Skip to main content

Taverna-cdk

The Taverna project is very interesting, in my not so humble opinion, because of the potential that workflows have. A workflow is a complete description of an experiment; that can now be shared through the myexperiment site.

The central point of a scientific experiment is that it should be repeatable, by the researcher and by others. Many bioinformatics journal papers describe experiments of a sort that will not be repeatable years down the line, by anyone.

A concrete example is this paper by CH Robert and PS Ho, which describes an analysis of water bridges in proteins. A crucial line in the methods section is this :
"All programs were written with FORTRAN 77 on a Silicon Graphics Iris workstation or with MATHEMATICA...on a Macintosh IIci computer."
Which is really great if, 10 years later, you want to re-run their method on more than the 100 high-resolution structures that were available at the time. Do their programs still exist? Do I have access to an Iris machine (I used them in Birkbeck once, I think) let alone a Macintosh IIci!

So, if at all possible, could anyone doing some computational research (I'm looking at you, PhD students) use some kind of tool like Taverna or Kepler and then provide a reference in the paper to a site with the workflow on it. Hopefully, with source code repository information, and revision numbers, even the particular version of the programs used could be retrieved.

Is it a lot to ask?

Comments

Popular posts from this blog

Adamantane, Diamantane, Twistane

After cubane, the thought occurred to look at other regular hydrocarbons. If only there was some sort of classification of chemicals that I could use look up similar structures. Oh wate, there is . Anyway, adamantane is not as regular as cubane, but it is highly symmetrical, looking like three cyclohexanes fused together. The vertices fall into two different types when colored by signature: The carbons with three carbon neighbours (degree-3, in the simple graph) have signature (a) and the degree-2 carbons have signature (b). Atoms of one type are only connected to atoms of another - the graph is bipartite . Adamantane connects together to form diamondoids (or, rather, this class have adamantane as a repeating subunit). One such is diamantane , which is no longer bipartite when colored by signature: It has three classes of vertex in the simple graph (a and b), as the set with degree-3 has been split in two. The tree for signature (c) is not shown. The graph is still bipartite accordin

Király's Method for Generating All Graphs from a Degree Sequence

After posting about the Hakimi-Havel  theorem, I received a nice email suggesting various relevant papers. One of these was by Zoltán Király  called " Recognizing Graphic Degree Sequences and Generating All Realizations ". I have now implemented a sketch of the main idea of the paper, which seems to work reasonably well, so I thought I would describe it. See the paper for details, of course. One focus of Király's method is to generate graphs efficiently , by which I mean that it has polynomial delay. In turn, an algorithm with 'polynomial delay' takes a polynomial amount of time between outputs (and to produce the first output). So - roughly - it doesn't take 1s to produce the first graph, 10s for the second, 2s for the third, 300s for the fourth, and so on. Central to the method is the tree that is traversed during the search for graphs that satisfy the input degree sequence. It's a little tricky to draw, but looks something like this: At the top

1,2-dichlorocyclopropane and a spiran

As I am reading a book called "Symmetry in Chemistry" (H. H. Jaffé and M. Orchin) I thought I would try out a couple of examples that they use. One is 1,2-dichlorocylopropane : which is, apparently, dissymmetric because it has a symmetry element (a C2 axis) but is optically active. Incidentally, wedges can look horrible in small structures - this is why: The box around the hydrogen is shaded in grey, to show the effect of overlap. A possible fix might be to shorten the wedge, but sadly this would require working out the bounds of the text when calculating the wedge, which has to be done at render time. Oh well. Another interesting example is this 'spiran', which I can't find on ChEBI or ChemSpider: Image again courtesy of JChempaint . I guess the problem marker (the red line) on the N suggests that it is not a real compound? In any case, some simple code to determine potential chiral centres (using signatures) finds 2 in the cyclopropane structure, and 4 in the