Software Engineer (Research) -BIB Lab

GENERAL SUMMARY OF POSITION:

We are seeking an experienced Research Software Engineer to join our Genomic Data Science lab. Your work will involve developing and contributing to open-source software libraries to support mining, analysis, exploration and visualization of very large and numerous data sets derived from next-generation sequencing technologies for genomic research. This position is ideal for someone interested in applied software engineering with an emphasis on applications to biological data analysis, and looking to make a substantial contribution to an exciting research area with ample opportunities for development and discovery.

You will build out novel technologies to accelerate bioinformatic and computational biology research and migrate classical workflows to modern data science ecosystems. Your work will push forward research agendas through interdisciplinary collaborations on including but not limited to epigenomic, 3D genomic, spatial, and single-cell multi-omic research.

About the Abdennur Lab

We are a team of computational biologists, data scientists, and developers dedicated to creating the next generation of Genomics Data Science tools and applying them to answer important questions and solve big problems. We value tinkerers, interdisciplinary thinkers, and people with a passion to use their skills for scientific discovery. The Abdennur Lab was founded in June 2022 at the University of Massachusetts Chan Medical School, is part of the Genomics and Computational Biology department. We have active research collaborations with experimental investigators and funding support from collaborative initiatives like the NIH Multi-omics for Health and Disease (MOHD) and 4D Nucleome (4DN) Consortia, the Common Fund Data Ecosystem (CFDE), and NCI's Program for Informatics Technology Development (ITCR).

Dr. Nezar Abdennur completed his PhD in Computational and Systems Biology at MIT, specializing in the 3D organization of the genome (3C/Hi-C technologies), its relationship to the epigenome, and its influence on gene regulation. His postdoctoral work expanded to profile the underappreciated diversity of silent chromatin states and how they change in disease. Nezar is a core contributor to HiGlass, a web-based visualization platform that enables fast, multiscale, and multimodal comparative exploration of vast amounts of (epi)genomic information. He co-founded Open2C, a community of computational biologists developing open source tools for 3D and functional genomics.

The Abdennur lab develops and supports foundational infrastructure for computational genomics that interoperates with the broader data science ecosystem, including tools like bioframe, oxbow, and anywidget.

MAJOR RESPONSIBILITIES:

Acquire an understanding of the group's research topics, working closely with research staff and domain experts.
• Identify bottlenecks, propose and implement reusable solutions to data analysis, data engineering, and other scientific workflows.
• Design, implement, and contribute to critical open-source libraries.
• Act as an ambassador for our group in relevant open-source communities, and foster collaborative projects to achieve shared goals.
• Promote a culture of sustainable research software development.

REQUIRED QUALIFICATIONS:

• Bachelor's degree in a quantitative field such as computer science, engineering or physics, OR an advanced degree in the life sciences with a track record of software engineering experience.
• 2+ years of prior experience relevant to the responsibilities of this position.
• Proficiency in Python and extensive experience with its scientific ecosystem of numerical, statistical and machine learning libraries, packages and data structures, including Jupyter notebooks and related infrastructure.
• Experience with software development best practices, including version control, documentation, unit testing, continuous integration, and issue tracking.
• A history of, or strong interest in, contributing to open-source projects.
• A passion for interdisciplinary work and excellent written and verbal communication skills.

PREFERRED QUALIFICATIONS:

• Experience (and ensuing frustration) with bioinformatics.
• Experience with web development OR systems-level programming (e.g. C/C++, Rust).
• Experience working in cloud environments (AWS, GC) and with containerization.
• Experience in the implementation and deployment of machine learning models.