Data files

To be described

Bioreactor data acquisition - part 1

Bioreactor data acquisition - part 2

5L culture of CH10-12, 37°C batch/fed-batch culture with induction at 28°C for 12h

5L culture of CH10-12, 37°C batch/fed-batch culture with induction at 28°C for 12h

5L culture of CH10-12, 37°C batch/fed-batch culture with induction at 30°C for 10h

5L culture of CH10-12, 37°C batch/fed-batch culture with induction at 30°C for 10h

5L culture of CH10-12, 37°C batch/fed-batch culture with induction at 33°C for 6h

5L culture of CH10-12, 37°C batch/fed-batch culture with induction at 33°C for 6h

5L culture of CH10-12, 37°C batch/fed-batch culture with induction at 37°C for 6h

5L culture of CH10-12, 37°C batch/fed-batch culture with induction at 37°C for 6h

5L bioreactor culture of recombinant strain E. coli CH10-12. Protein induction promoter when biomass reached 30 g cdw/L and at 29°C for 38 h

5L bioreactor culture of recombinant strain E. coli CH10-12. Protein induction promoter when biomass reached 30 g cdw/L and at 29°C for 38 h

5L bioreactor culture of recombinant strain E. coli CH10-12. Protein induction promoter when biomass reached 30 g cdw/L and at 32°C for 35 h

5L bioreactor culture of recombinant strain E. coli CH10-12. Protein induction promoter when biomass reached 30 g cdw/L and at 32°C for 35 h

5L bioreactor culture of recombinant strain E. coli NbF12-10. Protein induction promoter when biomass reached 30 g cdw/L and at 29°C for 37 h

5L bioreactor culture of recombinant strain E. coli NbF12-10. Protein induction promoter when biomass reached 30 g cdw/L and at 29°C for 37 h

5L bioreactor culture of reference strain E. coli WK6. Protein induction promoter when biomass reached 25 g cdw/L and at 29°C for 28 h

5L bioreactor culture of reference strain E. coli WK6. Protein induction promoter when biomass reached 25 g cdw/L and at 29°C for 28 h

Samples taken in the 5L bioreactor BR01 in the culture of E. coli WK6 in batch and fed-batch strategy

Samples taken in the 5L bioreactor BR02 in the culture of recombinant strain E. coli CH10-12 in a batch/fed-batch strategy at 37°C. Protein induction promoted when biomass reached 25 g cdw/L and at 28°C for 12 h

Samples taken in the 5L bioreactor BR03 in the culture of recombinant strain_ E. coli_ CH10-12 in a batch/fed-batch strategy at 37°C. Protein induction promoted when biomass reached 25 g cdw/L and at 30°C for 10 h

Samples taken in the 5L bioreactor BR04 in the culture of recombinant strain E. coli CH10-12 in a batch/fed-batch strategy at 37°C. Protein induction promoted when biomass reached 25 g cdw/L and at 33°C for 6 h

Samples taken in the 5L bioreactor BR05 in the culture of recombinant strain E. coli CH10-12 in a batch/fed-batch strategy at 37°C. Protein induction promoted when biomass reached 25 g cdw/L and at 37°C for 6 h

Samples taken in the 5L bioreactor BR06 in the culture of recombinant strain E. coli CH10-12 in a batch/fed-batch strategy at 37°C. Protein induction promoted when biomass reached 30 g cdw/L and at 29°C for 38 h

Samples taken in the 5L bioreactor BR07 in the culture of recombinant strain E. coli CH10-12 in a batch/fed-batch strategy at 37°C. Protein induction promoted when biomass reached 30 g cdw/L and at 32°C for 35 h

Samples taken in the 5L bioreactor BR08 in the culture of recombinant strain _E. coli _NbF12-10 in a batch/fed-batch strategy at 37°C. Protein induction promoted when biomass reached 30 g cdw/L and at 29°C for 37 h

Samples taken in the 5L bioreactor BR09 in the culture of _E. coli _WK6 in a batch/fed-batch strategy at 37°C. Induction simulation with 1 mM IPTG when biomass reached 25 g cdw/L and at 29°C for 28 h

Excel file containing the data anlysis of the BR01 culture: mass balances, specific growth rate, bioreactor volume, oxygen uptake rate (OUR)

Excel file containing the data anlysis of the BR02 culture: mass balances, specific growth rate, bioreactor volume, oxygen uptake rate (OUR)

Excel file containing the data anlysis of the BR03 culture: mass balances, specific growth rate, bioreactor volume, oxygen uptake rate (OUR)

Excel file containing the data anlysis of the BR04 culture: mass balances, specific growth rate, bioreactor volume, oxygen uptake rate (OUR)

Excel file containing the data anlysis of the BR05 culture: mass balances, specific growth rate, bioreactor volume, oxygen uptake rate (OUR)

Excel file containing the data anlysis of the BR06 culture: mass balances, specific growth rate, bioreactor volume, oxygen uptake rate (OUR)

Excel file containing the data anlysis of the BR07 culture: mass balances, specific growth rate, bioreactor volume, oxygen uptake rate (OUR)

Excel file containing the data anlysis of the BR08 culture: mass balances, specific growth rate, bioreactor volume, oxygen uptake rate (OUR)

Excel file containing the data anlysis of the BR09 culture: mass balances, specific growth rate, bioreactor volume, oxygen uptake rate (OUR)

Execution of a LEARN step: The case of growth coupled production hydrocarbons using S. cerevisiae

Gas analyzer (INNOVA 1313, Lumasense Technologies) Channel 4: gas out - BR01 Channel 6: gas in (reference) Sampling time: 60 s Flushing time: 45 s Analysis time: 15 s

Gas analyzer (INNOVA 1313, Lumasense Technologies) Channel 3: gas out - BR02 Channel 4: gas out - BR03 Channel 6: gas in (reference) Sampling time: 60 s Flushig time: 45 s Sampling time: 15 s

Gas analyzer (INNOVA 1313, Lumasense Technologies) Channel 3: gas out - BR04 Channel 4: gas out - BR05 Channel 6: gas in (reference) Sampling time: 60 s Flushig time: 45 s Sampling time: 15 s

Gas analyzer (INNOVA 1313, Lumasense Technologies) Channel 3: gas out - BR06 Channel 4: gas out - BR07 Channel 6: gas in (reference) Sampling time: 60 s Flushig time: 45 s Sampling time: 15 s

Gas analyzer (INNOVA 1313, Lumasense Technologies) Channel 3: gas out - BR08 Channel 4: gas out - BR09 Channel 6: gas in (reference) Sampling time: 60 s Flushig time: 45 s Sampling time: 15 s

This is the template that can be used to populate your project using the IBISBA Populator software that is part of the IBISBA Hub. More information can be found here https://ibisba.github.io/handbook/ibisba_hub/project/

The monitor_and_extract_metadata.py script is designed to monitor a specified parent folder for new subfolders containing a Result.xml file. It extracts selected metadata from the Result.xml file and saves this metadata in both JSON and XML formats within the same subfolder.

Summay of results form fermentations

This is an example of workflow run with target muconic acid. The results is a tar with a collection of SBML, fused with GEM SBML model (yeast in this case)

Template to collect input data for LEARN step

The unlock metadata template using a modified version of the ISA structure.

This is superseded by https://hub.ibisba.eu/file_templates/1