JPhysChem Modeling Package

04/26/2008. A few more words about the modifications. The parameter graph editing tool -- that can be found in the download section -- is embedded in a NetBeans platform application. The basic mathematical functionality provided in the August 2007 version has been extended towards mass spectrometry. As an independent part of the software a molecular fragmentation generator module (Cs. Peltz, I. Kövesdi, K. Újszászy, L. Drahos, J. Dombi, Automated Interpretation of Mass Spectra by Incremental Learning of Probabilistic Fragmentation Rules, 17th Intenational Mass Spectrometry Conference, 2006, Prague, pdf) and mass spectrometric data management routines were added. Later, these will be interfaced with the parameter graph editor / model building part, to provide and easy theoretical model building functionality.

04/24/2008. After 8 months 'without development' I'm back. Well, it wasn't really without development. I've put together several things in the field of mass spectrometry and I realized that I should publish them together in an IDE-like environment. Everything changed since the last version, even the name of the package. I wasn’t sure if I should keep the 'J' in the project name (I've done some .NET developments). So the next version will come soon. I don’t know if anybody will be interested in it, but I think it doesn't really matter.

08/29/2007. A basic functional version of the modeling tool is available (binary and source package) in the download area. Included features are graph drawing, syntax checking, evaluation. Basic mathematical and few vector manipulation functions provided and a sample graph demonstrating the definition of linear regression "from scratch". Missing features include specific mass spectrometric data manipulation functions, a larger set of statistical-mathematical functions and the ability of easy definition of new functions (without the modification of the source). Most of these features are in testing and bug-checking phase and will be available soon to the public.

08/28/2007. Reaction scheme editor module published (both binary and source), now capable of generating a C++ source code of a reaction mechanism. Future versions will be embeddable in JPhysChem main module.

JPhysChem is an open source Java-based OS-independent physico-chemical modeling tool. The program is designed to help building complex calculation models with a "few clicks" and to support testing of the model without a single line of coding. The goal is achieved by building graphical calculation/derivation trees. The nodes of the tree are arbitrary type parameters, which are connected to each other by functions. A base kit of standard mathematical functions is provided and the ability to define custom functions. In the future modules of functions will be available in the area of physical chemistry / mass spectrometry.

The graphical interface of the program is based on the open source JGraph graph visualization project, while the treatment of the abstraction layer (ie. the uniform treatment of the functions and expressions connecting the parameters) is based on the Java Expression Parser project. The newer versions of the modeling tool are built on the top of the NetBeans Platform.

Binary and source packages are available at the Sourceforge.net project page in the download section and on CVS.

The entire source of the project is written and maintained by Csaba Peltz. The software is distributed under GNU Lesser General Public License.

If you have further questions concerning the project, please contact the author: Csaba Peltz, peltz@users.sourceforge.net.


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