Frequently asked questions

Watershed is a modern operating system designed to fix the real bottlenecks in impactful bioinformatics. Watershed’s powerful hardware and intelligent software supports rather than replaces the bioinformatics developer by providing familiar, industry-standard coding tools, and getting out of the way of data-driven research and development. At the same time, our software layer provides single-button access to dedicated workhorse computers, scalable HPC environments, and industrial GPUs*, removing the need for a bioinformatician to moonlight as a cloud-ops engineer. Similarly, Watershed makes it effortless to convert analytical notebooks to UI-powered dashboards, letting dry-lab and wet-lab scientists collaborate on their data, and giving a first-class analytical experience to everyone on your team regardless of coding ability.

*not all access tiers have on-demand access to GPUs

Watershed is designed for any team where computational developers and wet-lab experts need to collaborate without barriers to either group. Our users include biologists, bioinformaticians, software engineers, and CSOs within discovery R&D groups, proteomics cores, sequencing facilities, informatics consulting orgs, and academic centers of excellence. The OS's flexibility makes it adaptable to a wide range of applications, but it shines for groups that need fast and robust computational workflows that don’t box out their wet-lab experts.

Watershed specializes in bioinformatician-friendly hardware and software working together. On the hardware side, our proprietary, purpose-built stack delivers informatics-focused (read: high-RAM, low-latency) machines with on-demand state-of-the-art GPUs without complex cloud-ops baggage wherever you need it. Meanwhile, our software focuses on effortless collaboration with non-coding colleagues and a workflow language that allows easy parallelization, HPC dispatch, caching, and tracking while seamlessly blending with unix tools and familiar notebook environments.

Watershed is founded on the belief that bioinformatics developers are real scientists doing real science, and no software solution can ever replace them. Rather than offering a range of pre-existing “one-size-fits-all” software pipelines that try to remove the bioinformatician from bioinformatics and ultimately serve no research groups’ needs perfectly, Watershed exists to empower and support the bioinformatician in accessing the resources they need and giving them the tools to share their work in an impactful manner. At the same time, our focus on collaboration across coding levels is central to our belief that the best scientific teams are those where everyone’s expertise is valued, and every user is treated as a first-class contributor on an equal playing field.

We have a wide range of users that work and develop in Watershed every day.  Check out our Resources Page to read our latest case studies and testimonials from our current customers. If you don’t see something similar to what you want to do, reach out; we’re happy to set up a no-cost consultation.

Watershed has a tiered access fee and bills monthly for compute & storage usage. We pride ourselves on transparent billing: we have no fees or limits on seats or number of projects, and no data ingress/egress fees on storage.

Schedule a demo with us today! We’ll share some of the magic that makes Watershed special, find out more about your compute, data, & storage needs, and help find the best Watershed package for you.

We are headquartered in Cambridge, MA, but serve clients all over the world!

Experts across all domains! We have PhD-level bioinformaticians, computational biologists, many talented engineers, and outstanding operations & commercial staff.

Watershed supports AI/ML workflows with the same rock-solid foundation of purpose-built hardware and software that powers all of our users projects. Watershed’s notebook interface allows for rapid iteration and exploration of data and model results, and the ability to attach workhorse GPUs like A100s with a click of a button means that compute capacity is never the barrier to accessing the kind of AI models your work needs.

We have active integrations with Benchling, S3, host RStudio and a number of other custom applications. Projects on Watershed can be granted internet access too — install whatever you need, whenever you need it!

Very! Security is paramount at Watershed, and is considered in every decision we make. Our CEO has built infrastructure used for securely exchanging millions of dollars per day, and has brought the same level of rigor to how Watershed has been constructed. We are currently undergoing SOC II Type II certification.

Absolutely! We onboard and provide orientation to all clients. If you need informatics support or advice, our consulting partners are all trained and certified by Watershed. We’ll happily connect you with one of our partners based on your needs! If there is something unexpected in system behavior, you can always reach out to us and we’ll investigate.

If it's data from a biological experiment, we can host it! A few examples include: fastqs, mzMLs, BAMs, BEDs, etc. - but the possibilities are vast.

Alphafold is an AI system that intelligently predicts the 3D structure of an amino acid sequence. Watershed scientists and customers alike have had a lot of fun exploring this and other deep learning algorithms.