Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology

Area of Science:

• Bioinformatics
• Systems Biology
• Computational Biology

Background:

• Biological systems rely on complex interactions within genes, regulatory circuits, and metabolic networks.
• Existing software lacked integrated tools for combining and visualizing these diverse biological data types.
• There was a need for tools to support metabolic flux modeling and interpret high-throughput omics data.

Purpose of the Study:

• To enhance the Pathway Tools software for integrating and analyzing biological pathway and network data.
• To improve capabilities for metabolic modeling and omics data interpretation.
• To provide efficient query and visualization tools for biological knowledge discovery.

Main Methods:

• Development and enhancement of the Pathway Tools software suite.
• Integration of multi-omics data analysis tools, including Omics Dashboard and pathway collages.
• Implementation of improved algorithms for metabolic modeling and data interpretation.
• Enhancement of core pathway/genome database management features.

Main Results:

• Pathway Tools now supports web-based metabolic model execution and improved gap filling.
• New tools for spatial grid organism community modeling and multi-omics data analysis are available.
• Enhanced database management includes multi-organism search, improved graphics, and faster performance.
• Redesigned gene and metabolite pages offer better data accessibility.

Conclusions:

• The enhanced Pathway Tools software provides a comprehensive platform for biological data integration and analysis.
• The software facilitates advanced metabolic modeling and interpretation of complex omics datasets.
• Updated features improve usability and performance for researchers in systems biology and bioinformatics.