KNIME is a graphical programming environment that many are considering for use in cheminformatics. One of the limitations of KNIME at the present is its relative lack of low-level cheminforamtics software components (nodes) compared to Pipeline Pilot, for example. Previous articles have introduced KNIME as a tool for cheminformatics and outlined a method for creating a KNIME node developer environment.

It’s a simple and increasingly common question: how can I enable users to search my website by chemical structure? Text search can be done relatively easily, but chemical exact structure and substructure search are considerably more complex. This article offers a high-level overview for non-experts of what’s needed to create a structure-searchable chemical database.

Did you know that United States Food and Drug Administration (FDA) maintains a Substance Registration System (SRS) that aims to centralize information on every ingredient contained in domestically-marketed foods, drugs, and medical devices? A central component of this system is the Unique Ingredient Identifier (UNII). The key documentation and resources on this system are scattered and extremely difficult to locate.

If you work in cheminformatics and you use Java, you’ll eventually face the problem of how to generate InChIs in Java. This blog has covered a few approaches to integrating InChI over the years, including the use of SWIG to statically link to the InChI code and NestedVM to compile the InChI C source into Java bytecode. NestedVM ports much better than SWIG, but at the price of a performance penalty on the order of 10-20 fold.

Ein Fehler ist aufgetreten. Sieh dir dieses Video auf www.youtube.com an oder aktiviere JavaScript, falls es in deinem Browser deaktiviert sein sollte. More online is available here. This is not just an example of fascinating research. The group at Cornell demonstrates how easy it is to reach a wide audience using what the Web offers cheaply or for free. Few in chemistry have caught on to this simple idea. Thanks to Mat Todd for the heads up.

The previous article in this series introduced KNIME as a data pipelining engine for cheminformatics. One of the conclusions from that article was that the possibilities for doing interesting things with an out-of-the-box KNIME installation were somewhat limited. This article briefly describes how to set up a KNIME developer environment in preparation for creating our own custom KNIME cheminformatics nodes.

Are you involved in Drug Discovery? Are you interested in how new technologies could change the rules of the game? Will you be in San Francisco on October 21st? Then you might consider registering (free) for the 4th Annual Collaborative Drug Discovery Community Meeting.

Whether you consider visual workflow/data pipelining environments like Pipeline Pilot useful or not, there’s no denying they’re popular. Within the last few years, KNIME has joined Pipeline Pilot as a widely-used visual programming platform. But unlike Pipeline Pilot, KNIME is released under an open source license, which makes it interesting from the perspective of disruptive technology.

If you’ve ever published in an ACS journal, you may remember a short form you need to fill out in which you transfer copyright to the ACS. Well, the rules are apparently set to change in the next few weeks. Read on to find out how.

You may have noticed some changes to Depth-First recently. This post highlights some of these changes, particularly in the parts you can’t see. What’s Wrong With Blogging Software? In its four-year history, Depth-First has run off of two blogging systems. The first was an ancient, lovable beast called Typo. The second was a custom-built replacement called Hubbub that I wrote, partly to teach myself about some newer technologies.

[Flash Content Scrubbed] Definitely worth checking out Node.js.