KSG for Engineers

The Knowledge Systems Group (KSG) is an applied genomics software and data sciences group, focused on enabling cancer genomics research and precision cancer medicine at Dana-Farber Cancer Institute (DFCI).

If you are a software engineer, and the concepts above are not familiar, this page aims to provide an introduction to our work.

#CodeForCancer

First and foremost, we focus on cancer. Dana-Farber Cancer Institute (DFCI) is one of the leading cancer centers in the world. It is a recognized leader in cancer research and cancer care, and it attracts some of the best minds in the world.

Every day you work here, you feel the mission of DFCI. And, while we at KSG do not see patients directly, our code makes it to real patients. There are very few places in the world where you can write code that has such a direct impact on real people, and we aim to create the most vibrant community of engineers who want to make the world a better place.

For a quick video regarding DFCI, check out the PanMassChallenge (PMC) Video below. The PMC is a bike riding fundraiser that raises money for DFCI. Since its inception in 1980, it has raised a total of $654 million for the Institute.

Open Source

Second, we focus on open source software. We have a deep and abiding belief in the power of open source, and believe our software should be freely available to all.

Our flagship project is the cBioPortal for Cancer Genomics, an open source project developed across multiple cancer centers. It is the most widely used platform for cancer genomics visualization and analysis (last year we had ~200K unique visitors), and everything about the project is open and available on GitHub. We have also developed MatchMiner, an open source platform for matching cancer patients to clinical trials.

It’s all about DNA

Much of our work is focussed on understanding the molecular basis of cancer.

In a nutshell, cancer is caused by mutations in DNA. With the advent of new technologies, we can “read the DNA” of every patient’s tumor, and use this information to perform research studies, develop new drugs, determine individualized treatments, and match patients to clinical trials. For an example of how this is done, check out the video below regarding the Profile Project.

Teams, Tools and Space

KSG is divided into multiple teams, and each team follows a Scrum process, with a product owner and scrum master, and we usually work in 1-2 week sprints. We have wonderful space at 360 Longwood Avenue, with lots of break out rooms, Google hangouts for video conferencing in each break out room, and tons of light. Caffè Nero is also one elevator ride away.

Each new member of KSG gets to pick their computer set up upon starting (usually a Mac or Linux laptop w/ an external large monitor). Depending on the project, we use a variety of tools, including GitHub, GitLabs, Slack and Hipchat, and continuous integration via Jenkins and Travis CI. We also have a strong culture of test-driven development and code reviews.

Technology Stack

Our technology stack varies by project. For example, our cBioPortal project is Java in the backend with a MySQL database, a REST-based API and a ReactJS front end. Most of our other projects tends to by Python and MonogDB in the backend, a REST-based API and ReactJS in the front-end. Several of our projects are "cloud native", running Kubernetes on Google Cloud.

Remote Policy

Having the option to work remotely is important for all members of KSG, and we find that working remotely can frequently result in a substantial boon to productivity. Sometimes there is nothing better than working at home with no interruptions and just cranking on some code. That said, much of our work is very complex and inter-disciplinary and there is no substitute for gathering around a white board to hash out a problem and come to a common understanding.

Over the years, we have therefore developed a KSG policy of a "remote day bank" — each member of KSG can work remotely up to 5 days / month, and we simply track days via a common google spreadsheet.

6 Week BootCamp for New Engineers

New engineers at KSG usually go through a 6-week “bootcamp”. We usually pick three projects for rotation, and the new person will spend 2 weeks on each project, getting to know each project and each team. This gives you an introduction to the scope of work going on here, and also enables you to meet everyone and start your initial contributions.

Supporting Full Stack Engineers and Continued Career Growth

We tend to hire people for an initial specific area of expertise, e.g. front end or dev-ops. But, we support all of our engineers in becoming full-stack engineers. And, we support engineers in continued career growth via online course subscriptions, mentoring, and conferences.

For engineers looking to learn biology and/or bioinformatics, the Longwood area of Boston and Kendall Square in Cambridge are epicenters of cancer genomics and there is a continual series of seminars across Dana-Farber Cancer Institute, Harvard Medical School, and the Broad Institute.

KSG Blog

  • Blog Post

    Mar 20, 2019

    Hello, world! We are rebooting our KSG web site. Stay tuned for future blog posts...

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