ConvAn

ConvAn (Convergence Analysis) is a novel software tool that helps the user in friendly GUI to gather, compare, analyze and make predictions about optimization behaviour in a statistical way based on previously obtained results of optimization runs.

 

About

ConvAn (Convergence Analysis) is a novel software tool that helps the user in friendly GUI to gather, compare, analyze and make predictions about optimization behaviour in a statistical way based on previously obtained results of optimization runs. ConvAn also advises the best method from an internal database for a particular model parameter set, that can save time and effort by optimizing the model in the most efficient way.

ConvAn is developed in C# programming language. ConvAn has versions to work with Microsoft SQL Server 2008 or PostgreSQL database system. ConvAn works on machines running Windows XP operating system or higher and Microsoft .NET Framework version 4.0, however it is possible to run ConvAn in other OS by using the open-source Mono Framework.

The first version of ConvAn was released on 25.05.2011. The latest version of ConvAn is available here.

CovnAn was developed with funding sources of a project of European Structural Fund Nr. 2009/0207/1DP/1.1.1.2.0/09/APIA/VIAA/128 "Latvian Interdisciplinary Interuniversity Scientific Group of Systems Biology"

 

Installation

ConvAn was developed in C# programming language. ConvAn and other necessary files can be downloaded from the list below. ConvAn versioning considers two-part notation, where the first part represents important new functionality and the second part represents some small changes and improvements of already existing functionality. ConvAn versioning starts from version 1.0.

Latest version

Release date 28.05.2012. Compatible with Microsoft SQL Server 2008.

  • Discretization and statistical calculation report file creation function has been added;

  • The function of the stepwise representation of graphs has been added;

  • Data load functionality has been improved.

Older versions:

 
 

 

User manuals:

User manual (version 2.0)

User manual (version 1.0)

 

Installation process:

The installation process consists of a few steps:

  1. Install Microsoft SQL Server 2008 Express R2 Compact Edition version 3.5 or PostgreSQL in case of Windows OS or PostgreSQL in case of other platforms. Settings for PostgreSQL: Port=5432; User Id=postgres; Password=postgres; SSL=true; SslMode=Prefer; Database=ConvAn_db.

  2. In case of Windows OS check if you have already installed .NET Framework v4.0 on your machine by executing .NET Framework file. As a result operating system will start the installation process or notify that .NET Framework is already installed on your machine.

  3. ConvAn works with a point decimal separator that means that the user must check if the decimal separator is a point. On Windows machines it can be done under Start > Control Panel > Region and Language, where in Format tab under button 'Additional settings' decimal symbol is located: input field.

  4. Extract ConvAn archive on your machine and you can freely start using ConvAn by running ConvAn vx.x.exe located in an extracted folder (in case of Windows OS).  On other platforms, ConvAn can be run on the open-source Mono Framework.

 

IMPORTANT! Do not delete any file in the extracted folder, because they all are used by ConvAn.

Screenshot of the ConvAn interface:

 

ConvAn Sample Files

This sample pack contains:

  • Sample data series of:

    • 1,5,10, and 15 adjustable parameters of design tasks (maximization tasks) of Evolutionary programming optimization method;

    • 1,5,10, and 15 adjustable parameters of design tasks (maximization tasks) of Particle Swarm optimization method;

    • 4 adjustable parameters of parameter estimation tasks (minimization tasks) of Evolutionary programming optimization method;

    • 4 adjustable parameters of parameter estimation tasks (minimization tasks) of Particle Swarm optimization method.

Sample data of design tasks of Evolutionary programming optimization method:

Sample data of design tasks of Particle Swarm optimization method:

 

Sample data of parameter estimation tasks of Evolutionary programming optimization method:

This archive contains sample data series of 4 adjustable parameters of parameter estimation tasks (minimization tasks) of Evolutionary programming optimization method.

Sample data of parameter estimation tasks of Particle Swarm optimization method:

This archive contains sample data series of 4 adjustable parameters of parameter estimation tasks (minimization tasks) of Particle Swarm optimization method.

 

Citation

Kostromins A., Mozga I., Stalidzans E. ConvAn: a convergence analyzing tool for optimization of biochemical networks. Biosystems, Volume 108, Issues 1–3, April–June 2012, Pages 73-77, ISSN 0303-2647, 10.1016/j.biosystems.2011.12.004.