Research Programmer Iv - Su Lab

ABOUT US: Scripps Research is ranked one of the most influential institutions in the world for its impact on innovation. We expand basic knowledge in the biosciences and use these fundamental advancements to develop profound innovations that improve wellbeing. Our educational and training programs mold talented and committed students and postdocs into leading edge scientists. Scientists in the institute’s five academic research departments work hand-in-hand with researchers of the Scripps Research Translational Institute and Calibr to merge foundational studies in biology, chemistry and computer science with translational science to produce pioneering drugs and advances in digital and precision medicine. Together, we cultivate new scientific leaders and expand the frontiers of knowledge to deliver medical breakthroughs to better human health around the globe. If you have a passion for making a difference, this could be your opportunity to join our transformative team.
POSITION TITLE: Research Programmer IV

POSITION SUMMARY:

This position will initially focus on the NSF-funded “Prototype Open Knowledge Graph” (Proto-OKN) project (www.nsf.gov/pubs/2023/nsf23571/nsf23571.htm), the goal of which is to build “an interconnected network of knowledge graphs supporting a very broad range of application domains”. These application domains include areas as diverse as biomedical science, toxicology, criminal justice, commercial supply chains, agriculture, energy, healthcare and more. Our team focuses on building infrastructure to integrate knowledge graphs from disparate domains and teams. We will build an “interconnecting fabric” that allows for integrative queries across all these domains. This position will focus on the use of Wikidata (wikidata.org) as a foundational layer of our Knowledge Fabric. Wikidata serves at least two roles - as an interstitial graph that links many independent knowledge graphs, and as a unifying source of identifier mappings across many ontologies and domains.
Beyond the specific Proto-OKN project, this position will generally work on the development of backend systems to efficiently access biomedical data, and/or DevOps to deploy and maintain software infrastructure. The hiring laboratory is involved in numerous projects to build software infrastructure and tools for bioinformatics, genetics, and genomics research. We have a particular emphasis on building large scale data integration infrastructure and on community platforms that enable collaboration and crowdsourcing. Representative projects include outbreak.info, the BioThings SDK for building APIs (biothings.io), and mygene.info. The broader research team includes a mix of software engineers and scientists; of graduate students, postdoctoral researchers, and staff; and of geographically and demographically diverse individuals. We actively cultivate an inclusive work environment.

REQUIREMENTS:

• Bachelor’s degree in Computer Science, Information Systems or related field or an equivalent combination of education, training and/or experience. Minimum of eight years programming experience, though relevant scientific experience and/or an advanced degree may reduce this requirement.
• Must have prior experience with knowledge graphs and/or semantic web technologies, including the use of RDF triple stores and/or labeled property graphs.
• Must be capable of leading a team and/or mentoring more junior developers.

PREFERRED SKILLSET:

Prior experience with the one or more of the following is preferred:

• Querying and editing Wikidata using the Wikidata API
• Familiarity with biomedical research and methodology, especially genetics and genomics.
• Experience developing scalable system architectures that adhere to good software engineering principles
• Ability to tackle, open-ended research questions independently and as part of a team
• Bioinformatics or computational biology experience
• Experience working within a diverse, interdisciplinary team.
• Experience contributing to open source software projects.
• Large scale data processing experience.

In addition, experience with one or more of the following technologies (or functional alternatives) is preferred:

• SPARQL and/or GraphQL
• Neo4j and/or GraphDB
• Elasticsearch
• Nginx
• Linux server (Ubuntu Server) administration
• Amazon Web Services setup and management
• Automated deployment
• Docker/Docker-compose, and automated CI/CD workflow setup

COMPREHENSIVE BENEFITS INCLUDE:

• Eligibility for retirement plans with employer contribution.
• Full suite of Health and Welfare plans including three medical plan options (including an HSA available option), dental, vision, life insurance, disability, EAP and more.
• Access to Flexible Spending Accounts (Medical/Dependent Care).
• Competitive vacation and sick leave policies.
• Free, on-site Counseling Center which provides confidential counseling services to benefits-eligible employees and their family members.
• Free, on-site parking.
  The above statements describe the level of work performed and expected in general terms. The statements are not intended to list all the responsibilities, duties and/or skills required of employees so classified, and the content herein is subject to change due to the business needs of Scripps Research, with or without notice. Furthermore, nothing in this job description shall be interpreted to be in conflict with or to eliminate or modify in any way the employment-at-will status of Scripps Research staff.

This individual will contribute to the design and implementation of technical solutions to facilitate integrative queries across the Proto-OKN knowledge graphs. These solutions will involve the creation of new software tools and components, which will be released as open-source code. This work will require extensive cross-team communication and collaboration, and this individual will be our primary representative to the other sites on the team.