Infer non-variable controls

[mwes]

In GitLab by @jakebeal on Aug 21, 2019, 06:53

Each modality of measurement implies some non-variable controls, which can be automatically inferred from the measurement table.

• Flow cytometry implies a rainbow bead control
• Plate reader implies a fluorescein dilution series and LUDOX and water controls (following the iGEM 2016 protocol https://jakebeal.github.io/Publications/PLOSONE-QuantificationOfFluorescence-2018.pdf)

I don't think the omics measurements have any fixed calibrants at present, though RNAseq should be using SRM 2374, a NIST calibration system for RNAseq https://www-s.nist.gov/srmors/view_detail.cfm?srm=2374

[mwes]

In GitLab by @jakebeal on Oct 14, 2019, 10:17

removed assignee

[mwes]

In GitLab by @jakebeal on Oct 25, 2019, 10:31

Related to #92 , might be obsolete depending on how @mweston's tables actually look.

[mwes]

In GitLab by @mweston on Oct 25, 2019, 10:47

These should be declared explicitly, not inferred - not all measurements include these control elements unless it's actually part of the design. We have support for this in the SR by three booleans:

has_fluorescence_calibration has_size_calibration has_igem_calibration

Example: https://gitlab.sd2e.org/sd2program/cp-request/blob/master/input/structured_requests/nand_2_0_omics.json#L131

Presence of these automatically inlines a re-usable measurement for each of these controls:

https://gitlab.sd2e.org/sd2program/cp-request/blob/master/references/flow_bead_fluorescence_calibration.json https://gitlab.sd2e.org/sd2program/cp-request/blob/master/references/flow_bead_size_calibration.json https://gitlab.sd2e.org/sd2program/cp-request/blob/master/references/igem_plate_reader_calibration.json

[mwes]

In GitLab by @jakebeal on Oct 27, 2019, 12:36

OK, @mweston, per your comment we won't infer controls. Instead, let's transform this into a warning in the validator when expected controls are not present.