Interactively AUDIT Your Growth Curves with a Suite of R Packages
Bibliographic record
Abstract
Bottlenecks often occur during data analysis when studying microbial growth in liquid culture at large scale. A researcher can collect thousands of growth curves, repeated measures of a microbial liquid culture, at once in multiple micro titer plates by purpose-built robotic instruments. However, it can be difficult and time-consuming to inspect and analyze these data. This is especially true for researchers without programming experience. To enable this researcher, we created and describe an interactive application: Automated Usher for Data Inspection and Tidying (AUDIT). It allows the user to analyze growth curve data generated from one or more runs each with one or more micro titer plates alongside their experimental design. AUDIT covers input, pre-processing, summarizing, visual exploration and output. Compared to previously available tools AUDIT handles more data, provides live previews and is built from individually re-usable pieces distributed as R packages.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.012 | 0.049 |
| Meta-epidemiology (narrow) | 0.004 | 0.002 |
| Meta-epidemiology (broad) | 0.003 | 0.003 |
| Bibliometrics | 0.005 | 0.003 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.004 | 0.004 |
| Open science | 0.003 | 0.004 |
| Research integrity | 0.001 | 0.004 |
| Insufficient payload (model declined to judge) | 0.137 | 0.098 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".