The Cambia Grove Innovator Fellowship Program embeds innovators within world class health care organizations to solve complex problems with emerging technologies and talent. This fellowship program was created using feedback from the innovator and health care systems communities during Cambia Grove’s Data Solution Series.
In collaboration with the Fred Hutchinson Cancer Research Center, Cambia Grove is seeking its inaugural fellowship cohort to develop a biological data catalog to expose valuable clinical and molecular data through consistent web-optimized application programming interfaces. These efforts will help researchers worldwide find effective treatments or even cures to cancer.
Fellowship Description: Ingesting & Processing Data for use in Research
Data science and visualization in Cancer Biology often requires use of reference data sets. Unfortunately, many of these resources are stored in formats and systems that are not optimized for web delivery. To help accelerate research, the program aims to automate the ingestion transformation and loading of various datasets into AWS and expose them using REST services. Exemplar datasets Include:
- Gene sets from Molecular Signatures Database (MSIG DB)
- Pathways from Pathway Commons
- Gene annotations from GeneCards
About the 2019 Cambia Grove Innovator Fellowship Program
Fellows will be selected to work as a team with Fred Hutchinson Cancer Research Center leaders part time for six weeks. A $750 per week stipend will be provided.
Fellows will have the opportunity to interact with Fred Hutch researchers and staff in various ways over the course of the fellowship, such as lunches with researchers, attendance at seminars, conversations with Hutch Data Commonwealth engineers, and opportunities to pitch concepts.
Technical Description of Work:
Fellows will create Extract Transform Load (ETL) scripts that pull data at regular intervals from public websites and process them for consumption through web-based APIs. ETL scripts will be written and integrated into the Airflow workflow platform and configured as directed acyclic graphs (DAGs). Methods will be containerized and made available as reusable methods for biological data processing. Example data to be ingested include: gene alias resolutions, gene metadata, and large-scale reference omics datasets from programs such as The Cancer Genome Atlas (TCGA), the IGSR 1000 Genomes Project, and Autism Speaks.
Accepting Applications: May 7 – June 7, 2019
Selected Fellows Announced: June 26, 2019
Fellowship Program: Part time between August 12 – September 27, 2019
Post Fellowship Presentations: October 3, 2019
Must be able to participate on site in Seattle, WA during the duration of the fellowship program.
Must be able to complete mandatory paperwork:
- Background check
- Confidentiality Agreement
- Copyrights Agreement
- Inventions Agreement
- Non-Employee Info Form
Candidate meets technical qualifications:
- Minimum of 3-5 years’ experience with back end development processes
- Skills/Experience with the following preferred:
- Python (pandas, scikit-learn, boto, nltk, numpy/scipy, Jupyter)
- GraphQL / Rest Services
- AWS cloud (API Gateway, S3, EC2, S3-Select, Athena, Lambda)
- Shell scripting (bash, sed/awk)
- Code/data-driven ETL (not UI tools)
- R (RStudio, tidyr, Shiny, ggplot2)
Candidate meets non-technical qualifications:
- Has experience interacting with both technical and non-technical teams
- Has experience working with teams
- Displays interest in engaging with Fred Hutch community
Candidate displays the ability to improve current data resources:
- Help to accelerate research to automate the ingestion transformation and loading of various datasets into AWS and expose them using REST services
Terms and Conditions
- Applicant must be eligible to participate.
- Applications will not be accepted after the deadlines posted.
- Fellows will participate in public presentations on October 3, 2019 at Cambia Grove.
4. Fellows will participate in promotional activities for the inaugural Cambia Grove Innovator Fellowship as well as subsequent fellowship programs