We’re looking for a developer to ramp up our efforts with Nextstrain.org. Job advertisement follows:
A developer position is available immediately in the Bedford lab at the Fred Hutch to improve backend infrastructure of Nextstrain.org and work with public health and academic partners to streamline data sharing and real-time analysis.
In collaboration with Neher lab at the University of Basel, we’ve built the Nextstrain platform to conduct real-time genomic epidemiology to aid understanding of pathogen spread and improve outbreak response. Pathogen genomic data can reveal otherwise hidden connections between infections and be used to infer patterns of epidemic growth, geographic spread and adaptive evolution. However, only through open sharing of genomic data can these inferences be fully realized. Our aim with Nextstrain.org is to provide a platform for both data sharing and analysis. This platform won the Open Science Prize in Feb 2017 and has already been instrumental in analysis of Ebola spread in West Africa, Zika spread in the Americas and is used by the World Health Organization to aid in the process of influenza vaccine strain selection.
The codebase is completely open source at github.com/nextstrain. Currently, we use a data parsing / cleaning module to canonicalize data from disparate sources, a RethinkDB database to host clean data, an informatic / pipeline module to process genomic data into annotated evolutionary trees and a browser-based frontend to display interactive visualizations. All backend / compute is written in Python and all frontend is written in JavaScript. At this point, the frontend has seen more development than the backend. We are now looking to improve backend infrastructure to allow easier sharing of data from outside groups and to automatically run builds when new data appears. This developer position would be in charge of backend infrastructure, but also work directly with public health and academic partners to incorporate new datasets and make an effective platform for applied genomic epidemiology.
The ideal candidate would have expertise in Python, databasing, bioinformatics and compute infrastructure. Database knowledge is required to host genomic data and provide APIs to outside groups to push data to a shared database. Informatics and compute knowledge is necessary to deploy automatically spin up builds as new data appears. This broadly aligns with experience in backend web development. Experience with frontend web development, particularly JavaScript, React and D3 would be a plus, but not at all a requirement. The ideal candidate should also have excellent communication skills as interfacing with collaborators is a key aspect.
Primary job responsibilities include: (1) managing Nextstrain database, (2) working with collaborators to keep data flowing through Nextstrain pipeline and (3) building infrastructure to streamline (1) and (2).
The Fred Hutch is located in South Lake Union in Seattle, WA and offers a dynamic work environment with cutting-edge science and computational resources. The position is available immediately with flexible starting dates. Informal inquires are welcome. Applications will be accepted until the position is filled. We offer a competitive salary commensurate with skills and experience, along with benefits. The Fred Hutch and the Bedford lab are committed to improving diversity in the computational sciences. Applicants of diverse backgrounds are particularly encouraged to apply. Depending on the applicant, this position could be a full-time salaried employee, a part-time employee or a contracted consultant.
For more information about the lab, please see the our website at bedford.io. To apply for the position please send (1) current resume, (2) code samples or links to published/distributed code and (3) contact information for two references to trevor@bedford.io.