Growth Balance Analysis

Growth Balance Analysis

Growth balance analysis

To get started, upload your GBA model by clicking "Choose File" and selecting your .ods file. If you don't have the GBA template yet, you can download it by clicking "Download GBA Template." After uploading your model, ensure its validity by clicking "Check Model." You'll be notified immediately if any issues are detected. For more control, you can use the advanced options to change the solver type for Non-linear Optimization (default is L-BFGS). Once you're ready, click "Run" to begin the optimization process for your uploaded model.

Upload your model

audio

Number of Conditions
Maximum Growth rate
 h-1
Average of Total Protein Concentration
 [g L-1]
Number of Converged Optimization

Interactive Plots

In this section, you can visualize the results by selecting different axes, such as Growth Rate, Protein Fractions/Concentrations, Fluxes, and more.



Your GBA Model

Here, you can view your uploaded GBA model. The first tab displays the Mass Fraction matrix (M) of your model. Even after optimization, you can modify any parameters and rerun the optimization by clicking "Run" in the last tab to see the changes. Additionally, you can download the updated model by clicking "Download" in the same tab.


Here, you can view your uploaded GBA model. The first tab displays the Mass Fraction matrix (M) of your model. Even after optimization, you can modify any parameters and rerun the optimization by clicking "Run" in the "Condition" tab to see the changes. Additionally, you can download the updated model by clicking "Download" in the same tab.


This section displays the Michaelis Constant (Km) matrix of your uploaded GBA model. Make sure each substrate in your reactions has a valid Km value; otherwise, a default value of 0.1 g/L will be used. You can also search for Km values in the table below, sourced from the BRENDA database. Please ensure Km values are mass balanced and converted to g/L by multiplying the Km values in molar units by the molecular weights of the respective substrates.



This section displays the Inhibition Constant (KI) matrix of your uploaded GBA model. You can modify the values directly here.


This section displays the Activation constant (KA) matrix of your uploaded GBA model. You can modify the values directly here.


This section displays the Turnover Number (kcat) matrix of your uploaded GBA model. You can search for kcat values in the table below, sourced from the BRENDA database. Ensure that kcat values are mass balanced and converted to 1/h (mass of product/mass of enzyme/hour) by multiplying the kcat values in 1/h units by the molecular weight of the respective product and dividing by the mass of its enzyme. "kcatf" and "kcatb" indicates the kcat for forward and backward reactions, respectively.



This section displays the External Concentration and Cell Density matrix. The parameter "Rho" represents the cell density in your model, while the other rows show the external concentrations. Ensure that all external concentrations are labeled with "x_". You can modify these values and rerun the optimization by clicking "Run" to see the changes. To download the latest version of your edited GBA model, click "Download."

Download

Pathway Visualization

In this section, you can view the network visualization of your GBA model. The dot size represents metabolite concentrations, while the line thickness indicates protein concentrations, both as results from the optimization. You can download the visualization results below.

Growth balance analysis

Create your model

Here, you can create your GBA model by selecting the number of metabolites and reactions. The first tab displays the Mass Fraction matrix (M) of your model. Ensure that the M matrix is mass normalized: the sum of metabolite fractions should equal -1, and the sum of product fractions should equal +1 for each reaction.

audio

This section displays the Michaelis Constant (Km) matrix of your created GBA model. Make sure each substrate in your reactions has a valid Km value; otherwise, a default value of 0.1 g/L will be used. You can also search for Km values in the table below, sourced from the BRENDA database. Please ensure Km values are mass balanced and converted to g/L by multiplying the Km values in molar units by the molecular weights of the respective substrates.


This section displays the Inhibition Constant (KI) matrix of your uploaded GBA model. You can modify the values directly here.

This section displays the Activation constant (KA) matrix of your uploaded GBA model. You can modify the values directly here.

This section displays the Turnover Number (kcat) matrix of your created GBA model. You can search for kcat values in the table below, sourced from the BRENDA database. Ensure that kcat values are mass balanced and converted to 1/h (mass of product/mass of enzyme/hour) by multiplying the kcat values in 1/h units by the molecular weight of the respective product and dividing by the mass of its enzyme. "kcatf" and "kcatb" indicates the kcat for forward and backward reactions, respectively.


This section displays the External Concentration and Cell Density matrix. You can select the desired number of conditions and external metabolites. The parameter "Rho" represents the cell density in your model, while the other rows show the external concentrations. Ensure that all external concentrations are labeled with "x_". You can modify these values and rerun the optimization by clicking "Run" to see the changes. To download the latest version of your edited GBA model, click "Download."

Download
Number of Conditions
Maximum Growth rate
 h-1
Average of Total Protein Concentration
 [g L-1]
Number of Converged Optimization

Interactive Plots

In this section, you can visualize the results by selecting different axes, such as Growth Rate, Protein Fractions/Concentrations, Fluxes, and more.



Pathway Visualization

In this section, you can view the network visualization of your GBA model. The dot size represents metabolite concentrations, while the line thickness indicates protein concentrations, both as results from the optimization. You can download the visualization results below.

About us

What is Growth Balance Analysis (GBA)?

Growth Balance Analysis (GBA) is a computational framework designed to study the balanced growth of cells in biological systems. Cells grow and divide while operating under several physical and chemical constraints, such as mass conservation, biochemical reaction kinetics, and limitations on cell density. GBA provides a method for modeling these complex systems and determining the optimal growth rate of cells by analyzing how resources are allocated across cellular reactions. At optimal growth, only a minimal subset of reactions remains active, leading to more efficient resource use and providing insights into cellular fitness. GBA has become an important tool for understanding fundamental principles of resource allocation, cellular economics, and the trade-offs involved in cellular growth and metabolism.

About GBApp

GBApp is a web application developed to simplify and enhance the implementation of Growth Balance Analysis for metabolic models. The platform allows researchers and educators to easily upload or create their own metabolic models, perform in-depth growth balance analysis, and visualize results through intuitive and interactive plots, as well as metabolic network diagrams. With GBApp, users can streamline the complex processes of metabolic modeling, making advanced computational tools accessible to a wider audience of scientists.

Whether you are looking to understand resource allocation in microbial systems or explore cellular growth patterns under different conditions, GBApp offers a comprehensive and user-friendly platform for conducting cutting-edge research in systems biology and metabolic modeling.

Contact us via Email: ghaffas@hhu.de