MonaLisa

 

 

 

 

 

 

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MonaLisa is a Java-based tool that allows you to carry out a biochemical network analysis. This portable application is utilized for studying metabolic models from humans, the food web, and cancer cells. You can test the functionality of the software by checking different model formats.

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MonaLisa Description:
MonaLisa is an advanced Petri net-based application specialized in analyzing biochemical networks. You can check models for structural faults and identify biological modules, as well as visualize the computed results.

The comfort of working with portable tools

The portable running mode ensures your Windows registry does not get bloated with extra entries. You may get rid of the utility by simply deleting the files that you have downloaded from the Internet.

Copying it on USB flash drives or other devices is also possible. You can run the program by opening the executable file. This is a Java-based tool so you need to previously install the working environment on your computer.

Support for different techniques

The application works with various analysis techniques which are related to network decomposition and knockout analysis, and offers support for the computation of elementary modes (T-invariants), P-invariants, maximal common transition sets (MCT-sets), T-clusters, minimal cut sets (MCS), degree distribution, and cluster coefficient distribution.

User interface and importing options

The GUI can be described as practical. You can work with three main panes: ones is used for project management, other for visualizing the PN model, while the last one provides access to a set of configuration settings.

The program offers you the possibility to import data from various systems biology and graph-theoretic formats, such as SBML, KGML, PNT, APNN, MetaTool, and PNML.

Project management

MonaLisa allows you to save projects to a file so you can easily import data in the future for making adjustments, view a list with recently used projects, set up the approaches, define the settings, and export the results and/or PN model to one of the file formats used for importing data.

Visualizing the PN model and configuring several settings

The application lets

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Stress on reactive networks usually occurs in a metabolic network due to an overproduction of specific products such as toxic compounds, or adverse environmental conditions. The metabolic response to stress occurs in a timely manner through a specific alteration of the expression of the genes encoding for enzymes involved in metabolic reactions. The transcriptional program is accompanied by an overall reduction of the protein content, an adaptation process which is related to the induction of a specific set of genes called stress genes. The analysis of the transcriptome and proteome of several organisms under different conditions has become an essential tool of the Systems Biology. Indeed, PN-based models have been utilized for a number of purposes such as the study of complex metabolic networks, metabolic engineering, cell communication, and the design of synthetic circuits. The Network Decomposition (ND) is a comprehensive analysis of large networks which allows identification of modules in which specific reactions operate. A canonical example in which the use of ND has been implemented is the analysis of the carbon metabolism. Carbon is one of the most important nutrients in cells and a major source of energy for bacteria. The cellular uptake of carbon involves the expression of a large number of genes. The enhanced expression of these genes facilitates the ability of bacteria to scavenge carbon from the environment. The carbon metabolism is currently of interest because of its role in controlling the metabolism of the cell. According to the state of the carbon metabolism, the cell will generate energy by glycolysis or aerobic respiration. However, the transition between the two pathways involves a major restructuring of the membrane and associated processes. In order to assure that the cell will generate energy in the correct way, the carbon metabolism has to be strictly regulated. Indeed, if the carbon enters the cell in a way that is not related to energy production, the cell could damage the membrane. The cellular homeostasis is regulated by the activity of several transcription factors called repressors. The analysis of the transcriptome and of the proteome in bacteria such as Escherichia coli under stress conditions has been shown that the synthesis of specific enzymes is down-regulated. This is part of a global stress response in which genes encoding for such enzymes are called stress genes. In the specific case of the degradation of the carbon source (glucose), four stress genes play a role. The deletion of one of these genes (lacI) is sufficient to increase the resistance of cells to glycolysis inhibitors. The most extensively studied stress genes are the lacI, lacZ, and cat lac genes in E. coli
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MonaLisa is an advanced Petri net-based application specialized in analyzing biochemical networks. You can check models for structural faults and identify biological modules, as well as visualize the computed results.
The comfort of working with portable tools
The portable running mode ensures your Windows registry does not get bloated with extra entries. You may get rid of the utility by simply deleting the files that you have downloaded from the Internet.
Copying it on USB flash drives or other devices is also possible. You can run the program by opening the executable file. This is a Java-based tool so you need to previously install the working environment on your computer.
Support for different techniques
The application works with various analysis techniques which are related to network decomposition and knockout analysis, and offers support for the computation of elementary modes (T-invariants), P-invariants, maximal common transition sets (MCT-sets), T-clusters, minimal cut sets (MCS), degree distribution, and cluster coefficient distribution.
User interface and importing options
The GUI can be described as practical. You can work with three main panes: ones is used for project management, other for visualizing the PN model, while the last one provides access to a set of configuration settings.
The program offers you the possibility to import data from various systems biology and graph-theoretic formats, such as SBML, KGML, PNT, APNN, MetaTool, and PNML.
Project management
MonaLisa allows you to save projects to a file so you can easily import data in the future for making adjustments, view a list with recently used projects, set up the approaches, define the settings, and export the results and/or PN model to one of the file formats used for importing data.
Visualizing the PN model and configuring several settings
The application lets you view the representation of the PN model of the carbon metabolism. The metabolites are displayed with the aid of circle while the reactions (transitions) are revealed using rectangles. Gray-filled circles indicate clone markers, and you may save the current representation to PNG or SVG file format, and alter the colors used for analysis, knockout analysis and background.
When it comes to managing all modelling and visualization settings, you can alter the highlighting of elementary models and place invariants and maximal common transition sets. In addition, you may divide the elementary elements into several categories.
An overall reliable scientific tool
In conclusion, MonaLisa

What’s New in the?

MonaLisa is a Java application for analysis of biochemical networks. The tool is mainly designed to analyze carbon metabolic networks. It provides a graphical user interface (GUI) for creating, saving, and importing different graph structures; finding structural faults and identifying functional modules.
There are also tools for analyzing knockout sets, models for knockout analysis, minimal cut sets, and P-invariants. Besides, the application allows working with isolated reactions, elementary modes, transition sets, and cluster coefficients. A comprehensive documentation provides access to the application and instructions for using it.

This product can be downloaded from the official site.

This application can be downloaded from the official site.

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