While testing ChemPhoto, it became necessary to test the chemical structure imaging application with SD Files containing several hundred thousand records. Although it’s tempting to meet this need by constructing “dummy” files with the same record or small set of records repeated, tests are always far more illuminating when real data is used.
Occasionally you may want to install Open Babel into your home directory, or some other non-root directory. This problem most commonly crops up when using a server on which you don’t have root privileges. Another reason could be that you’re practicing or experimenting, and just want to keep the mess out of your system directories. The following tip shows how to install Open Babel to an arbitrary directory on your filesystem.
The August issue of The Scientist ran an article on using online tools to find a job in which I was quoted. The article summarizes five tools for prospective job seekers: SciLink; NotchUp; VisualCV; Jibber Jobber; and Meeting Wave. It’s no coincidence that these are all social networking tools. The problem is that only one, SciLink, even makes an attempt to appeal to scientists specifically.
If you’re into cheminformatics and like well-written analysis, Rajarshi Guha’s new blog is well worth reading. Rajarshi is a longtime contributor to the world of open source cheminformatics, including the CDK and Open Babel projects. His interest in the quantitative side of cheminformatics is apparent in recent articles on faster substructure search, faster fingerprinting, and CDK performance.
A recent article on the chemical spreadsheet is currently the first item returned in a Google search for the term. And it’s not the first time something like this has happened. I’ve talked with many scientists who like the idea of blogging but insist there just isn’t any time to do it. To them I ask: how important is publicizing your work? The honest ones admit that publicity is an essential element of a successful scientific career.
The next salvo in the ongoing battle to decide whether the Federal Government should be in the scientific publishing business has been fired. H.R. 6845 seeks to preempt the recently-passed law (PL 110-161) requiring recipients of NIH funding to deposit copies of their peer-reviewed manuscripts into PubMed Central. The move is hardly surprising. The aim of PL 110-161 was on face value to promote Open Access.
In reading through Bruno Lowagie’s excellent book iText in Action, I noticed several references to JavaScript. I knew it was possible to do a lot of interesting things with PDF to promote interactivity. But JavaScript? It turns out Adobe has even published about 1,000 pages worth of documentation on the subject in the form of the Acrobat JavaScript Scripting Guide and the Acrobat JavaScript Scripting Reference.
One of the difficulties in creating applications that can write to a user’s filesystem is dealing with the real possibility that a simple, honest, garden-variety mistake can result in consequences ranging from the mildly frustrating to the disastrous.