Closed joewandy closed 1 year ago
Something for consideration here:
Parts one and two are quite straightforward. Part 3 could be done in one of two ways:
This goes (I think) to the bottom of the choices to be made...
For the particular example mentioned...
Thoughts?
Maybe an alternative is that we pass all scans to the state to update itself. And we then pass an MS1 scan, and it sends back a ranked list of the MS1 in the scan?
Vinny is on holiday but he left a comment on slack, summarised below:
For the experiment using optimal controller with peak picking in a loop, I wrote something that roughly did this before. In sequence manager OptimalMultiSampleExperiment, no idea whether it still works. Depends whether optimal controller still works I guess.
This does roughly what @joewandy's first comment on this issue asks. It just doesn't do it the way @simon suggested. The code is also in a serious need of reengineering. It made logical sense when I first wrote it, then became very clear soon after that my logic wasn't that solid. My number initial thoughts were to rearrange it with a separate section for processing, so this could be done on another core etc.
There is a half complete notebook called multi sample controllers in OneDrive. The first numbered section generally work and show roughly what the sequence manager can roughly do in terms of basic sequenced runs and gridsearch. There are some examples further down that run samples that are dependent on previous results, but these may not work any longer. I was in the process of updating these but hadnt quite got round to it yet
TODO: check the codes above and see how much can be reused, and what needs to be modified.
Briefly discussed in the meeting earlier.
Experimental manager (temporary name)
Use case:
Basically it's something that can define a workflow:
Not sure this is still needed, but sounds like something nice to have. Something to think about.
State has now been implemented as 'grid' in Ross' work.
We would like a flexible architecture that can cover a wide range of possibilities and experiments, e.g. DsDA style analysis, case-control study, etc:
For the next experiment, we aim to to test the following experiment on the machine:
@vinnydavies is there anything in https://github.com/sdrogers/vimms/blob/master/vimms/SequenceManager.py that can do the above? or needs to be completed?