This site contains three different PathCase applications, under the umbrella of “PathCase”:
PathCase System, developed during 2003-2008, is an integrated software system
for storing, managing, analyzing, and querying biological pathways at different levels of
genetic, molecular, biochemical and organismal detail. At the computational level,
PathCase allows users to visualize pathways in multiple abstraction levels, and
to pose predetermined as well as ad hoc queries using a graphical user interface.
Pathways are represented as graphs, and implemented as a relational database.
PathCase has multiple levels, with multiple tools at each level. Currently,
users can access three different PathCase system applications, each employing
a different metabolic pathways database:
PathCaseSB System, currently being developed by a grant from NSF Biology,
features PathCase Systems Biology Workbench that links metabolic pathways with systems biology models.
The aim of the PathCaseSB project is to build a framework and tools towards effective and efficient
systems biology model development for multiscale mechanistic models of biological systems. Our approach
is to integrate the model database with our metabolic network database PathCaseKEGG in order to build
“one-shop” querying, visualization, simulation, and modeling capabilities. While the PathCaseSB system
is continually being improved and its database is being expanded, it currently has the following components:
The browser interface is built primarily for viewing the information related to
(a) systems biology models from Biomodels [BioM, BioM06] (and later from other sources,
such as CellML [CellML]) in conjunction with metabolic pathway fragments from KEGG [Kegg]
that these models employ, and
(b) metabolic pathways from KEGG, in conjunction with BioModels models, with a focus
on presenting the relationships that exist between the various entities of the two types i.e.,
models and pathways.
(a) SimCom (Simulation and Compare) Tool allows users to simulate one or more models for
a chosen metabolic patway side-by-side and compare their simulations side-by-side. Users can also choose
to change the parameters of the models for simulation with different set of parameters. Another novel
feature of this tool is to allow users to add/change experimental values for the chosen pathways
behaviour and compare the experimentally observed behavior of the pathway with the simulation results
from chosen the model. This tool is aimed to be a basic building block and a major step forward in
helping Systems Biologists in composing and designing new models for pathways.
(b) iModel (User-Uploaded Models) Tool allows users to visualize and use simulation and comparison features in PathCasSB for their own models. Users can upload their model specified in SBML, using a user friendly interface (by just choosing the file to upload their file containing the model).
PathCaseMAW system, currently being developed by a grant from NSF Biology,
features PathCase Metabolomics Analysis Workbench that is designed for metabolomics analysis. Towards
this end, PathCaseMAW database contains a fully hierarchically compartmentalized metabolic network for
mammalians (humans and mice). Full compartment hierarchy refers to the multi-tissue (e.g., liver, adipose
tissue, muscle, etc) environment as well as a complete biological compartment distinction (e.g., liver-cell,
liver-cytosol, liver-mitochondrion, etc.). The network is being entered manually via an editor.
Recently, we have developed three frameworks for automated analysis of metabolomics data in terms of the
dynamic behavior of the metabolic network:
In more detail, MQL enables users to specify multiple and different classes of queries, such as
(a) computing (and visualizing) “Activated/Inactivated (metabolic) Paths” with increased and decreased
fluxes under specified physiological conditions (MQLAIP queries), (b) identifying/verifying “Potential
Futile Cycles”, (c) querying for required metabolic concentration change sets to prevent a particular
futile cycle, (d) searching for concentration change sets which lead to the (in)activation of a
user-specified metabolic subnetwork, and (e) exploring the metabolic behavior of a set of (possibly reversible)
reactions. At this point in time, within the MQL framework, only MQLAIP is being implemented.
PathCase is accessed from all around the world by anonymous researchers every day. The following map shows approximate locations of PathCase users.
The PathCase web client is a web-based interface
to the PathCase Database, and provides a web-based toolset via a Java applet
loaded within a browser window. It is designed as an intuitive and easy-to-use
tool, with no need to study user manuals.
The PathCase Desktop Client is a desktop application for browsing and interacting with the PathCase database.
The desktop client is discontinued, and the latest version can be found under the "Legacy Software" link on the left.