Data · dataset · 2021
Data for "Signal Amplification in Synthetic Bacterial Communication"
Listed in CaltechDATA
The files provided here contain the data and Python code referenced in the PhD thesis entitled "Signal Amplification in Synthetic Bacterial Communication".
Description
Python analysis and simulation files are in the tar archive `analysis.tgz`, in which the top-level directories `platereader`, `microscopy`, and `omnitray-modeling` correspond respecting order to platereader experiments, microscopy experiments, and simulations. Microscopy data are stored in tar archives and are labeled by date codes as YYMMDD.tgz.
When these archives are extracted to the directory `microscopy/data` they can be accessed by the `viewing_aquisitions.ipynb` or `200626_analysis.ipynb` Jupyter Notebooks. The time lapse microscopy images are unprocessed TIFF files. Raw and processed platereader data are in the `biotek_data.tgz` tar archive and related MCMC walker traces are in `mcmc_outputs.tgz'.
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The analysis code includes Jupyter Notebooks, Python modules, and SLURM job scripts. The job scripts are unchanged and unsuitable for the out-of-the box use. However, a user may need to adapt these scripts in order to perform processing or simulation before exploring data or generating figures in a Jupyter Notebook.
Links
Where it is published
- CaltechDATA record data.caltech.edu/records/ktbey-my740 ↗
landing page · from data caltech edu
- DOI doi.org/10.22002/d1.1928 ↗
DOI / persistent id · from data caltech edu
Catalogue records · 1
- InvenioRDM API data.caltech.edu/api/records/ktbey-my740 ↗
metadata API · from data caltech edu
Topics
- Stated by source
- synthetic ahl signaling wave propagation bacteria
- From keywords
- Earth & Environmental Science · Engineering · Humanities · Life Sciences · Social Science
- Inferred from text
- Communications engineering 74% · Image 65% · Microscopy 75% · Simulation 75%
Provenance · 1 source records, 16 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| CaltechDATA | ktbey-my740 | 12 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · data caltech edu | connector:data_caltech_edu@1.0.0 | |
| concepts[field].anzsrc:group:4006 | enrichment · data caltech edu | taxonomy-embedding@1.0.0 | title+keywords+description (74%) |
| concepts[field].local:field:earth-environmental | mapping · data caltech edu | connector:data_caltech_edu@1.0.0 | |
| concepts[field].local:field:engineering | mapping · data caltech edu | connector:data_caltech_edu@1.0.0 | |
| concepts[field].local:field:humanities | mapping · data caltech edu | connector:data_caltech_edu@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · data caltech edu | connector:data_caltech_edu@1.0.0 | |
| concepts[field].local:field:social-science | mapping · data caltech edu | connector:data_caltech_edu@1.0.0 | |
| concepts[method].local:method:simulation | enrichment · data caltech edu | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[modality].local:modality:image | enrichment · data caltech edu | keyword-concept-rules@1.0.0 | title+description (65%) |
| concepts[modality].local:modality:microscopy | enrichment · data caltech edu | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[topic].invenio_subject:data_caltech_edu:synthetic-ahl-signaling-wave-propagation-bacteria | source · data caltech edu | connector:data_caltech_edu@1.0.0 | |
| description | source · data caltech edu | connector:data_caltech_edu@1.0.0 | /metadata/description |
| publication_date | source · data caltech edu | connector:data_caltech_edu@1.0.0 | |
| title | source · data caltech edu | connector:data_caltech_edu@1.0.0 | /metadata/title |
| updated_date | source · data caltech edu | connector:data_caltech_edu@1.0.0 | |
| version_label | source · data caltech edu | connector:data_caltech_edu@1.0.0 |