# [CM-BASED REDUCED-ORDER MODEL FOR BIOREACTORS]

This readme file was generated on 2023-05-29 by Hector Maldonado

<help text in angle brackets should be deleted before finalizing your document>
<[text in square brackets should be changed for your specific dataset]>
<details on reccomended minimum content found at https://libraries.ou.edu/content/how-make-readmetxt-file

## Project organization
- PG = project-generated
- HW = human-writable
- RO = read only

- Title of Dataset: 

- Date of data collection: 2023-01-24

- Geographic location of data collection:  TU Delft, Delft, The Netherlands (via VPN)

- Information about funding sources that supported the collection of the data: TU-Delft

```
Author/Principal Investigator Information
Name: Hector Maldonado
ORCID:
Institution: TU Delft
Address: Van der Maasweg 9, 2629HZ Delft, The Netherlands
Email: h.a.maldonadodeleon@tudelft.nl

Author/Associate or Co-investigator Information
Name: Cees Haringa
ORCID:
Institution: Biotechnology Department - TU Delft
Address: Van der Maasweg 9, 2629HZ Delft, The Netherlands
Email: cees.haringa@tudelft.nl

Author/Associate or Co-investigator Information
Name: Adrie Straathof 
ORCID:
Institution: Biotechnology Department - TU Delft
Address: Van der Maasweg 9, 2629HZ Delft, The Netherlands
Email: A.J.J.Straathof@tudelft.nl

```

```
.
├── .gitignore
├── CITATION.md
├── LICENSE.md
├── README.md
├── requirements.txt
├── bin                     <- Compiled and external code, ignored by git (PG)
│   └── external            <- Any external source code, ignored by git (RO)
├── config                  <- Configuration files (HW)
    └── jsubmit?fluent.sh   <- This file is the bash file that submits the work to be run in the HPC (i.e, DelftBlue or HPC13 in text mode)
    └── commands.jou        <- This is the journal file that tells the HPC what files to run, i.e,. case and data files, initialization, patching, iterate, etc.   
├── data                    <- All project data, ignored by git
│   ├── processed           <- The final, canonical data sets for modeling. (PG)
│   ├── raw                 <- The original, immutable data dump. (RO)
│   └── temp                <- Intermediate data that has been transformed. (PG)
├── docs                    <- Documentation notebook for users (HW)
│   ├── manuscript          <- Manuscript source, e.g., LaTeX, Markdown, etc. (HW)
│   └── reports             <- Other project reports and notebooks (e.g. Jupyter, .Rmd) (HW)
├── results
│   ├── figures             <- Figures for the manuscript or reports (PG)
│   └── output              <- Other output for the manuscript or reports (PG)
└── src                     <- Source code for this project (HW)

```

## License

This project is licensed under the terms of the [MIT License](/LICENSE.md)

SHARING/ACCESS INFORMATION

Licenses/restrictions placed on the data: 

Links to publications that cite or use the data: 

Links to other publicly accessible locations of the data: 

Links/relationships to ancillary data sets: 

Was data derived from another source?
If yes, list source(s): 

Recommended citation for this dataset: 


## DATA & FILE OVERVIEW

File List: <list all files (or folders, as appropriate for dataset organization) contained in the dataset, with a brief description>

    requirements.txt        <- File describing the different packages and dependencies that are needed to run the project (RO) 
    bin                     <- Compiled and external code, ignored by git (PG)
        external            <- Any external source code, ignored by git (RO)
    config                  <- Configuration files (HW)
        jsubmit_fluent.sh   <- This file is the bash file that submits the work to be run in the HPC (i.e, DelftBlue or HPC13 in text mode)
        commands.jou        <- This is the journal file that tells the HPC what files to run, i.e,. case and data files, initialization, patching, iterate, etc.
    data                    <- All project data, ignored by git
        processed           <- The final, canonical data sets for modeling. (PG)
        raw                 <- The original, immutable data dump. (RO)
        temp                <- Intermediate data that has been transformed. (PG)
    docs                    <- Documentation notebook for users (HW)
        manuscript          <- Manuscript source, e.g., LaTeX, Markdown, etc. (HW)
        reports             <- Other project reports and notebooks (e.g. Jupyter, .Rmd) (HW)
    results
        figures             <- Figures for the manuscript or reports (PG)
        output              <- Other output for the manuscript or reports (PG)
    src                     <- Source code for this project (HW)
     


Relationship between files, if important: 

	jsubmit_fluent.sh, and commands.jou must be in the same folder (working directory) for the server to find it. commands.jou might 
	get the full path for reading-writing case and data files (if needed, but strongly adivised to avoid ending up with a messy collection
	of files). You can find proper comments on this file. 


Additional related data collected that was not included in the current data package: 

Are there multiple versions of the dataset? Probably yes, I have a template script (this) but versions of it are on my folder depending on the cases
I'm running. Keep an eye on the lastest version available, drop me a message if you find a typo or want to know more details about the script. 
You can find the last time I updated the file below. 

If yes, name of file(s) that was updated: 
	jsubmit_fluent.sh
	commands.jou

Why was the file updated? The contents were merged with the suggested folder structure from the RDM 101 course. 
When was the file updated?  2023-05-29


## METHODOLOGICAL INFORMATION

- Description of methods used for collection/generation of data: <include links or references to publications or other documentation containing experimental design or protocols used in data collection>

- Methods for processing the data: <describe how the submitted data were generated from the raw or collected data>

- Instrument- or software-specific information needed to interpret the data: <include full name and version of software, and any necessary packages or libraries needed to run scripts>

- Standards and calibration information, if appropriate: 

- Environmental/experimental conditions: 

- Describe any quality-assurance procedures performed on the data: 

- People involved with sample collection, processing, analysis and/or submission: 


## DATA-SPECIFIC INFORMATION FOR: [FILENAME]
<repeat this section for each dataset, folder or file, as appropriate>

Number of variables: 

Number of cases/rows: 

Variable List: <list variable name(s), description(s), unit(s) and value labels as appropriate for each>

Missing data codes: <list code/symbol and definition>

Specialized formats or other abbreviations used: