Senior Software Engineer, GA4GH

2 weeks ago

Cambridge, United States Broad Institute Full time

General information

Location

Cambridge, MA

Ref #

39189

Job Family

Research

Date published

30-Apr-2024

Time Type

Full time

Description & Requirements

Job Description

The Global Alliance for Genomics and Health (GA4GH) is an international open-science organization dedicated to creating genomic data standards for the benefit of human health and medicine. Formed in 2013, GA4GH brings together 600+ leading organizations working in healthcare, research, patient advocacy, life science, and information technology to create frameworks and standards to enable the responsible, voluntary, and secure sharing of genomic and health-related data.

GA4GH is supported by an international staff based at five sites around the globe, including the Broad Institute of MIT and Harvard in Cambridge, MA. As the organization grows and gains more support from the global genomics community, GA4GH is now actively building its in-house technical team.

As the GA4GH senior software engineer, you will support the development and implementation of open-source technical standards for genomic data sharing. These APIs and other standards will be implemented by genomic data projects from around the world to improve health outcomes. You will contribute to standards development work across the six Technical Work Streams based on timing and priorities, including critical tasks that are necessary to complete standards development but are unlikely to be carried out by external contributors. Day-to-day activities may include building frameworks, writing documentation, performing compliance testing, leading and managing projects, defining tasks and their priorities, and may mentor 2 to 3 software engineers. You will also play an important role in helping to disseminate, maintain, and version GA4GH standards. You will also be important in maintaining a strong connection between GA4GH and the Data Science Platform (DSP) community within the Broad.

While your direct line manager will be the Director of Strategy and Engagement (GA4GH), you will report in practice to the GA4GH Chief Standards Officer located at EMBL-EBI and a mentor within the DSP. As a member of the GA4GH technical team, you will have the opportunity to meet and work with leading international software engineers in the area of genomics. You will help to enable the work of a vast community of active contributors, many of whom contribute to GA4GH standards development outside of their day-to-day job functions. You may be expected to attend the bi-annual GA4GH Connect Working Meetings, which take place in an international location every spring and fall.

Key Responsibilities

Support the delivery of high-quality technical standards, by supporting projects through the product approval process Design, Develop and Maintain open source implementations for approved GA4GH technical standards, including APIs and new bioinformatics file formats. Design and Develop software to support the implementation of GA4GH technical standards worldwide, such as testbed platforms and documentation tools Work on GA4GH Tech Team Projects with minimal supervision. Define tasks and enable prioritization ensuring the organizational objectives are in-line with the Tech team’s objectives. Write clear and comprehensive technical documentation Join project calls with international collaborators to develop and prototype new specifications and features, and provide updates and tutorials/demonstrations to aid GA4GH standard implementations. May oversee the daily activities of and mentor one to two Software Engineers.

Qualifications

University degree in computer sciences, software engineering, bioinformatics, or equivalent 5+ years of professional experience in software development which may include a Master’s degree in computer sciences, software engineering, bioinformatics, or equivalent Professional experience with Java and/or Python is a must Proficient with version control (git) and collaborative project management platforms (GitHub, Slack) Proficient with automated software testing and continuous integration (e.g. Github Actions, Travis CI) Excellent communication skills (listening, written, and verbal), both in articulating your ideas and gathering input from a variety of collaborators in remote settings Resourceful team player who excels at building trusting relationships with customers and colleagues Knowledge of bioinformatics/genomics or experience in an international project is an asset but not essential Experienced with deploying applications through a public cloud provider, such as AWS, Azure, or Google Cloud Experienced with authentication and authorization standards (OAuth, OIDC) and associated providers Experienced with packaging software as Docker images, running Docker containers and Dockstore.

Preferred Skills

Experienced with widely used bioinformatics file formats (BAM, VCF) and toolkits (samtools, GATK) and working with large volumes of genomic data Experienced with writing reusable workflows in Nextflow, Snakemake, Workflow Description Language (WDL), or Common Workflow Language (CWL) Experienced with additional programming languages, such as JavaScript, Golang, and C Knowledge of the OpenAPI Specification to define and describe APIs is an asset Experience developing RESTful APIs with server-side web development frameworks (Flask, Spring Boot, Express, etc.) Strong interest in genomics and life science Knowledge of different GA4GH Standards and Workstreams

PERSONAL ATTRIBUTES

Inspired by challenging problems Independent and self-motivated Capable of managing effort across multiple parallel projects Thrives in a fast-paced, dynamic environment Collaborative Able to work flexible hours on occasion

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