vu.nl<mailto:b.teusink@vu.nl> Richard Notebaard (RUMC) Richard.Notebaart(a)radboudumc.nl<mailto:Richard.Notebaart@radboudumc.nl> 12:45 - 13:30 Lunch Lunch Lunch 13:30 - 14:30 Genome annotation Jasper Koehorst (WUR) jasperkoehorst(a)gmail.com<mailto:jasperkoehorst@gmail.com> FAME Brett Olivier b.g.olivier(a)vu.nl<mailto:b.g.olivier@vu.nl> SBML models, tools & databasesL Brett Olivier (VU) b.g.olivier(a)vu.nl<mailto:b.g.olivier@vu.nl> 14:30 - 15:30 FAIR data and models Katy Wolstencroft (LU) k.j.wolstencroft(a)liacs.leidenuniv.nl<mailto:k.j.wolstencroft@liacs.leidenuniv.nl> 15:30 - 16:00 Coffee Coffee Coffee 16:00 - 17:00 Zheng Zhao (DSM) zheng.zhao(a)dsm.com<mailto:zheng.zhao@dsm.com> Ahmad Zeidan (Chr Han) DKAHZE(a)chr-hansen.com<mailto:DKAHZE@chr-hansen.com> Final wrap-up & discussion 17:00 - 17:30 Wrap-up & discussion Wrap-up & discussion 17:30 - Drinks (BioSB) Dinner (self organised) BioSB Education Programme 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<http://www.biosb.nl>. Kind regards, Celia van Gelder, BioSB Dr. Celia W.G. van Gelder Education Manager BioSB Coordinator Education CMBI Programme Manager Learning DTL/ELIXIR-NL tel. +31613375327 e-mail: Celia.vanGelder(a)radboudumc.nl<mailto:Celia.vanGelder@radboudumc.nl> websites: www.nbic.nl<http://www.nbic.nl/>, www.biosb.nl, www.cmbi.ru.nl<http://www.cmbi.ru.nl/>, www.dtls.nl Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre PO Box 9101 6500 HB Nijmegen The Netherlands 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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Machine Learning in Systems Biology, 10th international Workshop
by Dijk, Aalt-Jan van 14 Apr '16

14 Apr '16

Call for Papers & Highlight track abstracts: 10th International Workshop Machine Learning in Systems Biology (MLSB-2016) Organized as a ECCB pre-conference workshop, September 3-4, 2016, World Forum, The Hague, Netherlands SUMMARY Biology is rapidly turning into an information science, thanks to enormous advances in the ability to observe the molecular properties of cells, organs and individuals. This wealth of data allows us to model molecular systems at an unprecedented level of detail and to start to understand the underlying biological mechanisms. This field of systems biology creates a huge need for methods from machine learning, which find statistical dependencies and patterns in these large-scale datasets and that use them to establish models of complex molecular systems. MLSB is a scientific forum for the exchange between researchers from Systems Biology and Machine Learning, to promote the exchange of ideas, interactions and collaborations between these communities. TARGET AUDIENCE The aim of this workshop is to contribute to the cross-fertilization between the research in machine learning methods and their applications to systems biology (i.e., complex biological and medical questions) by bringing together method developers and experimentalists. WORKSHOP TOPICS (NON EXHAUSTIVE) Methods: Active learning/Experimental design, Bayesian Methods, Clustering/Biclustering, Data integration/fusion/multi-view learning, Feature/subspace selection, Graph inference/completion, Kernel Methods, Machine Learning Algorithms, Multitask/Structured output prediction, Probabilistic inference, Semi-supervised learning, Systems identification, Time-series analysis Applications: Biomarker identification, Epigenetics, Genome-wide association studies, Metabolic modeling and reconstruction, Metabolomics, Protein function and structure prediction, Protein-protein interaction networks, Rational drug design methods, Regulatory genomics, Sequence Annotation, Signaling networks, Synthetic biology IMPORTANT DATES May 30, 2016: Full length manuscript submission May 30, 2016: Highlight track abstract submission June 30, 2016: Decision notifications for manuscripts and abstracts July 20, 2016: Final camera-ready manuscript submission August 19, 2016: Registration deadline September 3-4, 2016: Workshop INVITED SPEAKERS Prof. Ziv Bar-Joseph, School of Computer Science Carnegie-Mellon University, USA Prof. Jukka Corander, Department of Mathematics and Statistics, University of Helsinki, Finland Prof. Lodewyk Wessels, The Delft Bioinformatics Lab, Delft University of Technology, The Netherlands Prof. Yvan Saeys, VIB Inflammation Research Center, Ghent University, Belgium SUBMISSIONS We encourage submissions bringing forward methods for discovering complex structures (e.g. interaction networks, molecule structures), statistical machine learning methods for analysis of various high-throughput omics data, and methods supporting systems-level data analysis. The submissions are organized into the following two tracks: 1. Manuscripts (preferentially up to 5000 words) describing original work on machine learning in systems biology. These should describe method development and applications broadly in the topics listed above (see Workshop topics). Accepted proceedings track papers will be published in BMC Bioinformatics. The publications need to match the standards of the journal; please prepare your submissions using the BMC instructions (http://www.bioinformatics.nl/MLSB2016/BMC_guidelines.pdf) The publication is subject to open access fee (special reduced price negotiated by MLSB). 2. Highlights Track abstracts (1-2 pages) describing computational aspects of work that has been recently published in a journal (or are “in press”) as well as unpublished/on-going work. Submissions will be evaluated by at least three reviewers from an international programme committee of experts in the field. The most relevant and most original submissions will be accepted as full oral presentations and/or as poster presentations at the workshop. Submission is through the Easychair system: https://easychair.org/conferences/?conf=mlsb2016 REGISTRATION Registration via the general ECCB2016 registration system http://www.eccb2016.org/registration/ PROGRAMME COMMITTEE Antti Airola Chloé-Agathe Azencott Alexis Battle Michael A. Beer Andreas Beyer Karsten Borgwardt Céline Brouard Gal Chechik Chao Cheng Manfred Claassen Florence D’Alché-buc Dick de Ridder Saso Dzeroski Pierre Geurts Markus Heinonen James Hensman Lars Kaderali David Knowles Stefan Kramer Anshul Kundaje Harri Lähdesmäki François Laviolette Christina Leslie Hiroshi Mamitsuka Martin Renqiang Min Yves Moreau Alan Moses Sara Mostafavi Bernard Ng Mahesan Niranjan William Noble Uwe Ohler Tapio Pahikkala Nico Pfeifer Gerald Quon Magnus Rattray Juho Rousu Yvan Saeys Guido Sanguinetti Li Shen Motoki Shiga Oliver Stegle Koji Tsuda Giorgio Valentini Aalt-Jan van Dijk Jinbo Xu

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bytemal Aachen conference
by Cirillo Elisa (BIGCAT) 14 Apr '16

14 Apr '16

Dear all, We are excited to announce that after the great start of the conference series byteMAL in Maastricht, the next conference is coming up in Aachen on 17th June 2016. byteMAL - Bioinformatics for Young inTernational researchers Expo - is a conference series that is directed especially at young researchers in the fields of bioinformatics and computational biology and aims to provide a new networking platform for the exchange of knowledge and expertise across borders. We are very happy that Prof. Dr. Ben MacArthur from University of Southampton, Prof. Dr. Ines Thiele from University of Luxembourg and Prof. Dr. Olaf Wolkenhauer from University of Rostock will give the keynote presentations. Furthermore, participants will have the chance to present their projects during the poster session or their newly developed tools during the application showcase session. Online registration is possible until 20th May 2016. For more information about the event, please visit our website (http://projects.bigcat.unimaas.nl/bytemal/aachen/) or take a look at the flyer attached. You can also find us on Facebook (www.facebook.com/bytemal<http://www.facebook.com/bytemal>) or Twitter (https://twitter.com/byteMAL_Aachen) We are looking forward to seeing you there! Thank you and best wishes On behalf of the Organisational Team Lisa Turnhoff Doctoral Candidate AICES Graduate School Joint Research Center for Computational Biomedicine (JRC-COMBINE) RWTH Aachen University Augustinerbach 2a 52062 Aachen Germany Phone: +49 241 80 99210 Web: http://www.combine.rwth-aachen.de<http://www.combine.rwth-aachen.de/>? ?

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BioVis at ISMB 2016 Call for Participation
by Jan Aerts 14 Apr '16

14 Apr '16

The BioVis Interest Group (http://www.biovis.net) is organizing a meeting at ISMB in 2016. This meeting brings together researchers from the visualization, bioinformatics, and biology communities with the purpose of educating, inspiring, and engaging visualization researchers in problems in biological data visualization, as well as bioinformatics and biology researchers in state-of-the-art visualization research. BioVis@ISMB 2016 is co-located with ISMB 2016 <http://www.iscb.org/ismb2016> and will be taking place on July 8in Orlando, Florida at the Disney World Resort Swan and Dolphin hotel <http://www.iscb.org/ismb2016-accommodation>. The main ISMB 2016 conference will run from July 8 through July 12. There are three possible ways to participate in BioVis@ISMB: [1] New Research: Participants are invited to submit an abstract describing high-quality original research. Abstracts will be reviewed by the program committee and all accepted abstracts will be included in the poster session. The authors of selected abstracts will be asked to give a brief oral presentation during the SIG meeting. [2] Highlights: Participants may submit an abstract describing work published in the previous year as well as additional work undertaken since publication. The program committee will review these abstracts. Additionally, the BioVis SIG program committee may also invite authors of outstanding publications from other venues. The authors of selected abstracts will give an oral presentation during the SIG meeting. [3] Posters: We seek work in progress and preliminary results; previously published work from other venues; visualization challenges. Key Dates for BioVis@ISMB: - May 3, 2016 - Submission deadline for the Highlights Track and New Research Track - May 17, 2016 - Submission deadline for Poster Track - May 20, 2016 - Notifications for Highlights, New Research, and Posters For more info on BioVis@ISMB see: http://biovis.net/2016/ismb/ BioVis is also holding a meeting at IEEE VisWeek in 2016. For more info on BioVis@VIS see:http://biovis.net/2016/ieeevis/ General chairs - G. Elisabeta Marai, University of Illinois at Chicago, USA - Jan Aerts, KU Leuven, Belgium Paper chairs - Daniel Weiskopf, University of Stuttgart, Germany - Marc Streit, Johannes Kepler University Linz, Austria Poster chairs - Michel Westenberg, Eindhoven University of Technology, The Netherlands - William Ray, The Ohio State University, USA Publication chairs - Alexander Lex, University of Utah, USA - Florin Chelaru, MIT, USA Primer & challenges chair - Eamonn Maguire, CERN, Switzerland Highlights chair - Julian Heinrich, CSIRO, Australia Data contest chairs - Raghu Machiraju, The Ohio State University, USA - Cagatay Turkay, City University, London, UK Design contest chairs - Ryo Sakai, KU Leuven, Belgium - Francis Rowland, EBI, UK Industry and fundraising chair - Hector Corrado Bravo, University of Maryland, USA Website chairs - Tuan Dang, University of Illinois at Chicago, USA - Anamaria Crisan, University of British Columbia, Canada Publicity chairs - Jillian Aurisano, University of Illinois at Chicago, USA Steering Committee - Kay Nieselt, University of Tuebingen, Germany - Nils Gehlenborg, Harvard Medical School, USA - Jessie Kennedy, Edinburgh Napier University, UK - Jos Roerdink, University of Groningen, The Netherlands - Raghu Machiraju, The Ohio State University, USA (Chair) ================================================ Prof Jan Aerts * Visual Data Analysis Lab (vda-lab.be) * Data Visualization Lab (datavislab.org) * Bioinformatics - ESAT/STADIUS, Faculty of Engineering ( www.kuleuven.be/bioinformatics) * iMinds Medical IT Department (www.iminds.be) KU Leuven - University of Leuven Kasteelpark Arenberg 10 bus 2446 3001 Leuven-Heverlee ORCID: http://orcid.org/0000-0002-6416-2717 Tel: +32 16 321053 Fax: +32 16 321970 VAT BE 0419 052173

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[Gtpb] ARANGS16 - ARANGS16 Automated and reproducible analysis of NGS data
by Pedro Fernandes 13 Apr '16

13 Apr '16

ANNOUNCEMENT / REMINDER Applications for ARANGS16 - ARANGS16 Automated and reproducible analysis of NGS data with Darin London and Rutger Vos are OPEN IMPORTANT DATES for this Course Deadline for applications: May 2nd 2016 Course dates: May 9th - May 13th 2016 Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. Description Next generation sequencing (NGS) technologies for DNA have resulted in a yet bigger deluge of data. Researchers are learning that analyzing the data efficiently requires the creation of sophisticated pipelines, typically using command line tools in a Linux or other Open source Unix variant compute environment. Many researchers have created these pipelines to successfully analyse their data. Now they are faced with the challenge of making these pipelines available to their colleagues. The issue of reproducibility has emerged as a major issue, as researchers, peer reviewers, and even pharmaceutical companies discover that the software and data used to produce a particular research finding are either not available, poorly documented, or targeted to specific compute infrastructures that are not available to the wider research community. To remedy this, funding agencies and journals are creating policies to promote software reproducibility. In this brief workshop we will establish several best practices of reproducibility in the (comparative) analysis of data obtained by NGS. In doing so we will encounter the commonly used technologies that enable these best practices by working through use cases that illustrate the underlying principles. Building on the basis of an existing pipeline of command line utilities, we will illustrate how the entire compute environment used to run the pipeline can be packaged into a unit that can be shared with other researchers such that they can make full use of the environment on their own machines, or on standard cloud compute environments such as Amazon or Google. Best practices Command line scripting of analysis steps Provisioning systems to standardise software environment requirements Packaging of compute environment into static, portable units Sharing of compute environment packages Technologies Next generation sequencing platforms Command-line executables, command line scripting and batching Provisioning Systems: Puppet, Dockerfile Virtualization with Virtualbox and Vagrant Containerization with Docker More details at the GTPB website http://gtpb.igc.gulbenkian.pt/bicourses/ARANGS16/ 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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Vacancy for a tenure track lecturer in structural bioinformatics at Vrije Universiteit Brussel
by Stefan Weckx 13 Apr '16

13 Apr '16

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TransMed 2016 (ISMB - Florida, July 8) - Call for abstracts
by Johann Pellet 12 Apr '16

12 Apr '16

We are happy to announce the TransMed 2016: Translational Medicine Informatics & Applications meeting, to be held during the ISMB 2016, (Orlando, USA), on July 8, 2016. Knowledge-based translational medicine is a rapidly growing discipline in biomedical research and aims to expedite the discovery of new diagnostic tools and treatments by using a multi-disciplinary, highly collaborative, "bench-to-bedside" approach. Large amounts of multi-omics, imaging (medical and molecular) and clinical data can now be captured for given patient populations. In addition to the challenges of data curation and harmonisation, new computational methods are required to identify molecular signatures that suggest disease subtype. These signatures may be predictive of outcome or progression, and impact on disease management by suggesting personalised therapeutic strategies for patients. Such approaches will further the development of a new taxonomy of disease. In the TransMed SIG meeting, we will explore the current status of computational biology approaches within the field of translational medicine. Authors are invited to submit abstracts (1 page) for presentations and posters by April 15, 2016. Details of submission process are available on the TransMed2016 SIG website: http://transmedit.org/Main_Page. Keynote Speakers Confirmed: Prof. Russ Altman, Professor of Bioengineering, Genetics, Medicine and Computer Science; Director, Biomedical Informatics Training Program, School of Medicine, Stanford University Prof. Sean Mooney, Professor of Biomedical Informatics and Medical Education, University of Washington; Chief Research Information Officer (CRIO) of UW Medicine Prof. John Overington, Director of Bioinformatics at Stratified Medical, Visiting Professor at the Institute of Cardiovascular Science, University College London and the Farr Institute Key dates: Abstract submissions deadline: April 15, 2016 Poster and Presentation acceptance notifications: May 6, 2016 Final program available: May 27, 2016 TransMed 2016 SIG: July 8, 2016 If you have any further questions regarding the submission of abstracts, do not hesitate to contact our committee at the following email address: transmed-coord(a)googlegroups.com.

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Open Positions at Coimbra Genomics
by Pedro Lopes 12 Apr '16

12 Apr '16

Hi! Coimbra Genomics S.A. is a young company working in Digital Health and Precision Medicine, which has recently sealed six partnerships for the global expansion of its first product ELSIE - a software platform developed by the company and designed to allow any doctor, anywhere, to use genomic information from patients to make better decisions on prescriptions and diagnosis, all in the setting of a regular medical appointment. More info at: www.coimbra-genomics.com Coimbra Genomics is looking for skilled candidates for 3 positions: - Bioinformatics Expert ( http://www.coimbra-genomics.com/news-posts/bioinformatics-expert-job-opening ) hands-on bioinformatics experience in genetic/genomics applications, preferably in the design and maintenance of NGS pipelines. Proficiency in Python and/or other languages is required. - Human Genetics Expert ( http://www.coimbra-genomics.com/news-posts/genetics-expert-job-opening) in-depth knowledge of human genetics; ability to work with small groups of specialists; be familiar with recent trends in genetics/genomics (e.g. WGS, WES, gene panels, gene mutation databases, etc). - Head of Marketing and Communication ( http://www.coimbra-genomics.com/news-posts/head-of-marketing-and-communicat… ) strong background in healthcare industry; previous experience in marketing genetics-related products or services would be a plus. The successful candidate will lead the creation and implementation of a global marketing strategy for the commercial deployment of ELSIE. The first two positions require frequent presence at the Biocant Park, in Cantanhede, but candidates wishing to remain based in other regions are encouraged to apply. The position for the Head of Marketing and Communication will be based in Portugal, Germany or UK, and will require frequent international travelling. Applicants should send a brief letter of motivation and a CV, in English, until 15th April to Sandra Tomé at sandra.tome(a)biocant.pt You can find the full job's description in the files attached to this email. Best, Pedro http://www.coimbra-genomics.com/

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