Software Engineer

Location
San Francisco, CA, United States
Posted
Sep 27, 2020
Ref
REQ-387
Hotbed
Biotech Bay
Required Education
Doctorate/PHD/MD
Position Type
Full time
Category:
Science
Lab/Area:

Pico Area

Description:

We are seeking a talented software engineer to develop compelling technology for network biology and biomedical research. You will be working with established local and distributed teams of open source software developers dedicated to putting tools in the hands of biomedical researchers and clinicians. We will be developing network visualization and analysis tools and resources to elucidate molecular profiles underlying major diseases.

You must have demonstrated experience with modern software engineering practices for developing web applications and web services. Your experience should be sufficient to inform project-specific implementation decisions regarding:

  • JS environments and specifications (Node, ES2015+, TypeScript)
  • Frameworks and Architectures (React, Angular, Redux)
  • Bundlers/Transpilers (Webpack, Babel)
  • Design systems (Material UI, Styled Components)
  • API definition, deployment and maintenance (REST, Swagger, JSON)
  • Scripted data processing and pipelines (R, Python, Jupyter notebooks)
  • Algorithm implementation and optimization (C++, Java, Python)


Additionally, you should be knowledgeable about deployment, continuous integration, testing, database and DevOps technologies. You are expected to be proficient at leveraging Amazon, Google and HPC systems for custom computing and service deployment (PaaS, GCP, AWS, containers). Prior experience with Java application development, including OSGi and Maven, is also desired. Familiarity with high-throughput biomedical data (e.g., scRNA-Seq and proteomics), network models of biology or Cytoscape/cytoscape.js is a plus. Some experience developing biomedical or biological research applications is expected.

You will be working with a lean, distributed team of agile developers with varying degrees of biology expertise, led by a PhD biophysicist and lifelong programmer (who still writes code) and organizes development communities for multiple open source software projects. All of our coding projects are open source. The work most relevant to this position can be found among the repos at https://github.com/cytoscape.

The Gladstone Institutes is an independent, not-for-profit research organization affiliated with the University of California San Francisco (UCSF), contributing to the health and well being of all people through medical research, education, and outreach in the areas of heart disease, HIV/AIDS, and neurological disease. Gladstone Bioinformatics hosts a convergence of cutting-edge research, omics analytics, biostatistics and technology development, and is one of the primary centers for the National Resource for Network Biology, an NIH-sponsored resource for broadly distributed network biology software and methods. Gladstone's approximately 550 employees receive exceptional benefits. We are located in an award winning building adjacent to UCSF's Mission Bay Campus.

Responsibilities
  • To develop software tools within an existing ecosystem of open source solutions as an active member of a community-driven (and grant aim-driven) team effort.
  • To participate in translating biomedical problems into technology solutions.
  • To be responsible for end-to-end life cycle development, including design, testing and documentation, employing best practices.
  • To work effectively with multiple stakeholders and collaborators, including experimental and computational researchers, as well as distributed teams of developers, participating in weekly team meetings and conferences.
  • To lead and support end-user workshops and training events.
  • To coauthor scientific publications highlighting your tools and their application to biomedical problems, and contribute to grant applications and periodic report related to your projects.

Qualifications:
  • Masters or equivalent experience in computer science or biomedical software engineering
  • Minimum of 2 years post-undergrad experience in a research and development environment
  • Prior experience developing biomedical or biological research applications is expected.
  • Strong web application and web services development skills required
  • Extensive experience with JavaScript and either Python, C++ or Java required
  • Prior Java experience should include Swing, OSGi and Maven
  • Prior experience with API development required
  • Deep software engineering experience and affinity expected:
    • Full life cycle, Agile, unit testing
    • PaaS: GCP, AWS
    • DevOps, VM administration, containers
    • Continuous integration, Jenkins
    • RESTful web services, APIs
    • UI/UX sensibilities
    • Open source, collaborative/remote dev teams
    • Trello, Slack and real-time collaboration/coordination tools
  • Experience with data mining, analytical methods and visualization
  • Familiarity with high-throughput biomedical data types and methods: mass spec, sequencing data and variant data in particular is a plus
  • Prior experience with graph theory, network models of biology or Cytoscape is a major plus



Additional Information:

  • Title and salary will be commensurate with education and experience.
  • Be a part of big ideas and consider Gladstone. Your difference will make a difference in human health.
  • Gladstone is an equal opportunity employer.