Cheminformatics has seen the introduction of a diverse array of new open source software over the last few years. Using it all to its fullest potential is not always easy; differing languages, dependencies, interfaces, and varying levels of documentation make the job especially difficult. Rubidium is a new open source project aimed at changing that. Rubidium is a full-featured cheminformatics scripting environment for Ruby.

Welcome to Wikipedia! We’re writing a complete encyclopedia from scratch, collaboratively. We started work in January 2001. We’ve got over 6,000 pages already. We want to make over 100,000. So, let’s get to work! Write a little (or a lot) about what you know. Read our welcome message here: Welcome, newcomers!

If you’ve spent any time using Java applets, you may have run across an annoying little “feature” of Internet Explorer 6/7. Before interacting with an applet, it’s outlined in gray and displays the mouseover message “Click to activate and use this control.” This may not seem like much of an inconvenience, but it seems wrong to waste precious time explaining this kind of thing away to hundreds of perplexed users.

Regardless of your views on Java the Programming Language, Java the Platform has a lot going for it. The ability to run the same executable on any system with a Java Virtual Machine (JVM), without recompilation, is a significant advantage in today’s heterogeneous computing environment.

Some time ago, a Depth-First article discussed some methods for compiling C to Java bytecode. Many factors make this approach attractive compared to the JNI approach. Some of them include security, portability, and use within applets. Unfortunately, none of the approaches discussed in the earlier article seemed particularly general.

Recent articles have discussed Rubidium, the cheminformatics toolkit for Ruby. In this article, the first in a series, I’ll go beyond the Ruby code to discuss the technical aspects of taking an Open Source idea from concept to release. Finding a Home Before setting up your Open Source project, you’ll need to decide on how to host it. Project hosting can be as simple or elaborate as you wish, but the basic services include: a website;