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Position: Senior Scientific Programmer/Bioinformatician
Institution: European Molecular Biology Laboratory
Location: Heidelberg, Baden‐Württemberg, United Kingdom
Duties: We are seeking an experienced Senior Scientific Programmer/Bioinformatician to join the Samples, Phenotypes and Ontologies team to deliver new components for our Semantics as a Service platform used by the OpenTargets platform, the GWAS Catalog and several industrial partners from large pharma. Leading the delivery of software for these services. Developing the technical strategy for ontology services at EMBL-EBI. Building on our existing code base and services to support new user requirements. Transitioning our infrastructure to containerised/cloud-based delivery
Requirements: You should have a bachelor's degree in either bioinformatics or computer science and previous experience in designing and delivering software in a production environment. You should be able to demonstrate technical abilities in: Multiple programming languages, especially Java, Python and JavaScript and also working in a UNIX based environment. Experience of Java frameworks such as Spring would be an advantage. We use a number of different database technologies including relational databases (Oracle, MySQL), documents stores (MongoDB), Graph databases and triple stores (Neo4j, Virtuoso) and search technologies (Apache Solr)
   
Text: Senior Scientific Programmer/Bioinformatician Location: EMBL-EBI Hinxton near Cambridge, UK Staff Category: Staff Member Contract Duration: Until 31.05.2020 Grading: 6 (monthly salary starting at £2,944.48 after tax). Closing Date: 2nd September 2018 Reference Number: EBI_01271 Job Description We are seeking an experienced Senior Scientific Programmer/Bioinformatician to join the Samples, Phenotypes and Ontologies team (https://www.ebi.ac.uk/about/spot-team) to deliver new components for our Semantics as a Service platform used by the OpenTargets platform, the GWAS Catalog and several industrial partners from large pharma. The platform is essential in big data approaches to biological data analysis and is funded from several sources including the CORBEL project - a cross lifesciences infrastructure project which consumes the platform. The tools are highly accessed, use cutting edge technologies, including Java Spring, Neo4j, MongoDB, Apache Solr, OWL/RDF and Docker. The postholder will join at team of > 30 people working on common problems in lifescience and will deliver tools for accessing, building and using ontologies. The Ontology Lookup Service that provides Web service to access over 200 biomedical ontologies The Zooma service is our curated knowledgebase for mapping free text to ontology terms The OxO ontology mappings service that is used to discover mappings between ontology terms Our Webulous toolkit that helps our users build and contribute new terms to ontologies using GoogleSheets. The Experimental Factor Ontology is our in-house application ontology that serves a large number of projects including OpenTargets, GWAS catalog, BioSamples, ArrayExpress and Gene Expression Atlas and the Human Cell Atlas projects. You will be involved in the shaping the future direction of these services, and develop new features to support our growing user base through working closely with an interdisciplinary team of scientists and software engineers to rapidly translate requirements into technical solutions. Your primary responsibilities will include: Leading the delivery of software for these services Developing the technical strategy for ontology services at EMBL-EBI Building on our existing code base and services to support new user requirements Transitioning our infrastructure to containerised/cloud-based delivery At EMBL-EBI, we help scientists realise the potential of ‘big data’ in biology by enabling them to exploit complex information to make discoveries that benefit mankind. Working for EMBL-EBI gives you an opportunity to apply your skills and energy for the greater good. As part of the European Molecular Biology Laboratory (EMBL), we are a non-profit, intergovernmental organisation funded by 23 member states and two associate member states and proud to be an equal-opportunity employer. We are located on the Wellcome Genome Campus near Cambridge in the UK , and our 600 staff are engineers, technicians, scientists and other professionals from all over the world. Qualifications and Experience You should have a bachelor's degree in either bioinformatics or computer science and previous experience in designing and delivering software in a production environment. Prior knowledge of ontologies is highly desirable as is experience of working and integrating biological data though experience of relevant technologies is more important. We're looking for someone with a variety of technical skills and a willingness to learn new technologies. You should be able to demonstrate technical abilities in: Multiple programming languages, especially Java, Python and JavaScript and also working in a UNIX based environment. Experience of Java frameworks such as Spring would be an advantage. We use a number of different database technologies including relational databases (Oracle, MySQL), documents stores (MongoDB), Graph databases and triple stores (Neo4j, Virtuoso) and search technologies (Apache Solr) Experience of operations that include deploying Web servers and working with container technology such as Docker. You should also be flexible and willing to learn new skills whilst being encouraged to introduce new ideas and technologies to the group. Our team follow agile development principles and work in short bi-weekly sprints and develop software with an open-source and collaborative spirit. As part of your day to day job, you can expect to interact with other groups at EMBL-EBI as well as our external collaborators. All members of the team are expected to travel internationally to present our work at conferences and project meetings and also contribute to report writing and publishing scientific papers. This means good communication skills and strong verbal and writing skills are essential. Benefits EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation. The remuneration package comprises a competitive salary, a comprehensive pension scheme and health insurance, educational and other family related benefits where applicable, as well as financial support for relocation and installation. We have an informal culture, international working environment and excellent professional development opportunities but one of the really amazing things about us is the concentration of technical and scientific expertise - something you probably won’t find anywhere else. If you’ve ever visited the campus you’ll have experienced first-hand our friendly, collegial and supportive atmosphere, set in the beautiful Cambridgeshire countryside. Our staff also enjoy excellent sports facilities including a gym, a free shuttle bus, an on-site nursery, cafés and restaurant and a library. Application Instructions To apply please submit a covering letter and CV, with two referees, through our online system. Additional Information Applications are welcome from all nationalities - visa information will be discussed in more depth with applicants selected for interview. EMBL-EBI is committed to achieving gender balance and strongly encourages applications from women, who are currently under-represented at all levels. Appointment will be based on merit alone. This position is limited to the project duration specified.
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