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Gepasi is a software tool that deals with kinetic and thermodynamic modelling of chemical reactions. It helps model a wide range of biochemistry such as metabolism, protein synthesis, DNA synthesis, etc. Due to its unique modular design, Gepasi can be used to model various biochemical transformations.
Not all reactions are processive. For instance a reaction producing DNA from a RNA primer can be stopped immediately after a single addition. However Gepasi can be used to model reactions with either processive or non-processive behaviour.
Gepasi is not a simulator, nor a reaction stoichiometrist. It is rather a system to produce kinetic (or thermodynamic) modelling of biochemical reactions. The energy at the origin of this modelling is the knowledge that the reaction description in terms of differential equations leads to a set of parameters that cannot be directly measured but that can be estimated using metabolite concentration measurements.
A detailed description of the Gepasi API is provided in the The Gepasi Application article.
The Gepasi Application:
The Gepasi Application is a collection of clients (Gepasi) and servers (Gepasi server) interacting with each other. Although the Gepasi application was not developed as a service, it has been developped as a service, since it can be used as such from within a JAVA application.
Each client is a Java class and can be started by a simple line of code. It can also be started by a Java application. The client can connect to the Gepasi server via TCP or UDP protocols, it can send and receive a message and request a model. All these interactions are made by the JAVA client using the Gepasi API.
The Gepasi application provides extensive documentation about the client application and API and can be used to develop an application that is specific to your needs and that fits with your work and that fits with your resources.
The Oasis web site is a global platform where scientists can interact with each other and publish freely accessible scientific work. The Oasis platform creates a database of the scientific literature from major publishers (e.g. Elsevier, Wiley) and from other providers (publications by researchers, open access research articles, etc).
The Oasis community member can, by registering to the Oasis platform, create a personal account and become a member of the community. Community members have access to the scientific publications that are published and stored. They can browse the
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Gepasi is a free open source software used for the simulation of biochemical and chemical kinetics. Gepasi is written in C++ with multi-threading support and based on the ideas of (B)POPULUS and GENSYS. Gepasi supports all general kinetics and balance equations: Michaelis-Menten, Hill, enzymatic, competitive, uncompetitive etc. It has in- and out-well well-compartmentalisation and can model a wide variety of kinetics.
Input and output are mainly via simulation results: solution of the equations, plots of reaction progress with time and status information about the simulation. With Gepasi there is no need to specify kinetics in an equation (though this is of course possible), but to provide the reaction rates (k1,…, kn) and amounts (b1,…, bk) with which the equations are solved. Gepasi will find a steady state solution of the equations for the specified rates and amounts.
The following videos show an example of what Gepasi can do:
Supported Operating Systems:
Cross-Platform (Linux as well):
Input and Output:
Gepasi takes different input and output types: you can view the solution of the equations with time or plot the solution values, the reaction progress is shown with different visualisations. It is also possible to get a graph of the steady state of the reaction progress over time. At the other end, Gepasi can take plots of input and output plots over time.
The equations in Gepasi all use the same syntax for the code:
Solution variable = k1*(concentration 1 at time t) + k2*(concentration 2 at time t) +…
Gepasi has the ability to describe bio/chemical kinetics of multiple reaction compounds, reaction compounds of one compound and also compounds in reaction compartments.
Gepasi is a software system for simulating biochemical and chemical kinetics.
Gepasi can support multiple reaction compounds that react in an overall kinetics description. One can provide different rates for each compound. Also, the compounds can be in different compartments and their
Gepasi is a computer program for solving (bio/chemical) kinetics. For more information about the current functionality of Gepasi see the Gepasi Paper on the ModelDB website, the Gepasi User Manual or the Gepasi website.
Gepasi was developed with the following objectives in mind:
Finding analytical solutions for complicated structures (analytical techniques such as Runge-Kutta integration)
Finding the numerical solution for complicated systems (numerical techniques such as Newton-Raphson and explicit Euler)
Overcoming of users’ lack of analytical skills when dealing with complicated nonlinear differential equations
Locating the solution space of a system of equations by local and global optimization methods
Providing an easy way to create and simulate simple or complex structures
Providing a structured environment for simulation and analysis of different issues
Overcoming the problem with regards to data storage (i.e. too much data resulting in many rows and columns to be read/written from/to files)
Gepasi consists of three different modules:
The main module provides the ability to develop and simulate models that follow bio/chemical kinetics. These models consist of complex structures such as subsystems and parameter variation. See the Gepasi User Manual for more information.
The menu module provides an interface for the GUI development and simulation. It provides an XML file for the graphical user interface, which allows the modeler to interact with Gepasi without having to learn any programming language. See the Gepasi User Manual for more information.
The editor module provides an easy way for the modeler to assemble his/her model. The editor module can be used independently from the GUI for the simulation, and the modeler can add more components to the model any time. This can be used for GUI development and simulation. See the Gepasi User Manual for more information.
A metabolic pathway is a system (or network) in which different metabolites are produced by biochemical processes, and have a limited lifespan because of their degradation by biochemical processes. Each step in a pathway is catalyzed by an enzyme (or set of enzymes).
Different metabolic pathways are different types of chemical processes. The term pathway in this context means a sequence of reactions or enzymes catalyzing specific chemical reactions.
The process starts and ends with stoichiometric reaction equations. A stoichiometric reaction equation is an expression where the right hand side is equal to the left hand side. For
What’s New In Gepasi?
The Gepasi application is a kinetic simulation/modelling application, which is used to analyse the kinetics of one or more biochemical pathways. It is written in Java and can be run in the Java Virtual Machine (JVM) in a computer with no graphical environment.
Gepasi provides the following features:
Digital, tabular, and graphical output.
Comprehensive graphical and tabular representations of the kinetics, that can be exported to graphics programs.
External controls for the simulation of subsystems.
A user-friendly and easy-to-use graphical front-end.
Gepasi is provided under the GNU General Public License v2 or later.
The main diagram that shows the main user interface.
These are the different options available for the analysis of the kinetics of one or more subsystems.
Subsystem A + Subsystem B + Subsystem C +…
In this example subsystem A is connected to subsystems B and C. In this case the model comprises an input of metabolites (subsystem A) and an output of products (subsystems B and C).
Subsystems can be selected from the subsystems menu and specified under the subsystems menu.
Subsystems can be connected to each other by drag and drop, which makes the model easier to handle. The connections are simulated by a Jars file (S.jars in the screenshot) that represents the connections and interaction between the subsystems.
When the model is saved the Jars files (.jars) are generated and make it easy to restart the model later.
A graphical representation of the model.
The graphical representation shows the changing rates of the metabolites in time.
You can select whether to have a dynamic simulation or a steady state simulation (plot bifurcation diagram).
Metabolites can be selected from the metabolites menu.
The metabolites are shown in the graph as coloured boxes.
Metabolites in subsystem A + Metabolites in subsystem B + Metabolites in subsystem C +…
If subsystems that have the same metabolites are connected the metabolites will appear in the graph twice (the metabolites from the new subsystem will be drawn in red).
The metabolites that are not connected (no edge between two metabolites) are shown in grey.
We can select the subsystems, the metabolites and the simulation mode, by selecting the appropriate entry from the menus.
Selecting the simulation mode should be
System Requirements For Gepasi:
OS: Windows 7, Windows 8/8.1, Windows 10
Processor: Intel Core i5 or better, 2.0 GHz Processor
Memory: 8 GB RAM
Graphics: NVIDIA GeForce GTX 550Ti or better
DirectX: Version 11
Network: Broadband internet connection
Storage: 4 GB available space
You will also need at least 100 MB of available space on your HDD.
OS: Windows 7, Windows 8/8.1, Windows