vimms

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Previously, some of the ViMMS internals were moved to [mass-spec-utils](https://github.com/sdrogers/mass-spec-utils/tree/master) so they could be used as a separate, lighter-weight library. Unfortunately, that repository is no longer maintained. Additionally, there is...

mcbrider5002

Currently `IndependentMassSpectrometer` supports two kinds of arguments to generate scan times. [(Example.)](https://github.com/glasgowcompbio/vimms/blob/dc6df673f6112132e72bf0cecf93f8c74901485a/vimms/MassSpec.py#L555) The first is a dictionary mapping MS-levels (int) to either static values or a callable (of no arguments)....

mcbrider5002

Initial ms1 scan of 1 peak

1

It appears that an initial MS1 scan of exactly 1 peak is always inserted at the start of a simulated run. I can't remember why we do this, but maybe...

joewandy

No Targeting Below 80 m/z

2

ViMMS seems to have problems when scheduling fragmentation events below 80 m/z, even though defined constants would indicate the minimum should be 70 m/z. Fragmentation events between 70 and 80...

mcbrider5002

After code-refactoring, the following features are no longer supported in the simulated mass spec. They should be re-implemented at some point: - Being able to define multiple isolation windows for...

joewandy

Bumps [requests](https://github.com/psf/requests) from 2.26.0 to 2.31.0. Release notes Sourced from requests's releases. v2.31.0 2.31.0 (2023-05-22) Security Versions of Requests between v2.3.0 and v2.30.0 are vulnerable to potential forwarding of Proxy-Authorization...

dependabot[bot]

Noise peaks will never be fragmented as we loop after chemicals when generating scans, and there are no chemicals associated with noise peaks. See https://github.com/glasgowcompbio/vimms/blob/master/vimms/MassSpec.py#L623-L630. Not sure if this is...

joewandy

Breaking Overlap Controllers with RT Drift, then Correcting

6

Currently we have multiple controllers that treat RoIs as boxes and use properties of overlap between these boxes for prioritisation. (e.g. Non-overlap controller uses the unique area of a box.)...

mcbrider5002

Cutoff parameterisation in Gaussian Chromatogram

2

We currently have this: https://github.com/sdrogers/vimms/blob/df473d640a0b02f547e0150ba234da62e438c665/vimms/Chromatograms.py#L136 When we make `GaussianChromatograms` here: https://github.com/sdrogers/vimms/blob/df473d640a0b02f547e0150ba234da62e438c665/vimms/ChemicalSamplers.py#L300 We pass 0 as the mean and sigma as the sd. Our chemical RTs are the start of the...

sdrogers

This happens even after the notebook has finished running, and we try to open the mzML file.  Temporary solution is to restart the kernel, but it would be better...

joewandy