Dan’s NAO Notebook

NAO Cost Estimate – Summary

The goal of this project was to build a model that allows us to:

NAO Cost Estimate MVP – Adding noise

Previously, we have worked out a deterministic model of the sequencing depth required to detect a novel pandemic virus by the time it reaches a fixed cumulative incidence (number of…

NAO Cost Estimate MVP – Optimizing the sampling interval

See previous notebook. The goal of this notebook is to use our simple, deterministic cost estimate to answer the question:

NAO Cost Estimate MVP

See Google Doc for background. See also Simple detection cost model for P2RA version.

Detection sensitivity to read count noise

See all-hands memo.

2023-10-24 Analysis of sludge dissociation test qPCR

2023-10-16 Analysis of recent protocol-comparison experiments

2023-10-11 Analyze qPCR standard curves

Test out the standard curves from qPCR standard curve troubleshooting.

2023-10-10 Analyze prefilter experiment qPCR

Determine which prefiltration method produces better nucleic acid results.

2023-10-05 Qubit data exploration

Trying to understand the Qubit output.

2023-09-28 qPCR Quality Control

Putting together a standard set of quality control checks and plots for qPCR. Includes standard curves and dilution series.

2023-09-13 PMMoV qPCR Analysis

NOTE: Need sample metadata. I don’t know what the samples are.

2023-07-18 Extraction Experiment 1 qPCR Analysis

Testing the efficacy of RNA extraction kits in influent samples. See experiment google doc.

Examine extraction-kit comparison experiment

2023-09-13 Extraction Experiment 2 qPCR Analysis

Testing the efficacy of RNA extraction kits in settled solid samples. See experiment google doc.

Airport experiment sequencing cost estimate

We are planning to…

2023-08-29 qPCR Analysis

Simple deterministic model of local and global prevalence

This is building on Mike’s notes. The objective is to have a very simple deterministic model of an exponentially-growing virus spreading from somewhere else…