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Running InChI Anywhere with WebAssembly
- 1. Running InChI Anywhere with WebAssembly Rich Apodaca (@rapodaca) Metamolecular
- 2. • Unique Key: Does this database have this molecule? • Foreign Key: What other databases have this molecule? • Permissionless (cf. CAS) The InChI Value Proposition
- 3. • 165,000 lines of code • Mostly C InChI Source Code
- 4. Deployment { } C Source 1001101010… 1100111010… 1110010101… Native Executables Build System
- 5. What About… ✓ Ubiquitous X Native Code not Allowed! Servers… Permission
- 6. The Most Important App https://www.wsj.com/articles/your-browser-is-the-most-important-app-you-havemake-sure-you-use-the-right-one-1537707600
- 7. •Browser debut in 1994 •Universal browser support •Pretty fast JavaScript
- 8. InChI to JavaScript Rewrite 160,000 lines of C to JS. Transpile 160,000 lines of C to JS. { } InChI Source https://github.com/metamolecular/inchi-js
- 9. •Ad hoc solution •Limited tooling •Limited scope •Gobs of glue code •Not built for speed JavaScript as Assembly Language { } C Source
- 10. • Binary instruction format • Fast, portable compile target • Sandboxed for security • Runs in all browsers, 2017 • W3C Standard, 2019 • Runs InChI? WebAssembly (Wasm)
- 11. • Minimal tooling • No auto-generated glue code • Use verbatim InChI source • In other words, a build system Goals InChI Wasm compile { } 1010100111…
- 12. InChI-Wasm Project { } C Wrapper Build Script ⚙️ InChI Wasm + LLVM Compiler { } + InChI C Source v1.06 https://github.com/rapodaca/inchi-wasm
- 13. Application Stack JS-Wasm Interface (2 KB) Standard Library (Static, 69 KB) User Interface InChI Wasm (601 KB)
- 16. C Wrapper Wasm interface Also, inchi_to_inchikey with help from Bob Hanson heavy lifting 💪 copy result (InChI or Error) JS error reporting
- 17. Build Script LLVM compiler Wasm Target Standard Library Obscure, hard-won hack Wasm options Standard build stuff
- 18. Data Schlepping in JS Inputs: molfile and options Byte wranglers Translate input } Write output Call InChI Wrapper Return result }
- 19. Performance “WebAssembly aims to execute at native speed by taking advantage of common hardware capabilities available on a wide range of platforms.” - webassembly.org
- 20. •114 K SureChEMBL Update •Test Wasm & native •Same InChI output •155 ChEMBL discrepancies •3 Errors Benchmark 0 550 1100 1650 2200 2750 Wasm Native InChIs/sec https://github.com/rapodaca/inchi-benchmark
- 21. Rethinking the Web Browser for Chemistry
- 22. Ertl et. al. https://doi.org/10.1186/s13321-015-0061-y
- 25. • Legacy code written in C, C++, or FORTRAN • Incentive for in-browser and/or serverless deployment • Compile to Wasm with LLVM • User Interface in HTML5 A Template for Future Work https://metamolecular.com
Editor's Notes
- Increasing the scope and reach of InChI
- What’s InChI’s irreducible value proposition? Answers two questions Permissions interfere
- One challenge: the code itself
- C has a long history, and for most of software deployment hasn’t changed much.
- This model excludes some very important platforms. … Often the solution is to run the native code on a server, but that creates a permission relationship.
- Thought experiment. As of midnight tonight I’m going to delete every app from all your devices except one. Which one will you keep?
- Major factor contributing to the success of the Web browser Items Re-cast InChI source as JavaScript?
- Two conceptual paths Rewrite Transpile
- Emscripten works, but it leaves some important things to be desired
- Recognizing these limitations, browser vendors worked together to deliver a new way to run software in Web browsers.
- To answer this question, I started with some goals.
- After several months of part-time work, success Items LLVM - suite of compiler and toolchain technologies Widely-supported and used Wasm support built in
- Zooming out, this is how an InChI-Wasm application might be structured. At the top…
- InChI-Wasm project contains an HTML test page, shown here
- A more user-friendly test page is available at chemwriter.com slash inch
- Important component in the project is the wrapper. Small bit of code written in C Purpose: expose a valid Wasm interface. …
- Orchestrating the compilation of InChI to Wasm is the build script, most of which is shown here. Ordinary shell script that calls clang, the LLVM compiler.
- Running on the browser side is a small amount of code that talks to the InChI Wasm instance. Vanilla JavaScript main functionality expressed in the molfileToInChI function. …
- Performance is always an important topic Indeed, the WebAssembly documentation itself makes a very bold claim.
- To judge the performance of InChI-Wasm, built a benchmark Within 2x of native Pretty good!
- Take a few steps back and talk about where I think projects like InChI-Wasm fit into chemistry. There’s this tendency to view the Web browser as a dumb data terminal. I think this sells the platform short.
- For a good example of this approach, consider the Wikipedia Chemical Structure Explorer. Structure search works offline.
- Many have used Jupiter Pyodide Python Notebook, including NumPy, Pandas, Matplotlib and parts of SciPy All running in a browser w/ Wasm
- Wasm steadily working its way into popular programming languages. All of the ones here have Wasm runtimes, can be compiled to Wasm, or both. This solves a thorny integration Native binaries create platform-specific problems
- To conclude, I’d like to propose a template for further work in this area.