Peruse the Octet API Documentation and you may find something surprising about the Molecule interface: it lacks mutator methods. Given that mutators enable the state of an object to change, how can a Molecule ever be created in the first place? Why would anyone even need immutable Molecules? Mutable Molecules are Unnecessary Most cheminformatics tools permit the unfettered modification of molecules after their creation.

InChIMatic is a simple Web application that uses Google to perform exact structure searches on the Web. After drawing your structure in the editor window, click the “InChI!” button to get a link. This link takes you to a Google query that displays matches for your molecule. You’ll need both Java and JavaScript enabled in your browser to use InChIMatic.

Yet another case of axial chirality in the recent literature comes in the form of ion channel openers described by Vrudhula et al. A previous Depth-First article illustrated how most popular cheminformatics tools are incapable of distinguishing axially chiral enantiomers such as those shown above. If your application suddenly needed to do so, could it cope?

What does it take to design products that are both simple and powerful? Woz’s interview is chock-full of lessons. Of course, it helps to be a genius. It also doesn’t hurt to have a clear vision of what you want to build. Living and breathing what you’re working on sure seems to be important. These factors all play a role, but in reading how Woz designed the Apple II, I was most struck by how important constraints were to his process.

A while back, Seth Godin gave a talk on things that are broken, why they are broken, and why they stay broken (video). Seth is one of those rare speakers who can entertain and inform at the same time. I especially liked how his talk identifies seven (maybe more) reasons for brokenness. As I watched Seth’s talk, it wasn’t hard to think of many examples in which chem(o|i)informatics is broken.

Rails excels as a rapid Web development platform. Deployment of Rails applications, on the other hand, has until recently been a lot less rapid and a lot more complicated. A new Rails technology called Mongrel is now set to change all of that. Mongrel is a fast Rails application container. It can be used in standalone mode - exactly like WEBrick.

The way that atoms, and particularly their masses, are modeled sets the stage for the kinds of problems a cheminformatics environment can solve. Many systems are currently in use, a reflection of the many different ways there are to think about this problem. This article will introduce the atomic mass system used by Octet, which provides atomic mass values and uncertainties cross-referenced to the primary literature.

What are the most reliable ways to fail in science? Of course, no scientist sets out to fail, but an understanding of that path can lead to a better understanding of the path to success. By way of Seth Godin’s Blog, I came across some interesting rules for failure. Seth’s article cites the above quoted essay.

An XML language is only as useful as the software tools that take advantage of it. Previous articles have discussed how the XML language FlexMol can solve a variety of molecular representation problems ranging from the multiatom bonding of metallocenes to the axial chirality of biaryls. Octet is a framework written in Java that speaks FlexMol natively. In this article, I’ll show how Octet can be used to read a sample FlexMol document.

One of the most important considerations when building an application is the choice of framework. As the quote from the Gang of Four implies, there’s much more to frameworks than just a collection of re-usable code.

The Web may be the most effective information-delivery platform ever created. Unfortunately, a variety of barriers, both technical and cultural, restrict the use of the Web for chemistry. In the last few years, three powerful forces for change have emerged: Open Source; Open Access; and Open Data. Most of what’s written on these subjects takes a theoretical angle that makes it difficult to visualize real benefits.