Jon’s Radio Comments

November 15, 2006

Tantalizing hints of the Knowledge Navigator

Filed under: Uncategorized — jonsradiocomments @ 7:15 pm

The original item is here.



  1. What do we have to do to get that javascript applet?

    Comment by Graham — November 16, 2006 @ 4:12 pm | Reply

  2. Dear Jon,

    I was pleased once again to read a particular column of yours that
    resonated with me (‘Just Give Me the Data’). I’m a bioinformatician (currently back in school), and I spent two years of my life recently wrestling with the flat file format of the PDB (

    I’m sorry to say that I never got round to taking advantage of the new XML format with which they republished the entire dataset about 3/4 of my way through the project. I’ve not looked for a few years, but your comments prompted me to go back. They have a few tools for format conversion, but it doesn’t seem like they’ve published tools simply for the extraction and recombination of data. There was a
    paper published recently about PDB, describing its growth, but also pointing out the low use of the new formats (there’s several) described by the paper as a slow adoption by the general community.

    You rightly state that the problem is a lack of ease, nobody is
    going to download an XML file if they don’t even know how to handle
    it. There must be so many professors, post-docs and graduate students sticking with the old format because they simply don’t know XML, just biochemistry and biophysics. What kind of difference would it make if a small program was published that allowed straight-forward extraction of the required chain segments without having to squint at the original file.

    The result of my old project ( is a
    web-interface that allows a 2D visualization of interactions between chains. I designed the applet to accept the results in an XML format of my own, which can also be downloaded, saved and used again in the future. At the time, I was self-congratulatory about ‘moving with the times’, but I now realize how restrictive the circumstances are, I myself did not publish any neat little scripts that helped the user to extract and manipulate subsets of the data.

    The Systems Biology/Bioinformatics community has been expounding on
    the problem for a while, because such science would jump forward in
    leaps and bounds if all the little datasets could be shared and
    intergrated with the ease that you envision. The central issue is the need to hammer out a universal format that encompasses every aspect of biology. What a daunting task as you can imagine, but I’m asking, is such a universal format needed? If any individual scientist could access and tie in data of their choice at ease, such as Avi did in his webcast, then, more than a universal format, we just need all the available data in XML/RSS, and an available collection of scripts, or even javascript bookmarklets, that empowers us.

    I should add that another problem we have as a community is the
    necessity to visualize data in its context. Whether this be the
    comparison of evolutionary conserved sequences, the 3D structure of a biomolecule or the network of protein interactions, we are drawn, time and time again to use different programs for each context that in turn dictate the formats, such as the applet I designed.

    A fantastic step, one that I wished I had time to invest in, would be to create visualization programs that are independent (if thats the right word) of the data constructs available, and is also ‘online’. In other words, to create visualization plugins for firefox that can interact with the data-handling adaptors (easy to write greasemonkey scripts perhaps) that in turn can handle any kind of personally or corporately designed XML format would be, well, as you say, the knowledge navigator.

    Finally, the community needs an ease with which they can share, modify, and tout or blog better/updated scripts which can be installed with a click, a ‘’.

    Comment by Sam — November 16, 2006 @ 5:50 pm | Reply

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