Job Description:
Berkeley Labs Environmental Genomics and Systems Biology Division (EGSB) has an exciting opportunity available for a Software Developer to develop advanced frameworks for biomedical data discovery using graph database systems. You will work primarily on the NIH Monarch Initiative which provides an integrated knowledge base and ontologies connecting diverse data about genotype-phenotype associations in humans and model systems. You will develop the next generation of the SciGraph API, providing advanced functionality for data exploration and discovery. The technology you develop will also form the basis for revealing new relationships between data in the NCATS Translator project. It will also be the backend for the Gene Ontology and the associated Noctua knowledge modeling environment. This position will be filled at the Level 3 or 4, dependent on experience. Specific Responsibilities: -Develop and extend APIs on top of graph databases and/or RDF triplestores. -Implement algorithms that integrate logical and probabilistic inference over biological data. -Devise methods that allow expressive queries to be executed efficiently. -Maintain pipelines for bulk upload and synchronization of data. In Addition To The Above, Specific Responsibilities - Level 4 -Devise novel algorithms for elucidating disease mechanisms, and publish on results. -Contribute to grant writing. -Provide technical assistance and training to collaborators at other sites. -Serve as a key contributor to troubleshoot and solve highly technical, complex problems and provide direction for the project. Required Qualifications: -Bachelors Degree and or equivalent experience in computer science, bioinformatics or related field and a minimum of 4-5 years of relevant experience. -Extensive knowledge of a variety of graph databases, including RDF triplestores. -Experience modeling and working with complex data (ideally biological). -Excellent software engineering skills. -Ability to work effectively in a diverse team environment. -Additional Desired Qualifications For Both Levels. In addition to the above, Required Qualifications for Level 4: -Knowledge of ontology and knowledge engineering frameworks, APIs, languages and techniques (e.g. OWLAPI, Jena, SPARQL). -Familiarity with a high-level JVM language, ideally Scala. -Experience with Apache Spark engine. -Knowledge of Apache Lucene frameworks (e.g. Solr, Elastic Search). -A good intuition for visualization techniques. -The posting shall remain open until the position is filled.
Additional Info:
Berkeley Lab (LBNL) addresses the worlds most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Labs scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the U.S. Department of Energys Office of Science. This is a full time 1 year term appointment with the possibility of extension or conversion to Career appointment based upon satisfactory job performance, continuing availability of funds and ongoing operational needs. Classification will depend upon the applicant's level of skills, knowledge, and abilities. Full-time, M-F, exempt (monthly paid) from overtime pay. Salary is commensurate with experience. This position is contingent on the successful completion of a background check. Work will be primarily performed at West Berkeley Biocenter (Potter St.) Bldg. 977, 717 Potter St., Berkeley, CA. Equal Employment Opportunity: Berkeley Lab is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status. Berkeley Lab is in compliance with the Pay Transparency Nondiscrimination Provision under 41 CFR 60-1.4. Click here to view the poster and supplement: "Equal Employment Opportunity is the Law.[Click Here to Access the Original Job Post]
Berkeley Labs Environmental Genomics and Systems Biology Division (EGSB) has an exciting opportunity available for a Software Developer to develop advanced frameworks for biomedical data discovery using graph database systems. You will work primarily on the NIH Monarch Initiative which provides an integrated knowledge base and ontologies connecting diverse data about genotype-phenotype associations in humans and model systems. You will develop the next generation of the SciGraph API, providing advanced functionality for data exploration and discovery. The technology you develop will also form the basis for revealing new relationships between data in the NCATS Translator project. It will also be the backend for the Gene Ontology and the associated Noctua knowledge modeling environment. This position will be filled at the Level 3 or 4, dependent on experience. Specific Responsibilities: -Develop and extend APIs on top of graph databases and/or RDF triplestores. -Implement algorithms that integrate logical and probabilistic inference over biological data. -Devise methods that allow expressive queries to be executed efficiently. -Maintain pipelines for bulk upload and synchronization of data. In Addition To The Above, Specific Responsibilities - Level 4 -Devise novel algorithms for elucidating disease mechanisms, and publish on results. -Contribute to grant writing. -Provide technical assistance and training to collaborators at other sites. -Serve as a key contributor to troubleshoot and solve highly technical, complex problems and provide direction for the project. Required Qualifications: -Bachelors Degree and or equivalent experience in computer science, bioinformatics or related field and a minimum of 4-5 years of relevant experience. -Extensive knowledge of a variety of graph databases, including RDF triplestores. -Experience modeling and working with complex data (ideally biological). -Excellent software engineering skills. -Ability to work effectively in a diverse team environment. -Additional Desired Qualifications For Both Levels. In addition to the above, Required Qualifications for Level 4: -Knowledge of ontology and knowledge engineering frameworks, APIs, languages and techniques (e.g. OWLAPI, Jena, SPARQL). -Familiarity with a high-level JVM language, ideally Scala. -Experience with Apache Spark engine. -Knowledge of Apache Lucene frameworks (e.g. Solr, Elastic Search). -A good intuition for visualization techniques. -The posting shall remain open until the position is filled.
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Additional Info:
Berkeley Lab (LBNL) addresses the worlds most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Labs scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the U.S. Department of Energys Office of Science. This is a full time 1 year term appointment with the possibility of extension or conversion to Career appointment based upon satisfactory job performance, continuing availability of funds and ongoing operational needs. Classification will depend upon the applicant's level of skills, knowledge, and abilities. Full-time, M-F, exempt (monthly paid) from overtime pay. Salary is commensurate with experience. This position is contingent on the successful completion of a background check. Work will be primarily performed at West Berkeley Biocenter (Potter St.) Bldg. 977, 717 Potter St., Berkeley, CA. Equal Employment Opportunity: Berkeley Lab is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status. Berkeley Lab is in compliance with the Pay Transparency Nondiscrimination Provision under 41 CFR 60-1.4. Click here to view the poster and supplement: "Equal Employment Opportunity is the Law.[Click Here to Access the Original Job Post]