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Related Experiment Video

Updated: May 27, 2026

TBase - an Integrated Electronic Health Record and Research Database for Kidney Transplant Recipients

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Published on: April 13, 2021

PathCase-SB architecture and database design.

Ali Cakmak¹, Xinjian Qi, Sarp A Coskun

¹Electrical Engineering and Computer Science Department, Case Western Reserve University, Cleveland, OH 44106, USA.

BMC Systems Biology

|November 11, 2011

Summary

This summary is machine-generated.

PathCase Systems Biology (PathCase-SB) integrates metabolic network models and data into a single database, enabling efficient systems biology research. This platform facilitates the development and analysis of kinetic models for biological systems.

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Introduction of an Integrated Pathology Image Management, Artificial Intelligence, and Reporting System

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Area of Science:

Systems Biology
Computational Biology
Bioinformatics

Background:

Effective systems biology research requires integrating metabolic pathway resources and regulatory metabolic network models.
Developing computational tools on an integrated platform enhances the study of metabolic network regulation.
Integrating regulatory metabolic networks and existing models into a unified database environment presents a significant computational challenge.

Purpose of the Study:

To present the architecture and database design of PathCase Systems Biology (PathCase-SB).
To describe the development of a database-enabled framework and web-based computational tools for kinetic model development.
To facilitate the integration of biological data from sources like BioModels and KEGG.

Main Methods:

Developed PathCase Systems Biology (PathCase-SB) with a focus on database architecture and design.
Integrated data from the BioModels database and KEGG into the PathCase-SB framework.
Created a web-based integrative framework with computational tools for modeling and analysis.

Main Results:

PathCase-SB provides a unified database environment for regulatory metabolic networks and models.
The system offers data and API access for multiple user interfaces and software tools.
PathCase-SB facilitates the development of kinetic models for biological systems.

Conclusions:

The PathCase-SB architecture and database are highly extensible and scalable.
The system provides easy and fast (real-time) access to integrated biological data.
PathCase-SB is currently utilized by researchers globally for systems biology research.