The Directory of Open Access Journals (DOAJ) currently lists 2420 Open Access scholarly journals. Of these, 52 currently fall under the category of chemistry. Although the organic chemistry subcategory only currently lists three journals, the general chemistry category actually contains several journals containing organic chemistry content, such as the Bulletin of the Korean Chemical Society, Chemical and Pharmaceutical Bulletin, and Molbank.

A previous article introduced OPSIN, an Open Source Java library for decoding IUPAC chemical nomenclature. In this tutorial, you’ll see how OPSIN can, when interfaced with freely-available chemical informatics software, generate 2-D structure diagrams from IUPAC names. Prerequisites This tutorial requires Ruby CDK (RCDK), which in turn requires Ruby, Java, and the Ruby Java Bridge.

In the ideal world for many Java developers, all software would be written in Java. The reality is that a great deal of software is written in other languages, one of the most widespread of which is C. This article discusses a unique approach to working with C code from Java, producing 100% pure Java bytecode that runs anywhere Java does.

IUPAC chemical nomenclature is everywhere. It can be found in journal articles, both new and old, on the Web, in databases, on Material Safety Data Sheets (MSDS), in chemical catalogs, and just about anywhere chemical information is found. The rules of this nomenclature are one of the first things taught in Organic Chemistry classes, and entire books are devoted to the subject.

Karwath and De Raedt are onto something more than just an innovative use of SMILES strings. When the majority of chemical informatics papers provide instructions for downloading both complete source code and complete data sets, the game will have changed forever. Advocating this postion in essays, presentations, emails, and letters is one way to make the case, and a very old one at that.

The Ruby Java Bridge (RJB) is one of the most useful Ruby integration packages available. For example, RJB enables the complete use of the Chemistry Development Kit (CDK) from within Ruby. Past articles have been written from a unix-centric perspective. This article will show how Windows users can join in the fun.

My laptop recently died. Depth-First hasn’t been updated lately due in part to the time it’s taken to get a working replacement. For my new system, I wanted to build a desktop from components and run Linux on it, which is the OS my old system was running. Now, anyone who has done this knows that assembling the hardware is actually the easy part.

A previous article in the Hacking PubChem series pointed out that the entire PubChem database can be downloaded via FTP. This article shows how simple tools written in Ruby can be used to efficiently process the massive amount of data on PubChem’s FTP-server. Prerequisites The only software you’ll need for this tutorial is Ruby. Organization of PubChem’s FTP-Server PubChem is a big database.

Open Source licensing is nothing short of revolutionary. Of all of the things an Open Source license makes possible, perhaps the most far-reaching is the right of licensees to create and distribute derivative works.

InChI identifiers can be viewed both as unique molecular keys and as a language encoding molecular structure. With the right software, it is possible to decode any InChI to arrive at a human-readable molecular structure. This tutorial will show how to convert InChI identifiers into 2-D molecular renderings using open source tools.

Ruby Chemistry Development Kit (RCDK) version 0.2.0 is now available. This version adds built-in support for Structure-CDK, a 2-D rendering framework. Simplifying the use of this library is a convenience layer enabling many common tasks to be accomplished with a single line of Ruby code. Installing RCDK-0.2.0 is simple.