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galaxyproteomics / tools-galaxyp

Galaxy Tool Shed repositories maintained and developed by the GalaxyP community
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Adding Visualization Tools for Proteomics #56

Open souravsingh opened 8 years ago

souravsingh commented 8 years ago

It would be nice if a tool for visualizing the results from Mass Spectrometry and peptide matching experiments.A tool which can visualize and show a list of peptide matches which can run from OpenMS. cc @jj-umn @bgruening @jmchilton

bgruening commented 8 years ago

@souravsingh I know that @jj-umn is working on some visualisations. Do you have any suggestions? Any nice JS library we could reuse or any web-component that you would like to see integrated?

souravsingh commented 8 years ago

I am thinking of creating a JS library from scratch, since we also wish to allow visualization from programs like ProtK in the long run.

bgruening commented 8 years ago

As soon as we have a JS vis it's trivial to add it to Galaxy. I would also recommend you to look at the http://biojs.io/ registry and look if some visualisations are useful. These can also be easily integrated in Galaxy.

jj-umn commented 8 years ago

@tmcgowan @souravsingh @bgruening
Tom McGowan has done some nice work with using datatables and incorporating the lorikeet browser.
You may want to see if any of his experience would be of help.

bgruening commented 8 years ago

@tmcgowan is this cool project anywhere available? This sounds great!

souravsingh commented 8 years ago

I am intending to do this project as a part of GSoC 2016.I am open to any suggestions on the project.

iracooke commented 8 years ago

Hi Sourav, that's awesome. It would be great if you could build on the work that @tmcgowan and @jj-umn have done already. They have already created tools to convert various proteomics formats to sqlite for visualisation, and built some visualisations on top of that. There is plenty more to do of course and it would be awesome if you could find a project that complements their existing progress. I am guessing that Tom or JJ will have some more specific thoughts.

Stortebecker commented 6 years ago

What about integrating (parts of) MZmine? The MS visualizations seem to be really nice and sufficient for everything from raw data to statistics. It is not only made for visualization, but maybe one could integrate a small part first. Mzmine is open source and Java-based, would that work? It seems to provide an API, but I could not find a good documentation of the API so far.

I asked the developers about documentation: https://github.com/mzmine/mzmine2/issues/386.

Stortebecker commented 6 years ago

... and the report: no, it does not seem like mzmine could be integrated. The provided API is only for data processing, not for visualization.