Cover Pages: Molecular Dynamics [Markup] Language (MoDL)

[July 29, 1999] As reported in a communiqué from B. Arun concerning the early results in the MoDL project:

MoDL - Molecular Dynamics Language (pronounced as 'model') is a "new XML application for simulation data from molecular dynamics. Chemical Simulations are an integral part of research in the field of Chemical Engineering/Sciences. The effort involved in making sense of the huge amounts of data that these simulations provide is enormous. We envisage that visualization of this simulation data will be of great assistance in the understanding of chemical systems and provide new insights as well. MoDL provides simple constructs like atom, bond, molecule and TRANSLATE that mark-up the simulation data. To rotate [a molecule] one has ROTATE. One can define atom and molecule types and then use them to build up a chemical compound. Plots can also be drawn in any position in the 3D scene using plot and curve. The MoDL file is converted to the VRML world using a program that uses the Perl XML::Parser module. The visualizations can then be viewed using a VRML plug-in inside a Web browser. More information and examples are provided on the project Web site." The authors have provided a MoDL tutorial and a MoDL XML DTD. Examples in VRML encoding are also supplied. A 'MoDL Authoring Tool' (under development) is available for download; XML::Parser and XML::DOM modules have to be installed for this to work. The project team (Dr. Swami Manohar, Prof. Vijay Chandru, B. Arun, A.D. Ganguly) request comments on the application; they may be sent via email to modl@violet.csa.iisc.ernet.in

[Note: if you'd like to (just possibly) be impressed and have not already surfed to the Web site: look first at the XML encoding for a molecule (e.g., 'Zeolite NaCaA Cage = Zeolite NaCaA with one CH4') and then look at the image on the main page.]

References:

MoDL - Molecular Dynamics Language Home Page
DTD of the Molecular Dynamics Markup Language; [local archive copy]
MoDL Tutorial
MoDL Authoring Tool Under development 1999-08-06, 'XML::Parser and XML::DOM modules have to be installed for this to work.'
Project Team: Dr. Swami Manohar, Prof. Vijay Chandru, B.Arun, and Ashes Dhanna Ganguly
Contact address: modl@violet.csa.iisc.ernet.in
Departmental project report by Ashes Dhanna Ganguly, in Postscript, (June 17, 1999), Thesis Report [DisMaL System] - The report discusses two new applications - an XML application for visualization of Chemical Simulations and Molecular Dynamics on the web; and an XML application framework for managing applications in handheld devices. Chemical Simulations are an integral part of research in Chemical Engineering/Science. Typically, the simulator programs output vast amounts of data after running a simulation. To go through the data, understand what exactly happened and make sense out of it is a very difficult task. If one is able to visualize the simulation, understanding the processes becomes a lot easier than to go through the numerical outputs. Chemical Visualization is thus a tool to readily gain insight into a natural process. Visualizations can also be used to demonstrate scientific concepts to others. In this part of the project we have designed a new markup language which allows the simulation data to be "marked up", and developed a tool for visualizing chemical simulations on the web. Information Markup [for] Handheld Computers are very different from general ones in many ways - the display is restricted, the keyboard may have 0 to 10 keys. These restrictions severely limit the way in which we can interact with such computers. Paradigms like virtual keys, voice browsing, voice appended with visual information become useful in such restricted enviroments. Our aim in this part of the project was to design an application framework which would be the interface between the user and application programs in handheld computers. Chapter 2 discusses our initial exploration into XML and what we came up with in the process - a Vector Markup Language (VML) browser, a Fig2VML converter, a Latex2MathML converter and a markup language for writing dissertations, DisMaL - this project report has been written in it. Chapter 3 goes into our major work in Molecular Dynamics Visualization over the Web, the design of the new markup language MoDL, the visualization using VRML, the MoDL to VRML converter, an authoring tool to easily markup simulation data and how to use all these tools. Chapter 4 discusses Information Markup and the new XML application for it; its domain and design; and the concepts of stylesheets and their usage in browsing. Chapter 5 gives a synopsis of the tools developed during this project and some examples of their outputs. Chapter 6 concludes this report and explores the future work anticipated in the two areas of Chemical Visualization and Information Markup." [local archive copy]
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