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

Written byJeff Perkel

| 2 min read

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 from a database or sorting results. There's nothing to download; you simply cut-and-paste atoms from the Scriptome Web site and paste it into a UNIX, Windows, or Mac OS command window (you'll need to have Perl, and possibly also BioPerl, installed). Suppose you want to sum the n'th column of a file containing tabular data. You go to the Scriptome Web site, find the atom "calc_col_sum", and cut-and-paste the text into a terminal window:perl -ne "BEGIN {$col=1}" -e "s/\r?\n//; @F=split /\t/, $_; $sum += $F[$col]; END {warn qq~Sum of column $col for $. lines\n~; print qq~$sum\n~}" file.tabGiven a file called 'file.tab' that looks like this:Fly 7 Human 14 Worm 28 Yeast 35The output is: Sum of column 1 for 4 lines 84That may seem trivial, but the atoms can be quite powerful when combined into "protocols". One pre-fab protocol combines five scripts to comb genome-vs-genome BLAST output files for potential orthologs. At the moment, the site has a relatively limited number of tools. But according to the Scriptome FAQ list, the project remains a work-in-progress: "We have several zillion ideas. We might decide to change the interface if biologists dislike the cut-and-paste + edit method. There are plenty of tools and protocols to write. We would like to add an "explain this" button to each tool, so that Perl students can get a detailed explanation of how the tools work."Given the project's target audience of biologists with little or no programming experience, that final item sounds like a worthy goal.

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

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