Kind of fermentation software to use based on the applications

The user final application will determine the kind of fermentation software to use. The potential applications include: fermentation process control, analysis of fermentation/cell culture data, process improvement or development and/or specific fermentation equipment software. The answer is that there are different tools that are not necessarily fermentation specific but they each are superior in their respective categories as follows: process control, data storage, data analysis and process modelling and simulation.

First all let’s mention process control software. The process control software monitors the data coming from the sensors and measuring instruments. All fermentation data analysis is preceded by data capture, archival and retrieval. As mentioned before the company that has really taken over process control is Emerson's DeltaV system. DeltaV is that software that in most cases does the data capture.

Data capture is followed by data storage. There are different software programs that store process data for the long term what is called a historian. DeltaV has a historian however OSI soft PI (better known only as PI) is the system that is the most popular and it archives data for the long-term. PI’s success has to do with its customer tools and support. PI customer tools include DataLink and ProcessBook that are good for generic process troubleshooting and support.

To obtain a better understanding of the main variables controlling bioprocessing not only fermentation but also cell culture is precise to use statistical data analysis. Again, there are different statistical programs but JMP from the SAS Institute is the most well-known and used software. JMP is a desktop stats software whose capabilities go from statistical design of experiments (DOE) to sophisticated analysis of the process main variables for process improvement and for troubleshooting to identify the main cause of specific production and quality problems.

For process simulation it is necessary to have accurate models that predict the process as closely as possible. However, that implies the use of many independent variables not only from the biological point of view but also from the process itself such as mass and energy balances, heat and mass transfer and the differential equations associated with it. The more accurate the bioprocess model is, the more equations are needed. A common approach for many companies I have worked with is to develop their own bioprocess models a task that can take 6 months to a year depending on the complexity associated with the new process. To solve the mathematical equations needed MathLab is an excellent tool to do it.

There are different tools available and all have a broad spectrum of prices and capabilities. For bioprocesses, SuperPro design has a clear advantage for bioprocess modeling and simulation because it has strong capabilities for batch processes that are the norm in fermentation and cell culture. Superpro has different fermentation models available to match the bioprocess kinetic characteristics combined with sophisticated process capabilities in order to achieve a process simulation as close as possible to the real process. Furthermore, all of this can be done in a short period of time that contrasts with the individual approach, I stated above and definitely is a tradeoff between time and accuracy.

A new software tool for bioprocess analysis that is advantageous when measured for price and benefit is called the Fermentertool and it is based on an Integrated Mathematical Model of Development (IMMD) for the calculations and assumes the presence in the bioprocess of dividing and non-dividing cells. This fermentation tool helps to design feeding rates and adjust substrate and nutrient ratios to improve/optimize cell growth and product formation. It works with different types of fermentations under different constrains such as product and substrate inhibition. The company also offer free trials at the following website

For equipment specific software for fermentation, I will mention some such as: Sartorius BioPAT® MFCS/win for supervisory bioprocess control and data acquisition and for upstream and downstream processing. It is a feature-rich, GAMP category 4 software package - based on over 25 years of experience and 3,000 installations worldwide. Eppendorf BioCommand® Software For Fermentors and Bioreactors to monitor and control fermentation and cell culture processes through personal computer. FNet - Fermentor Control Software: is a software for monitoring fermentation and cell culture processes with the LAMBDA MINIFOR laboratory fermenter. Among these equipment specific software Sartorius BioPAT® MFCS/win stands out for its capabilities to store data, to integrate with other software and for process control and optimization.

I have used all of the programs mentioned above and in general prices are associated with quality and capabilities and some of the software I stated is a little pricey. The statement you get what you paid seems to be a constant in life and in fermentation.


My recommendations are as follows:

DeltaV is a superior control system

OSI PI is a superior data historian

JMP is a superior data analysis software

Fermentertool: is the best choice when determined based on cost vs benefits for process improvement and optimization of nutrient feed rates and quantities.

For process simulation for fermentation and to fill the gap between fermentation and downstream processing and between process design and simulation for bioprocesses SuperPro design is a superior tool.

Sartorius BioPAT® MFCS/win for fermentation specific equipment and bioprocess control.

Additional information

Websites for the companies mentioned in this article:





Intelligen SuperPro Design:

Equipment specific software:

Sartorius MFCS/win:

Eppendorf BioCommand® :

Applikon Biotechnology software:

FNet - Fermentor Control Software:

BiofuelTech Consultants offers consulting helping customers to improve fermentation control, analysis, improvement, design and optimization.

keywords: fermentation software, cell culture, data analysis, multivariate, statistics