June 2019 - BBClist - maillist.psb.ugent.be

Researcher in Artificial Intelligence applied to life sciences (RRE) / Reference: 173_LS_AI_RRE
by BSC RRHH 13 Jun '19

13 Jun '19

Researcher in Artificial Intelligence applied to life sciences (RRE) Primary tabs *Context And Mission* The Life Sciences Department at the BSC integrates the independent research of senior scientists that work on various aspects of computational biology, ranging from bioinformatics for genomics to computational biochemistry and text mining. The Computational Biology group is involved in multiple projects in collaboration with experimental groups generating state-of-the-art genomics and epigenomics datasets, actively participating in the International Human Epigenome Consortium and with the general aim of enabling new approaches in personalized medicine. Current efforts involve integration of different types of omics data, with a particular emphasis on epigenomics. We are establishing methods to study genome architecture exploiting interdisciplinary tools such as machine learning and network theory. The mission of the Computer Science Department at the BSC is to influence the way machines are built, programmed and used: computer and system architecture, programming models and performance tools, resource management, Big Data and artificial intelligence. The HPAI (High Performance Artificial Intelligence) research group is part of the Computer Science department, and it performs research in Artificial Intelligence, focused on the solutions, problems and infrastructure provided by High Performance Computing. The group actively collaborates with researchers from other fields, with the goal of applying machine learning to challenging problems in a wide variety of domains. HPAI has active collaborations with several large tech companies, pursuing lines of research of common interest. The group is also involved in multiple research projects, both European and national. Although the HPAI is open to all aspects of AI, currently its main lines of research are deep neural networks and graph analytics. The post holder will collaborate with the Life Sciences department and the HPAI research group in the Computer Science department, with the goal of finding AI solutions to life sciences challenges. This will include working closely with researchers from both areas, programming, testing and dissemination of the research. The candidate will be able to develop an independent research programme within the broad topics mentioned above. The Researcher will work in a highly sophisticated HPC environment, will have access to state-of-the-art systems and computational infrastructures, and will establish collaborations with experts in different areas both at the local and international levels. *Key Duties* * Development of AI solutions, with special emphasis on machine learning methods, for the analysis and interpretation of biological data * Use predictive computational methods based on statistical and inference approaches to model complex biological processes * Integration of heterogeneous data sources using advanced data mining techniques *Requirements* * Education o PhD in computer science or bioinformatics with a strong AI component. o OR Alternatively, an MSc on AI or Bioinformatics, with a strong computer science background, or background on applied mathematics/physics with demonstrated experience in AI methods. * Essential Knowledge and Professional Experience o Experience in AI methodologies o Interest in the life sciences area * Additional Knowledge and Professional Experience o Knowledge and experience in life sciences research o Knowledge and experience in AI methodologies: - Data pre/post-processing (feature selection, feature reduction, plotting and visualization) - Supervised and unsupervised learning (classification, clustering, regression) - Knowledge representation - Complex networks (graph-based representation, graph analytics) - Deep learning (TensorFlow, PyTorch, Caffe, word embeddings) o Programming: Python (scikit-learn, numpy, matplotlib), Matlab, R, Java, C, C++, Git * Competences o Fluency in spoken and written English, while fluency in other European languages will be also valued o Capacity to explore new research lines o Good communication and presentation skills o Ability to work both independently and within a team *Apply here:* https://www.bsc.es/join-us/job-opportunities/173lsairre http://bsc.es/disclaimer

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Post-doc Researchers in Computer Science and Bioinformatics (R2) / Reference: 270_LS_ICB_R2
by BSC RRHH 13 Jun '19

13 Jun '19

Post-doc Researchers in Computer Science and Bioinformatics (R2) *Context And Mission* Professor Nataša Pržulj is looking for several post-docs to work in machine learning and network science. They will be developing new algorithms for computationally hard problems and applying them to analyzing large-scale molecular and patient data to aid drug discovery and personalizing treatment. The successful candidates will work on the prestigious ERC Consolidator grant of Prof. Pržulj. The successful candidates will address developing and applying sophisticated machine learning and network science models and algorithms. The algorithms will be carefully tuned to extract relevant biological and medical knowledge from systems-level real-world molecular and medical data. The aim is to utilize them to understand the structure of the data that would enable mining the data for new biological and medical insight that would further lead to improving diagnostics, discovering new biomarkers, improving patient stratification and treatment, personalizing treatment and facilitate rational drug development. The successful candidates will join a dynamic research group of Prof. Przulj within BSC. The students will work in a highly sophisticated HPC environment, will have access to systems and computational infrastructures, and will establish collaborations with experts in different areas. *Key Duties* * Conduct high-quality research * Publish in high impact journals and conferences * Present research at national and international conferences and meetings * Collaborate with various research groups across Europe and elsewhere * Help supervise PhD and MSc students * Participate in grant writing and organizational activities * Participate in educational and outreach activities *Requirements* * Education o PhD in Computer Science, Mathematics, Physics, Bioinformatics, or a related field * Essential Knowledge and Professional Experience o Good publication record for the career stage o Fluency in spoken and written English * Competences o Good technical skills including at least several of the following: algorithms, data analysis, graph, network and complexity theory, scientific computing, statistics, machine learning, programming in C, C++, a scripting language and Matlab, using a parallel computing environment, bioinformatics, network biology, network medicine, network analytics, medical informatics. *Apply here: *https://www.bsc.es/join-us/job-opportunities/270lsicbr2 http://bsc.es/disclaimer

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BSC: (bio-)informatician back-end engineers (RE12) / Reference: 97_LS_INB_RE12
by BSC RRHH 13 Jun '19

13 Jun '19

(bio-)informatician back-end engineers (RE12) *Context And Mission* The Spanish National Bioinformatics Institute (INB) is the major bioinformatics platform in Spain, and the Spanish representative in the European bioinformatics infrastructure ELIXIR. INB is fully oriented to complete a solid integration with International Bioinformatics infrastructures including specifically the ELIXIR consortium. *Key Duties* * Design, implement and document communication channels for data sharing honoring data ownership, and security * Contribute to the development of a Virtual Research Environment (VRE) for various research projects at the Life Sciences Department * Manage and support users of the INB computational resources, including computational equipment, databases, and software infrastructure * Develop, document and maintain software for the integration and biological data, following the guidelines of ELIXIR * Contribute to the management of data within the current projects * Maintain communication with ELIXIR platforms, communities, and management, participate in their regular meetings and discussions * Contribute to supervise junior members at the INB/ELIXIR-ES units *Requirements* * Education o BSc or MSc. in bioinformatics, computational biology or computer sciences with significant bioinformatics experience * Essential Knowledge and Professional Experience o At least 2 years of professional experience with a similar role o Experience in cloud computing o Experience in data management APIs and most common bioinformatic data sources and formats o Experience in database design and management (SQL and noSQL): MySQL/MariaDB, PostgreSQL, SQLite or similar; MongoDB, Elasticsearch, Cassandra or similar o Experience with advanced software packaging procedures o At least 2.5 years of professional experience on programming languages ecosystems such as C++, Perl, Python, PHP and/or Java o Vast experience working with Unix/Linux systems * Additional Knowledge and Professional Experience o Experience in modern authentication/authorization protocols o Experience on the development, generation and use of software containers e.g. Docker, Singularity and/or rkt, as well as their orchestration using docker compose, kubernetes, ansible and/or similar technologies o Experience on workflow managers such as Galaxy, Nextflow or similar o Experience on developing project technical specifications * Competences o Ability of understand scientific literature, and software documentation o Ability to communicate scientific results o Ability to work independently o Ability to represent the team in international project meetings o Used to work under pressure under strict deadlines *Apply here: *https://www.bsc.es/join-us/job-opportunities/97lsinbre12 http://bsc.es/disclaimer

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BSC: (bio-)informatician web front-end developer (RE12) / Reference: 96_LS_INB_RE12
by BSC RRHH 13 Jun '19

13 Jun '19

(bio-)informatician web front-end developer (RE12) *Context And Mission* The Spanish National Bioinformatics Institute (INB) is the major bioinformatics platform in Spain, and the Spanish representative in the European bioinformatics infrastructure ELIXIR. INB is fully oriented to complete a solid integration with International Bioinformatics infrastructures including specifically the ELIXIR consortium. *Key Duties* * Contribute to the development of front-end platforms and associated APIs for the current research projects in the Life Sciences department, in close collaboration with back-end engineers * Contribute to ensure appropriate user experience at the developed front-ends * Work together with other developers at INB/ELIXIR-ES and other ELIXIR nodes to ensure the appropriate implementation of previously agreed standards and methodologies * Contribute to supervise junior members at the INB/ELIXIR-ES units *Requirements* * Education o Software Engineer Degree or equivalent Bioinformatics related degrees * Essential Knowledge and Professional Experience o At least 2 year of professional experience in web frontend technologies such as NPM, yarn, Bower, Grunt, Gulp, webpack, or and HTML, CSS and JavaScript ecosystems o At least 2 year of professional experience with programming languages such as Ruby, Python and/or Java o Vast experience working with Unix/Linux systems * Additional Knowledge and Professional Experience o Experience in microservices software architecture o Experience with back-end frameworks, like Spring, Django or Laravel o Experience with front-end frameworks, like Angular, Vue and/or React will be highly appreciated o Familiar with software containers technologies such as Docker and/or Singularity o Familiar with design, implementation and deployment of relational databases (MySQL, PostgreSQL or similar) and/or non-relational databases (MongoDB, ElasticSearch, Cassandra) o Experience in designing, implementing and documenting data management APIs o Experience on developing project technical specifications * Competences o Fluency in English o Good writing and presentation skills o Strong personal soft-skills sets: Communicative, enthusiastic, highly collaborative, proactive, self-driven o Strong technical writing skills o Ability to work independently o Ability to represent the team in international project meetings o Used to work under pressure under strict deadlines *Apply here: *https://www.bsc.es/join-us/job-opportunities/96lsinbre12 http://bsc.es/disclaimer

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Master Student - R0
by BSC RRHH 13 Jun '19

13 Jun '19

*Master Student - R0* * * *Context And Mission* To develop novel algorithms on Neoantigen immunogenicity predictions. *Key Duties* * To assist in the new team working in Neoantigen predictions. *Requirements* * Education o Bachelor in Biotechnology, Bioinformatics or related field * Essential Knowledge and Professional Experience o Bioinformatics and python programming * Competences o Team work *Conditions* * The position will be located at BSC within the Life Sciences Department * We offer a full-time contract, a good working environment, a highly stimulating environment with state-of-the-art infrastructure, flexible hours, extensive training plan, tickets restaurant, private health insurance, fully support to the relocation procedures * Duration: Temporary - 1 year renewable * Salary: we offer a competitive salary commensurate with the qualifications and experience of the candidate and according to the cost of living in Barcelona * Starting date: July 1st *Apply here:* https://www.bsc.es/join-us/fellowships/14119lseapmr0 http://bsc.es/disclaimer

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Come join us as a postdoc or PhD student in Bioinformatics at HZI
by McHardy, Alice C. 11 Jun '19

11 Jun '19

Dear all, we are looking for postdocs and PhD students who would like to work with us in the Department of Computational Biology for Infection Research at HZI. More details can be found below and feel free to contact me with questions. https://tinyurl.com/yy6l7z9b Best, Alice McHardy Prof. Alice C. McHardy Computational Biology of Infection Research Helmholtz Centre for Infection Research ________________________________ Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Silke Tannapfel Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

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Fwd: [Programming-interest] Vacancy Data Steward for Rare Diseases Project at Radboudumc
by Gurnoor Singh 11 Jun '19

11 Jun '19

---------- Forwarded message --------- From: <Koen.tenHove(a)radboudumc.nl> Date: Tue, Jun 11, 2019 at 10:06 AM Subject: [Programming-interest] Vacancy Data Steward for Rare Diseases Project at Radboudumc To: <programming-interest(a)lists.dtls.nl> Dear all, Please find a vacancy for ‘Data Steward for Rare Diseases Project’ below. Could you please spread this to people, in your network, who could be interested (themselves, or might know someone)? https://www.radboudumc.nl/en/vacancies/66621-data-steward-for-rare-diseases… Thanks in advance! Kind regards, *Koen ten Hove* | Data scientist, team Data Stewardship Radboudumc | Information Management | Koen.tenhove(a)radboudumc.nl 06-15508235 - looproute 196 internal website: http://www.radboudumc.nl/intranet/rdl external website: www.radboudumc.nl/datastewardship *Radboud universitair medisch centrum* Postbus 9101, 6500 HB Nijmegen www.radboudumc.nl De informatie in dit bericht is uitsluitend bestemd voor de geadresseerde. Aan dit bericht en de bijlagen kunnen geen rechten worden ontleend. Heeft u deze e-mail onbedoeld ontvangen? Dan verzoeken wij u het te vernietigen en de afzender te informeren. Openbaar maken, kopiëren en verspreiden van deze e-mail of informatie uit deze e-mail is alleen toegestaan met voorafgaande schriftelijke toestemming van de afzender. Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The content of this message is intended solely for the addressee. No rights can be derived from this message or its attachments. If you are not the intended recipient, we kindly request you to delete the message and inform the sender. It is strictly prohibited to disclose, copy or distribute this email or the information inside it, without a written consent from the sender. Radboud university medical center is registered with the Dutch Chamber of Commerce trade register with number 41055629. _______________________________________________ Programming-interest mailing list Programming-interest(a)lists.dtls.nl https://lists.dtls.nl/mailman/listinfo/programming-interest -- Thanks & regards, Gurnoor Singh. Laboratory of Plant Breeding, WU Plant Sciences, Netherlands. Tel: +31-636474720

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training in Cloud Computing For Biomedical Researchers.
by Lieven Sterck 06 Jun '19

06 Jun '19

> From: "PHADWAL Kanchan" <Kanchan.Phadwal(a)roslin.ed.ac.uk> > Dear All > American Academy for Biomedical Informatics, Maryland, USA is organising a two > days ( August 6 th and 7 th ) hands on training in Cloud Computing For > Biomedical Researchers. This is aimed at all the Biomedical researchers. For > further details and registration please see the link below. > [ > https://www.eventbrite.com/e/cloud-computing-for-biomedical-researchers-reg… > | > https://www.eventbrite.com/e/cloud-computing-for-biomedical-researchers-reg… > ] > * Save With Early Bird Registration > Best Wishes > Kanchan > The University of Edinburgh is a charitable body, registered in Scotland, with > registration number SC005336.

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two upcoming HPC worskhops for Life Science Researchers
by Mateusz Kuzak 05 Jun '19

05 Jun '19

Dear all, SURFsara in collaboration with ELIXIR-NL and DTL is organising two High-Performance Computing workshops targeted at life science researchers. Both workshops will take place in Utrecht in SURF offices. "Cluster Computing for Life Sciences" is a two-day workshop. On the first day, participants will learn the basics of the Unix shell and how to work on the command line efficiently and how to access resources with more computing power (computer cluster) and run the computations remotely. On the second day, they will learn the basics of Python programming language and build a simple analysis pipeline with Snakemake and execute it on the computer cluster. Website and registration Time and Date: 9 am - 5 pm, 1-2 July, 2019 Location: SURF Utrecht. Kantoren Hoog Overborch (Hoog Catharijne), Moreelsepark 48, room 3.5, 3511 EP Utrecht ------------------------------- "Getting started on the high-throughput data processing platform" Vastly increasing data volumes and data complexity imply that researchers require novel solutions to large scale cluster computing. This workshop aims to provide an introduction and hands-on experience with our new solution to this problem: “a new and versatile platform for high-throughput data processing”. Website and registration Time and Date: 9 am - 5 pm, August 28, 2019 Location: SURF Utrecht. Kantoren Hoog Overborch (Hoog Catharijne), Moreelsepark 48, room 3.5, 3511 EP Utrecht — Mateusz Kuzak Scientific Community Manager | Dutch Techcentre for Life Sciences e-mail: mateusz.kuzak(a)dtls.nl | Tel. +31 643707254 twitter: @matkuzak | GitHub: mkuzak | skype: mkuzak orcid: orcid.org/0000-0003-0087-6021 Visiting address: DTL | Jaarbeurs Innovation Mile (JIM) | 6th-floor Beatrixgebouw Jaarbeursplein 6 | 3521 AL Utrecht

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Cloud developer position Ghent University
by Michiel Van Bel 03 Jun '19

03 Jun '19

Dear all, Ghent University and VIB are looking for a motivated software developer within the ELIXIR life sciences framework. Project The PLAZA platform for comparative, evolutionary, and functional genomics is a data resource that integrates gene and genome information ( [ https://bioinformatics.psb.ugent.be/plaza | https://bioinformatics.psb.ugent.be/plaza ] ). It offers a wide variety of tools to end-users through a web interface, in order to help speed up both small-scale and large-scale data analyses. Multiple independent instances of the platform exist, where each instance either focuses on a different phylogenetic clade, or uses improved gene annotations and genome assemblies compared to previous instances. In order to scale up the building of these instances, we are looking for a software developer to help with moving the PLAZA platform to cloud-based systems. Your tasks: * You are responsible for the design and implementation of the necessary tool-chain for building PLAZA instances in the cloud (e.g. OpenStack, Amazon cloud, Azure, etc.). * You assist with the building of new PLAZA instances, and help with the implementation of unit-tests to check the status and validity of newly build PLAZA instances. * You implement configuration and administration utilities for end-users, to facilitate building PLAZA instances. Profile You hold a degree of Master in computer science, bioinformatics, (bio)engineering, biotechnology or an equivalent degree * Hands-on experience with Linux/Unix environments and BASH scripting * Proficiency in at least one programming language (e.g. Java, Python, …) and one scripting language (e.g. Perl, Python, …) * Good working knowledge of relational databases and SQL How to apply? Click the link below to access the job-portal of Ghent University [ https://career5.successfactors.eu/career?career_ns=job_listing&company=C000… | https://career5.successfactors.eu/career?career_ns=job_listing&company=C000… ] Michiel Van Bel - Postdoctoral fellow Applied Bioinformatics And Biostatistics VIB-UGent Center for Plant Systems Biology Ghent University Technologiepark-Zwijnaarde 71 - 9052 Ghent - Belgium Tel. +32(0)9 331 36 95 [ http://www.psb.ugent.be/ | www.psb.ugent.be ] Genome editing, cutting-edge technology for a sustainable agriculture

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