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OpenChrom / OpenTyper

MALDI-TOF MS interface for OpenChrom/ChemClipse
https://lablicate.com/applications/maldi
Eclipse Public License 1.0
4 stars 4 forks source link

Batch processing #5

Open Mailaender opened 7 years ago

Mailaender commented 7 years ago

Current Freeware tools provided by Bruker Daltonics such as CompassXport are command line based and designed for the Microsoft Windows operating system only. I also haven't managed to get them up and running on my office/home PCs as they might need a connection to flexAnalysis (Setup.exe seems to install weird DLLs and COM connections) or the command and control server of the MALDI operator machine.

An easy configurable GUI to walk you through the data processing and exporting to replace this functionality can be achieved with an Eclipse wizard.

eselmeister commented 7 years ago

Yepp, using a wizard could be a nice solution. Since a while, we implement process wizards for specific tasks:

https://spectrometrylab.wordpress.com/2016/09/05/create-a-retention-index-cal-file https://spectrometrylab.wordpress.com/2016/08/23/enhanced-chemstation-quantitation

Is it possible to run the CompassXport tools under Linux/Mac using WineHQ?

Am 01.12.2016 um 07:22 schrieb Matthias Mailänder:

Current Freeware tools provided by Bruker Daltonics such as CompassXport are command line based and designed for the Microsoft Windows operating system only. I also haven't managed to get them up and running as they might need a connection to flexAnalysis (Setup.exe seems to install weird DLLs and COM connections) or the command and control server of the MALDI operator machine.

An easy configurable GUI to walk you through the data processing and exporting to replace this functionality can be achieved with an Eclipse wizard.

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Mailaender commented 7 years ago

Is it possible to run the CompassXport tools under Linux/Mac using WineHQ?

Not sure. My best guess is, that this tool was written in the early days when hardcore university researchers used it for automated data export. Nowadays R packages exist to read the .fid file format or you simply use the flexAnalysis pipeline to process the data with secret algorithms automated by convenient batch processing macros that are partly configurable with XML files and VBScript.

As I can't get it to run on Windows 7 not even on Bruker certified hardware, I am not sure if it is compatible with the latest flexAnalysis/Compass 1.4 and I am also not sure if the Bruker Software Support will be able to help me. My plan is to investigate it later when optimizing the mzXML converter. It or rather it's output could be used as some kind of official reference to develop against.