Engineer, Bioinformatics Cloud at Second Genome
South San Francisco, CA, US

Hi, we’re Second Genome.

We are a fast-paced and innovative venture-backed biotechnology company developing tomorrow’s breakthrough therapeutics at the interface of complex microbial communities and their host environments.  We are leaders in microbial ecology, metagenomics, and computer science. Our stellar informatics team works hand-in-hand with our expert lab scientists to propose and test novel scientific hypotheses based on compelling observations from large data sets. We love fresh approaches, we value process validation, and we welcome peer review.

In addition to our ground-breaking technology, we believe in embodying an authentically joyful workplace. Our Core Values:

  • We are Innovators

  • We are Driven to Action

  • We are Great Colleagues

  • We Work Smart

  • We Respect the Data

And we’re looking for a Bioinformatics Cloud Software Engineer.... otherwise known as a Genomic Data Science Cloud Platform Impresario. 

We’re on the search for a computer scientist, computational biologist, or software engineer with a passion for platform development. Our ideal candidate understands that their work directly supports multi-million dollar hypotheses - and is comfortable standing by their product. We want to meet a natural multi-tasker who embraces the rapidly changing demands of an industry environment. We value team players who understand the importance of communication and the fine balance between compromise and assertion. We’d love to work with someone who is personally driven but comfortable not having all the answers, and resourceful when working toward goals.


Responsibilities and Duties

  • Develop Second Genome’s best-in-class genomic and metagenomic data management and discovery cloud platform using software development lifecycle principles

  • Actively seek, evaluate, scale, and spearhead the adoption of new computational approaches to expand our data science capabilities

  • Communicate findings within the group and to stakeholders inside and outside the company


Qualifications and Skills

  • Fluency in Python and its numerical, scientific, and parallel computing libraries, including but not limited to numpy, pandas, scikit-learn, and multiprocessing

  • Fluency with MySQL or similar query language, database schema design, and the Python sqlalchemy library

  • Working experience with Amazon AWS cloud services and/or developing a serverless infrastructure

  • Knowledge of code versioning systems like SVN or git

  • Managing and communicating developments using a project management software like JIRA, Trello, or Redmine

  • Familiarity with R and Unix shell command line tools

  • Ability to effectively explain complex computational approaches to individuals from different disciplinary backgrounds

  • Committed to integrity, accountability, transparency, and reproducibility; results that can’t be reproduced by another are meaningless

  • Ph.D. in Computer Science, Applied Mathematics, Bioinformatics, or comparable, or a Master’s degree with about two years industry experience

  • Documented success in a multiple programmer DevOps team with specific experience with choosing related issues to address for a specific release, writing unit tests, preparing software branches for merging by the lead developers


Bonus Qualifications

  • Familiarity with prokaryotic biology, biological sequence data, and contemporary tools for analyzing and operating on biological sequences

  • Knowledge of public bioinformatics databases and tools

  • Familiarity with machine learning methods and multivariate statistics, feature selection methodologies and model validation strategies to minimize false discovery rates

  • Proficiency in visualization and presentation of large scale -omics data

  • Strong interpersonal communication skills


What’s it like to work at Second Genome?

We understand and appreciate the hard work and emotional investment on the part of all our team members - it takes a lot to be a contributor at a startup that’s leading its industry. We make it a priority to mindfully design our work environment and employee offerings with our unique and dedicated team in mind.

  • Competitive salary and employee stock options.

  • Fully stocked kitchen with sandwich materials, organic snacks, coffee (Peet’s or Stumptown - take your pick!) and beverages.

  • Four weeks paid time off, plus federal holidays.

  • Generous and comprehensive medical, dental, and vision plan options, including doctor house calls and in-office clinics.

  • 401(k) plan, HSA option, and pre-tax FSA accounts: dependent care, transit, healthcare, and parking.

  • Our WellBiome health and wellness program: a monthly health stipend, open standing desks, and weekly boot camp and yoga classes on-site.

  • Apple computer + all its fancy accessories.

  • Friendly and open office environment with great colleagues and an intentional culture that drives innovation, passion, collaboration, and fun!

  • A picture is worth a thousand words. Check out our Instagram @secondgenomelife for a glimpse into our unique team culture.


Second Genome provides equal employment opportunities (EEO) to all employees and applicants for employment without regard to race, color, religion, sex, national origin, age, disability or genetics. In addition to federal law requirements, Second Genome complies with applicable state and local laws governing nondiscrimination in employment in every location in which the company has facilities. This policy applies to all terms and conditions of employment, including recruiting, hiring, placement, promotion, termination, layoff, recall, transfer, leaves of absence, compensation and training.