Create exhaustive user settings page

wasimsandhu commented 2 years ago

Should allow the user to enter the following:

General settings

Google Drive user (for cloud backup)
Table for "registered" instruments
Text field for adding new instruments

Notifications

Table of users registered for Slack notifications
Text field for registering users for Slack notifications
Table of users registered for email notifications
Text field for registering users for email notifications

Internal standard QC settings

Text field dropdown for adding chromatographies
Dropdown for selecting polarity
Table for adding internal standard name, m/z, and RT

Biological standard QC settings

Text field dropdown for adding chromatographies
Dropdown for selecting polarity
Table for adding biological standard feature name, m/z, and RT

MS-DIAL parameters

See https://github.com/czbiohub/MSPipeline/tree/main/scripts/msDialParameter

All parameters should be stored in the database.

wasimsandhu commented 2 years ago

Navbar documentation in Bootstrap Dash: https://dash-bootstrap-components.opensource.faculty.ai/docs/components/navbar/

wasimsandhu commented 2 years ago

TODO: MS-DIAL parameter settings

#Data type
MS1 data type: Centroid
MS2 data type: Centroid
Ion mode: Positive
DIA file: 

#Data collection parameters
Retention time begin: 0
Retention time end: 100
Mass range begin: 0
Mass range end: 2000

#Centroid parameters
MS1 tolerance for centroid: 0.008
MS2 tolerance for centroid: 0.01

#Peak detection parameters
Smoothing method: LinearWeightedMovingAverage
Smoothing level: 3
Minimum peak width: 4
Minimum peak height: 50000
Mass slice width: 0.1

#Deconvolution parameters
Sigma window value: 0.5
Amplitude cut off: 0

#Adduct list
Adduct list: [M+H]+

#Text file and post identification (retention time and accurate mass based) setting
Text file: /mnt/storage/samba/shared/metabolomic/MsdialParam/DDA_HILIC_Pos/InternalStandardsPos.txt
Retention time tolerance for post identification: 0.3
Accurate ms1 tolerance for post identification: 0.008
Post identification score cut off: 85

#Alignment parameters setting
Retention time tolerance for alignment: 0.05
MS1 tolerance for alignment: 0.008
Retention time factor for alignment: 0.5
MS1 factor for alignment: 0.5
Peak count filter: 0
QC at least filter: True

wasimsandhu commented 2 years ago