Develop examples using real world fermentation data
tgadam opened this issue · comments
We need to develop a couple of examples demonstrating converting source (aka raw) fermentation data into the FSML data standard.
- Develop a public facing example that can be stored in fsml.org
- Develop an example using partner data
Here is an interesting example: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5320064/#bib1
Identified some partner data that we can use. The above link has a large volume of data that would be a good complete public example but it's pretty dense so it may not be a good intro dataset.
Still searching for a good intro public dataset.
We can use this dataset: https://abpdu.lbl.gov/resources/fermentation-bioreactor-sample-data/
We can use this dataset: https://abpdu.lbl.gov/resources/fermentation-bioreactor-sample-data/
This might be a good option because it's public and partner data. @tiffanydai @AndresPerezTesela can you look at this data and see if it would be a good dataset for creating an intro tutorial / user story for using FSML?
@mfero is seeing if we can use our previously identified partner example as a public example.
No, the Microbyre examples can not be used as public examples, however, they can be shared within BioMADE. Microbyre recommends checking the Beckman Coulter website for the Biolector white paper with examples.
@mfero to check if we could randomize the values in the csv files from Microbyre.
@AndresPerezTesela to check if we can select some data from the ABPDU dataset, as a working example.
@mfero still to check with Microbyre about randomizing their csv files.
@AndresPerezTesela Could you add some links here pointing to the datasets to be used as an interim example?
AMBR Data is dispersed in many different files. I've created this folder with AMBR's public data and start putting something together: https://drive.google.com/drive/u/0/folders/1db63-5T3skv6nfF6C-ehR1SQyymh4iHW. I've made a README file briefly describing the data contents.
Note that we might end up working with Phycus data initially though.
Seems like we have a real MicroByre example to be used publicly. Closing ticket for now.