If you’ve ever created Web documents containing source code, you may have wondered how to easily add syntax highlighting. Over at the Metamolecular Products Blog, we needed source code highlighting and decided to find the best solution available. Depth-First uses a highlighter that’s installed as a server-side plugin.
Nothing stimulates quality discussion in science like numbers. The numbers themselves don’t even need to be initially accurate or properly obtained - those things work themselves out in the end. Numbers simply offer a basis on which to form a hypothesis, which leads to re-analysis of the numbers, further data collection, and ultimately a more accurate picture of the phenomenon.
Metamolecular continues to compile its catalog of free chemistry databases and Web services. The newest entry covers SIDER, a remarkable tool that lets you explore the relationships between marketed drugs and their side effects.
Recently, Jean-Claude Bradley discussed improvements to the software his group uses to automate the determination of solubility from NMR spectra. The code, written by Andrew Lang, is available for download from the Open Notebook Science site. Now, there’s nothing wrong with sharing source code this way - it’s just that there’s a much more effective way - with GitHub. I’ve created a fork of Andrew’s NMR analysis code on GitHub.
As announced on the eMolecules blog, the eMolecules database can now be downloaded free of charge in a variety of fomats. Currently available are a SMILES dataset and a 2D SDF dataset. Future releases will include datasets with 3D coordinates for docking applications. The datasets contain chemical structure information along with the eMolecules identifier. These datasets do not include pricing, availability, and vendor information.
For those who may not have seen the news, the Royal Society of Chemistry (RSC) earlier this week announced the acquisition of ChemSpider, the free database of chemical structures and related data. The tone of the press releases and commentary around the Web has been congratulatory, which is to be expected given the dedication and hard work by ChemSpider’s creators.
It’s been over two years since Ruby CDK was first announced. For the unfamiliar, Ruby CDK offers a convenient way to use the Chemistry Development Kit from the MRI Ruby implementation. Over the least several months, I’ve received quite a few emails about Ruby CDK. Many of the questions and comments revolve around the library now being out of date with both Ruby and CDK.
Science doesn’t need journals. What we need is scientific communication.
Mat Todd poses some very good questions in response to a recent post on creating chemistry communities: It should be emphasized that whenever we talk about ‘chemists’, we’re really making generalizations about a heterogeneous group. Same applies to ‘software developers’. Keeping that in mind, here are some ideas for how the culture of professional chemists differs from the culture of professional programmers: Numbers.
