Closed sdrogers closed 4 years ago
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
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!
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.
Maybe for each listed task, best to put them into a single notebook?
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?
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.
If not, any volunteers?
I'm doing it
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
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
Methods 2.1. full scan 2.2. top-n 2.3. DIA 2.4 smartROI 2.5. Optimal controller
MultiSampleMethods 3.1 sequence manager 3.2 gridsearch (added) 3.3 DsDA ... others to be added
Evaluation 4.1. Scoring (added) 4.2 heatmap (edited)
Seems that @vinnydavies has done it
Following notebooks: