MonaLisa

MonaLisa is a cool application that focuses on analyzing biochemical networks using Petri nets. With this software, you can check your models for any structural faults and find biological modules. Plus, it helps you visualize the results you've computed, making things easier to understand.

Easy to Use and Portable

This app has a portable running mode, which means it won't clutter your Windows registry with extra stuff. If you ever want to uninstall it, just delete the downloaded files – it's that simple! You can even copy MonaLisa onto USB flash drives or other devices. Just open the executable file to run it. Remember, since this tool is Java-based, make sure you have the Java environment set up on your computer first.

Powerful Analysis Techniques

MonaLisa supports various analysis techniques related to network decomposition and knockout analysis. It also helps with computations 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-Friendly Interface

The graphical user interface (GUI) is pretty practical. You’ll find three main panes: one for managing projects, another for visualizing the Petri net model, and the last one gives access to different settings you can configure.

Data Importing Made Easy

This software allows you to import data from different systems biology formats like SBML, KGML, PNT, APNN, MetaTool, and PNML. So you're covered no matter where your data is coming from!

Save Projects for Later

MonaLisa lets you save your projects as files so you can easily come back later for adjustments. You can view a list of recently used projects too! It also lets you set up approaches and define settings before exporting results or the PN model into compatible file formats.

Visualize Carbon Metabolism

You can even see how carbon metabolism looks in a PN model! The metabolites are shown as circles while reactions are rectangles. Clone markers appear as gray-filled circles. And if you want to keep a snapshot of your work? Save it as PNG or SVG files! You can also change colors used in analysis and background.

Manage Your Model Settings

When managing all modeling and visualization settings in MonaLisa, you'll have options like highlighting elementary models or organizing invariants and MCT-sets into categories.

Conclusion: A Great Tool for Professionals

If you're looking for advanced features for visualizing and analyzing functional modules in biochemical networks, MonaLisa is an excellent choice—especially if you're a professional user!