Create simple notebooks for the simplest use cases

[sdrogers]

Following notebooks:

• Creating a chromatogram / fragment pickle file from an mzML
• Generating a set of random chemicals and creating the output mzML in fullscan and top-N mode
• Seeding from an existing mzML file

[vinnydavies]

Think this is already done. Need to double check that the current ones are still working and add a few new examples. DIA, SmartROI and sequence manager

[sdrogers]

Could you link them here please? I’m not sure I’ve seen all the above, but that obviously doesn’t mean they don’t exist!

[joewandy]

Could you link them here please? I’m not sure I’ve seen all the above, but that obviously doesn’t mean they don’t exist!

The notebooks are here https://github.com/sdrogers/vimms/tree/master/examples. These are the examples used for the paper (maybe best not to change them too much?).

Also I just checked, for the three tasks above, they're scattered in different notebooks.

• Creating a chromatogram / fragment pickle file from an mzML.
  • See 01. Download Data.ipynb section c (there are other stuff in the notebook).
• Generating a set of random chemicals and creating the output mzML in fullscan and top-N mode
  • First download and parse the HMDB database to get all the chemicals, see 01. Download Data.ipynb section b.
  • Then run for fullscan mode.
    • For a single sample, see 02. MS1 Simulations.ipynb.
    • For multiple samples, see 03. Multiple Samples Example.ipynb.
  • No example to run in top-N yet.
• Seeding from an existing mzML file
  • See 04. Top-N Simulations.ipynb

Maybe for each listed task, best to put them into a single notebook?

[sdrogers]

Yes, single notebooks for each of those simple cases, please. Separate from the paper ones (which should just be updated to reflect the new split between repositories).

@vinny are you working on notebooks?

If not, any volunteers?

-- Dr Simon Rogers Senior lecturer, School of Computing Science, University of Glasgow

On 9 Jul 2020, at 16:49, Joe Wandy notifications@github.com wrote:

 Could you link them here please? I’m not sure I’ve seen all the above, but that obviously doesn’t mean they don’t exist!

The notebooks are here https://github.com/sdrogers/vimms/tree/master/examples. These are the examples used for the paper (maybe best not to change them too much?).

Also I just checked, for the tasks above, they're scattered in different notebooks.

Creating a chromatogram / fragment pickle file from an mzML. See 01. Download Data.ipynb section c (there are other stuff in the notebooks). Generating a set of random chemicals and creating the output mzML in fullscan and top-N mode First download and parse the HMDB database to get all the chemicals, see 01. Download Data.ipynb section b. Then run for fullscan mode. For a single sample, see 02. MS1 Simulations.ipynb. For multiple samples, see 03. Multiple Samples Example.ipynb. No example to run in top-N yet. Seeding from an existing mzML file See 04. Top-N Simulations.ipynb Maybe for each listed task, best to put them into a single notebook?

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[joewandy]

If not, any volunteers?

I'm doing it

[vinnydavies]

I was working on examples for the sequence manager. Some part of those examples can be added into one of the examples that already exist. We should also add DIA examples

[joewandy]

1. Data 1.1 Creating a chromatogram / fragment pickle file from an mzML 1.2 Generating a set of random chemicals and creating the output mzML in fullscan and top-N mode 1.3 Seeding from an existing mzML file

2. Methods 2.1. full scan 2.2. top-n 2.3. DIA 2.4 smartROI 2.5. Optimal controller

3. MultiSampleMethods 3.1 sequence manager 3.2 gridsearch (added) 3.3 DsDA ... others to be added

4. Evaluation 4.1. Scoring (added) 4.2 heatmap (edited)

[joewandy]

Seems that @vinnydavies has done it