Cytoscape v3.0.2 on Mac OS X

Cytoscape 3.0.2 was released on 1st August, a bugfix release for the 3.x series. However, there is a compatibility issue with the latest Java update from Apple resulting in Cytoscape hanging on startup. I'd followed advice found elsewhere to update to the latest Java version with no success, until I found this post from Tim Hull, outlining a simple way to check what version you have installed.

/usr/libexec/java_home -v 1.6 -exec java -version

If the output contains “xM4508”, you have the broken version. If it contains "xM4509", this is probably a different issue...

If you find that you have the bad version, you can download the updated from Apple using the links below:

The updated Java fixed the problem for me.

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MetaboHunter (API)

MetaboHunter is a Python module for accessing the MetaboHunter web service for automated assignment of 1D raw, bucketed or peak picked NMR spectra. More information about the algorithm is available in the published paper: Tulpan, D., Leger, S., Belliveau, L., Culf, A., Cuperlovic-Culf, M. (2011). MetaboHunter: semi-automatic identification of 1H-NMR … More

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