A few weeks ago we put a number of spectra online using Bob Lancashire’s JSpecView applet. Specifically, using data supplied by John Meyers from our Advisory Group, we put up some IR data, Raman data and MS data associated with cocaine.

You should see a series of spectra that look like this.Mass Spec Picture
















The intention is to allow ChemSpider users to add their spectral data to records on the ChemSpider database to facilitate open access sharing of analytical data.

As commented, this is for Proof of Concept. We are seeing some dependencies on the Java Version as well as whether the browser is Internet Explorer, Firefox or Safari and whether it is on Mac or PC. We need your help. Please visit the cocaine page and scroll down to the bottom of the page and respond to this blog post with a comment regarding whether you can see the series of spectra or not. If not, then let us know what platform you are on in terms of PC or Mac, browser and version number and the Java version.

I have recently participated in a demo led by the RedHen Spectra group. Their efforts are definitely of interest in terms of a potential mash-up in the future.

If you are interested in submitting spectra onto ChemSpider in the future (we are presently accepting NMR, MS (non-hyphenated), IR, Raman etc.) please contact us directly at feedback@chemspider.com to initiate discussions.

Stumble it!

5 Responses to “Proof of Concept Viewing of Spectral Data on ChemSpider”

  1. Jean-Claude Bradley says:

    That’s great news. We have a bunch of H and C NMR spectra in JCAMP format for pure compounds – how do we submit them?

  2. Rich Apodaca says:

    I see five non-inited applets. My guess is that you’re using Java 1.6 to compile the applet. If you can get away with it, try using a 1.4.2 JVM, or switch the target JVM and see what happens. You should be able to reproduce the problem on any system by demoting the browser’s JVM – try 1.4 or 1.5.

    Check out the last item on this page:

    http://java.sun.com/docs/books/tutorial/deployment/applet/problemsindex.html

    platform=Linux
    browser=Firefox

    Here’s my Java console output: (REMOVED FOR BREVITY)

  3. valt says:

    I left a question on JSpecView about this problem: http://sourceforge.net/forum/forum.php?thread_id=1788205&forum_id=546074. Weird is that some of JDX are loaded while others no. I tried to compile with different JDKs (1.5+), but got no success (with Plugin 1.6). Also, it worked fine for me before I upgraded to JavaPlugin 1.6. Didn’t try to debug applet code yet, may be somebody will provide quick solution.

  4. Robert Lancashire says:

    The code is being compiled with 1.6_01 since there is a bug with SUN 1.6_02.
    The Eclipse antbuild is set to compile at 1.5 and I am surprised to hear that
    1.5+ is not working since we have compiled successfully with 1.5.10

    It is not possible to go back to 1.4 since some routines are using 1.5.

  5. ChemSpider News » Blog Archive » JSpecView Visualization Issues Now Resolved on ChemSpider says:

    [...] so that structure-spectra association is in place. We have described this in previous posts (1,2) and a technical note about depositing spectral data is available [...]

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