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NetherlandsMetabolomicsCentre / metitree

Metitree
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Comparing fragmentation trees #11

Open justinjjvanderhooft opened 12 years ago

justinjjvanderhooft commented 12 years ago

It is possible to include a button at the compare/match tab that produces visual output of where the two trees that have a match (score) actually are similar and where they differ? That would help in the manual interpretation of the generated matches.

michaelvanvliet commented 12 years ago

At this moment there is not. There is a manual way to do this using the SAMS lib from GitHub: https://github.com/NetherlandsMetabolomicsCentre/samsn. You download the CML files from Metitree and do the following:

Command to compare two fragmentation trees. USER/$ java -jar sams-0.1.git.jar -i1cml F002169_C15H9O4.cml -i2cml F002169_C15H9O4.cml compare

I will add this to the list of Feature requests

justinjjvanderhooft commented 12 years ago

Ok, thanks!, can I also use it within the browser environment of MetiTree? I am running it on a Windows computer, like almost everybody here at PRI has (except the BioInformatics people)

michaelvanvliet commented 12 years ago

No not yet. I think you should be able to get it running on Windows. Make sure you have Java, R, RServe, XCMS and graphviz installed.

The other option would be to have a Linux VM, like the Ubuntu VirtualBox image you used to run Metitree.