Rust+WASM spotted @ Ensembl genome browser -> possible whitepaper?


#1

Today I’m attending the conference “Visualising Biological information” (VIZBI2019). One of the posters is about how the Ensembl genome browser is replacing their 20 year old C/C++ server side codebase with a modern from-scratch rebuild, using (among others) Rust+WebAssembly.

For those without a bioinformatics background: Ensembl is one of the biggest resources in genome bioinformatics. They provide curated, annotated browsing of the reference genomes for all of the important species: i.e. the “SatNav” to make sense of our DNA blueprints of life.
They put the distilled essence of terabytes of information at your fingertips.

Since they are one of the core resources for the bioinformatics world, they have very high standards on performance, stability and long term maintainability, so if they pick Rust, we’re doing something right!

Their new client-side needs robust interactivity and high performance: for showing thousands of DNA objects and lots of annotation tracks in an interactive webbrowser view. They felt Rust+WAsm was the only obvious choice.
I spoke with their team leader, and they were very happy with the concerted efforts of the wasm-WG, they probably wouldn’t have picked Rust without their efforts, so big kudos to them! :heart:
Having said all of that, Rust is still a very new animal to the Ensembl team, so I’m doing my best to give them a flying start. Any tips and pointers are welcome!

Their experimental, wheels-might-come-off pre-alpha is being developed in the open starting today. If you want to give it a try: the announcement (with link to live demo) is here Ensembl 2020: pre-alpha release

Ensembl is developed at the EBI in Hinxton, near Cambridge (UK), so I pointed their Rust dev (unfortunately still singular) at the Cambridge Rust Meetup.
@therealjpster, @Istar-Eldritch: as organisers of said meetup: anything I should tell them?

I also approached them about maybe adding to our whitepaper collection, and they were quite enthusiastic about the idea. I’ll try to put them in touch with the community team.
If anyone has tips for how to engage, I’d love to hear them! :heart:

Edit: Tweet with their poster, proudly showing the Rust and StdWeb logos!


#2

Hey @juleskers, that is really cool and thank you for pinging us about it! I’m a bit ashamed I was not aware of it while working on the same industry and being in the same location. I would definitely love to get in touch with them and try something for them to speak about the project to the comunity, we do not have a well defined structure yet to deal with the process so I’m joining the slack channel they provided and I’ll try to continue from there.

Thank you again, if you had any other specific idea please, let me know.


#3

Glad to be of service!

I got the impression that they picked this conference as their “big reveal” of their prototype, and were working somewhat stealthily until now. Their repo has only been public for a few days, so unless you are literally down the hall of their office at EBI, I’m not sure which signals you could have picked up before today :slight_smile:

Unfortunately their Rust dev was not present in person. From the story, he was the one researching the possible alternatives, and arrived at Rust as the only sensible option for what they want to do. He apparently learned Rust during this process. So it seems all our documentation and wasm resources are doing good, if he could pick all of that up without support on the forum here or from the local meetup :smile:

I’ll also plan on joining their slack, let’s see if we can make their budding crustacean feel a little less lonely :heart:


#4

This is awesome! I’ve been pushing for Rust and Webassembly in our lab, and it works super well. I set up a demo in a blog post last year, and it’s great to see more and more bioinformatics moving in the same direction =]


#5

I’m in the UK, wish I was nearer Cambridge :frowning: