PubMed unchained. And, Oh, no, not another 'Ome!

I found two cool new tools today. The first, via Sourceforge, is PuMA, a standalone Java front-end to PubMed. PuMA (currently at version 1.0alpha) allows you to view bibliographic search results and abstracts in the same window, visually construct complex Boolean queries, and export data to EndNote, Reference Manager, ProCite, and BibTex. It also offers keyword highlighting, links to Google and Google Scholar (for instance, to find articles citing another's work), and an intuitive user interface. The second, via the bioinformatics blog nodalpoint, is a neat little project called Scriptome. My first thought on seeing the post was to dismiss the thing as yet-another-omic. But Scriptome, developed by the Computational Biology Group at Harvard's Bauer Center for Genomics Research, is anything but. Instead it is a collection of bioinformatics one-liners: simple Perl scripts (called "atoms") that complete a single defined task like fetching a sequence...