What’s the difference between computational chemistry and cheminformatics? Computational chemists encode all the hydrogens. This tongue-in-cheek statement, whose origins I don’t recall, isn’t far off the mark. It stands to reason that if hydrogens are going to be deleted, there needs to be a good way to bring them back. This article proposes some language intended to simplify what has become an unnecessarily complex problem.

I recently showed how to compile a complex C application to WebAssembly using Emscripten. Although effective, this approach comes at the cost of complexity. A lot of JavaScript glue code is produced, and an external tool chain is required. The former obscures the underlying principles, which makes improvement and extension difficult. The latter may not always be possible.

The word “blockchain” is working its way into scientific publications, symposia, and I suspect, grant applications. Several groups now seek to apply this technology to old problems such as ensuring data integrity in regulated environments including drug manufacturing and clinical trials.

As noted in a recent article, WebAssembly adds a powerful new suite of tools to the Web development workshop. In particular, WebAssembly clears a path to running software written in arbitrary languages within a Web browser securely, and at near native speeds. Unfortunately, taking advantage of this new potential is non-trivial given that it requires expertise in both Web technologies and traditional build systems.

Back in the summer of 2008 I published a post about JavaScript’s current and future roles in chemistry. In it, I cataloged the then-available smattering of chemistry software that had been written in JavaScript. I also said that despite poor performance and primitive tooling, JavaScript was uniquely positioned as a foundation for important chemistry software. Since then, a lot has happened. This article recaps some highlights.

Meet Jane, a Web developer tasked with implementing structure search on a customer website. Jane has just learned that small organic molecules can be represented by short text strings called SMILES. Relieved that the structure search problem isn’t nearly as complicated as it first sounded, Jane tells her customer not to worry — structure search will be ready ahead of schedule and within budget. Jane’s plan is simple.

Graph theory plays a central role in cheminformatics, computational chemistry, and numerous fields outside of chemistry. This article introduces a well-known problem in graph theory, and outlines a solution. Matching in a Nutshell A matching ( M ) is a subgraph in which no two edges share a common node. Alternatively, a matching can be thought of as a subgraph in which all nodes are of degree one.

Last year marked the 30th anniversary of David Weininger’s SMILES paper. Although the computing landscape has changed beyond recognition since 1988, the SMILES language has barely changed at all. Sure, there’s the alternative line notation InChI and the OpenSMILES specification. But the former hasn’t changed SMILES itself, and the latter has mainly narrowed the range of SMILES formulations seen in the wild.

Back in 1968, Edsger Dijkstra published his well-known “go to statement considered harmful” letter advocating the abolition of the GOTO statement from high-level programming languages: At the time, GOTO was well-regarded and widely-used, as evidence by the controversy surrounding Dijkstra’s letter and the length of time it took languages supporting GOTO, or its use in languages that sill support it, to decline.

Molecular structures are sometimes thought of a possessing language-like properties. Smaller units (atoms and bonds) are assembled into larger units according to well-defined rules of syntax and semantics.

Distributed systems pervade modern computer technology. Examples include multi-core CPUs, GPUs, computer clusters, and the Internet itself. Although many forms of distributed computing have been developed, their main purpose is to increase the utility of individual resources through cooperation, often involving some form of parallelization.