1. Desktop Environment

CSE-Online Desktop Environment is a graphic user interface for the Java On Demand Application Framework (JODAF), which is a software platform that allows distributed applications and data to be delivered on demand to the user CSE-Online desktop environment in a secure and transparent manner.

The applications available in CSE-Online are catergorized into different workspaces for different domains of computational science.  Each workspace has one application framework which serves as a single entry point for all user's needs in that domain.  In this release, we feature the MolDesign tool, which is the application framework for Computational Molecular Science. 

2. MolDesign: Computational Molecular Science Workspace

MolDesign is the application framework for Computational Molecular Science within CSE-Online.  It is the main entry point for all molecular modeling and simulation needs within CSE-Online cyber-environment.    MolDesign  provides a 3D graphic user interface that can link to a number of domain-specific and general utility tools.  

Tools that are integrated in MolDesign

1. SMICAR: A Web-Service tool for converting SMILES to Cartesian coordinates.
2. JChemPaint: An open-source 2D chemical structure sketcher.
3. Gaussian Input Builder: A Graphic User Interface for the Gaussian program.
4. Direct Links to the National Cancer Institute (NCI) and National Center for Biotechnology Information Structure Databases.
5. Global File Explorer: File system for both local and remote files.
6. GSub: Submit/monitor jobs to/on a Computing Grid using the Globus Technology (currently it can access theTeraGrid resources).
7. Jpeek: An image viewer.
8. Jpad: A Note pad tool.
9. Pandora: A general purpose 2D plotting tool.
10. User Feedback: Tool that allows users to provide feedback on specific applications to the developing team.

Standalone tools

1. Resource Broker: Submit/Monitor jobs on remote servers.
2. GAMESS-US Input Builder: A Graphic User Interface for the GAMESS-US program.
3. Quantum Chemistry Knowledge Management System
4. Sander-GUI: A graphic user interface for the Sander program (the MD simulation module of the AMBER package).
5. Protein Data Bank: A mirror site for the PDB database.
6. VASP GUI: A graphic user interface for the VASP periodic DFT program.
7. Thermo: A Web-Services tool for calculating thermodynamic properties of molecular species.
8. TheRate: A Web-Services tool for calculating rate constants of elementary reactions.
9. JEKS Spreadsheet: A speadsheet application.
10. Jmol: An open-source 3D structure viewer (Standalone application).
11. BioViewer: A graphic tool for viewing and analyzing bio-systems. 
12. Crystal Viewer: A graphic tool for viewing and analyzing crystal structures. 
13. SSH Terminal: SSH Terminal emulator.
14. CSEO messenger: Communication tool for text chat.

3. Computational Chemical Kinetics Workspace

Below are standalone applications. 

1. Mechanism Editor: A graphic user interface for viewing/editing/analyzing complex mechanisms.
2. PREMIX-GUI: A graphic user interface for creating input for the PREMIX program (part of the CHEMKIN II package).
3. SENKIN-GUI: A graphic user interface for creating input for the SENKIN program (part of the CHEMKIN II package).
4. Mechanism Database: Database for Mechanisms of combustion of hydrocarbons.
5. Flame Database: Database for experimental and calculated premixed flames.

4. Computational Life-Science Workspace

1. SWISS Homology: A graphic user interface for the SWISS homology model.

5. Materials Science Workspace

1. COD: A Java application that allows users to search for crystal structures.
2. JBabel: A Java wrapper for OpenBabel used to convert between different chemical file formats.
3. B: A Java biomolecular modelling package B, this has been adapted to be used with CSE-Online by the Lewis Group.