https://biotechsim.

ch
biotechsim.ch is a web application designed to aid in the production of recombinant enzymes and to assist with
biocatalysis using whole-cells. The web application provides an intuitive planning and analytical tool for batch
cultivation experiments. Essential inputs such as the maximum specific growth rate for a particular microorganism are
available through a library or can be calculated from one’s own experimental data and shared with others.

Planning

personally computed values or values from publications and public libraries (2,4)
1 Select the input values for the planned batch
experiment 1

2 Edit input values

3 2 7
3 Select units of biomass concentration

Select parameters for a particular microorganism

-values to a proprietary library

4
from the library
4
5 For low initial substrate concentrations [< 1 g/L],
include a reasonable Ks-value

6 To execute simulation, press the “Enter” key 5

7 Perform a what-if analysis to study effects of

input values on simulations

Adapt simulation to experimental data

Experiment 9 10 13

max
8 Edit measured data for biomass and substrate

Login: to save and share data from one’s own experiments and to save μ
concentrations; copy/paste from Excel is
possible
8
9 Define additional variables and extend the
table with measurement data

Take samples according to proposed optimum

10
sampling interval 11

11 Compare simulated data with measurements

12 Hide data from displaying in the graph by 12

clicking the legend

Adapt simulation inputs to fit measurement

13
data

Library: to access measurement data,

Analyse experimental data

Analysis
14 Automated* determination of maximum specific
growth rate (μmax) 14
* A straight line is fitted to a subset of datapoints for the 17
relationship ln(x)=f(t) by means of linear regression. 15 16
Additional points are included in the inital subset and
computations of maximum specific growth rate are
performed repeatedly as long as the slope is > 95% of
the maximum slope determined for the initial subset.
This method was adopted from a publicly available R-
package (3), the underlying algorithms of which had 17
been published previously (1).

15 Edit initial number of points used to compute the

slope by linear regression
16 Visually control the quality of fit

17 Save computed μmax-values in a proprietary or

public library

Please, cite with:

Looser, V., R. Gassmann, S. Weichart, A. Busin, R. Vorburger, and K. Kovar. 2019.
A mobile tool for planning and analysis of batch cultivation experiments, biotechsim.ch
Development of biotechsim.ch was funded by the “Innovation in Biocatalysis: A toolbox for sustainable bio-based production” programme of the
Competence Center for Biocatalysis (CCBIO), 2018. The web application and documentation are licensed under the terms of a Creative
Commons Attribution 4.0 International (CC BY 4.0) license.
References
(1) Hall, BG., H. Acar, A. Nandipati, and M. Barlow. 2015. Growth Rates Made Easy. Mol. Biol. Evol. 31: 232-38.
(2) Milo, R., P. Jorgensen, U. Moran, G. Weber, and M. Springer. 2010. BioNumbers-the database of key numbers in molecular and cell biology. Nucleic Acids
Res. 38:D750-3. http://bionumbers.hms.harvard.edu/search.aspx
(3) Petzoldt, T. 2017. growthrates: Estimate Growth Rates from Experimental Data. R package version 0.7.0. https://github.com/tpetzoldt/growthrates
(4) Richards, M. A., V. Cassen, B. D. Heavner, N. E. Ajami, A. Herrmann, E. Simeonidis, and N. D. Price. 2014. MediaDB: a database of microbial growth
conditions in defined media. PLoS One 9:e103548. https://mediadb.systemsbiology.net/defined_media/