Data Engineer

Location
San Francisco, CA
Posted
May 16, 2022
Hotbed
Biotech Bay
Required Education
Bachelors Degree
Position Type
Full time
Are you ready for the challenge of managing and processing Gordian’s vast in vivo single cell perturbation datasets, to help identify novel therapeutic targets for complex age-related diseases?

The Destination:
Gordian Biotechnology is a therapeutics company focused on diseases of aging, the major unmet medical need of our generation. Age-related diseases have complex causes that include interactions with the aged environment, and traditional ex vivo screening methods have failed to produce effective treatments.

To address this problem, Gordian’s platform delivers and tests hundreds of therapeutics in individual animals. We thus scale in vivo efficacy testing to cover every therapeutic target at the very beginning of the drug discovery process. This lets us choose targets that really impact disease biology, to develop and commercialize therapies for the world’s deadliest diseases, and eventually for the processes of aging itself. 

The Journey:
Our mission is audacious, and the path will be full of both challenges and excitement. Two things characterize the Gordian experience: 1) We work as a team, with ownership in our own roles and trust in each other. 2) We strive for extraordinary outcomes, and in doing so grow our skills and capability.

Team – Relying on each other begins with transparency. We set clear goals, visibly connecting individuals and teams to our company objectives. This empowers each of us to make autonomous decisions about our work, knowing how they will affect the bigger picture. Our communication happens out in the open. We give and receive feedback from a perspective of helping each other grow, share mistakes, and ask for help.
Extraordinary – Every day, we ask ourselves ‘could this process/outcome be even better?’. Knowing our overall mission, we do what we think helps us make the most progress, without asking for permission. We don’t shy away from big challenges or unknown territory, but find a way to excel. Our colleagues are amazing, both at what they do and as people. They inspire us to keep up, to not let them down, and be inspiring in return. 

Like any cutting-edge research environment, Gordian doesn't believe in a standard 9 to 5 day. We set ambitious project goals and support each other to meet them, while maintaining the balance individuals need to thrive and achieve excellence. Our team is geared towards helping each other out and maintaining a culture of intellectual and social fun. We like getting things done and keep standing meetings to a minimum. This year, in accordance with our unlimited vacation policy, each member took an average of 2.5 weeks of (offline) vacation, not including major holidays. We unwind with weekly team lunches, and support each others’ projects both experimentally and by ‘pre-mortem’ meetings to discuss possible failure modes and experimental design. 

If this environment sounds appealing, help us bring it to life. We are at the beginning of a long journey, and want both your ability and your personality along for the ride. Our culture is a source of great pride; it represents both who we are, and who we wish to be. You can dive deeper here: https://www.gordian.bio/s/Values.pdf

The Details:
Gordian aims to provide everything you need to thrive. Beyond our community and science, you’ll have enough equity to be a true stakeholder in the company, competitive salary, full health/dental/vision/life insurance, 401k with match, whatever vacation you need to be at your peak, remote work flexibility, and access to world-class mentors and advisors to support your professional growth. Our labs are in the Dogpatch, near UCSF Mission Bay. 
And you:
You have a history of successful execution, both in- and outside of your job description. You want a chance to do your best work, to immerse yourself and excel alongside people who will inspire you and whom you’ll be excited to spend your days with. 

You truly want to play a key role in an early-stage startup: A fast-paced environment full of both uncertainty and new challenges, demanding relentless resourcefulness. You have deep expertise, and broad curiosity.

You have experience managing and processing large and varied genomic datasets, and writing software to help fellow scientists (whether computational or not) to access, analyze, and gain biological understanding of these data. You are excited to make it easy and efficient to extract insight from our unique in vivo data, to find better ways to treat complex diseases. 

Your mission in this role is to take the software backbone of Gordian’s in vivo screening platform to the next level, by building pipelines and other software tools that can handle the ever growing amount of data we collect. Gordian has multidimensional data across many cell types, with thousands of biological perturbations, in many species. Our data is unique, and making sense of it will require methodological analysis not only within each dataset, but across all of them. You’re excited to use and extend state of the art tools for processing single cell transcriptomic data, in order to make these data accessible to all scientists at Gordian. You will also integrate complementary data modalities (including imaging, spatial transcriptomics, epigenetic sequencing) with our transcriptomic data. Your work will happen in constant dialogue with both bioinformaticians and biologists. The tools you build will be used by the whole company, and you’ll design and document them accordingly.

In your first six months you will take responsibility for Gordian’s single cell processing pipeline, increasing throughput and efficiency to match experiments which will generate 10x more data than we have previously. In addition, you will establish and maintain systems to enable anyone outside the computational biology team to access our data and run basic analyses and queries.  

Strong candidates will have managed genomics pipelines and created software tools used by teams for accessing and basic analysis of data. Your work or work you contributed to should be evident from github and/or publications and accessible interactive data  (e.g. http://www.copdcellatlas.com/). You have a strong data engineering background with knowledge of genomic and bioinformatic data types and processes and are thoroughly comfortable with python/R, github/gitlab, and with using workflow languages such as Nextflow, wdl/Cromwell or Snakemake in a cloud computing environment. You combine a mindset of process optimization and reliability with intrepid build-from-scratch creativity.