Transcript Sanner
Representation, Implementation, and Interaction: Challenges for Macromolecular Assemblies Michel F. Sanner The Molecular Graphics Laboratory The Scripps Research Institute La Jolla, California Workshop on Visualization of Biological Complexes Oct. 11-12, 2003 Berkeley, CA TSRI Interoperable Software Components for users Interoperable Software Components for programmers Software Components for programmers Monolithic Software Conflicting goals? • Increased models complexity • Increased data sets size and heterogeneity • Interoperation of interdisciplinary computational methods • Increased technological complexity • Increased usability • Increased flexibility • User-reconfigurable applications • Transparent computing Python to the rescue High level language as a scripting environment TSRI PMV: From Building Blocks to Applications TSRI PMV Architecture Generic Molecule Viewer built from reusable components But meant forViewerFramework programmers Msms Commands Mslib DejaVu MolKit Idle Numeric PyOpenGL Tkinter TSRI ViPEr: a Visual Programming Environment Does not require the scientist to Become a programmer AChE APBS TSRI ViPEr Architecture Web NetworkEditor Visualization DejaVu Standard MolKit SymServer Imaging Mslib SymServ PIL MolKit Your Library Your Code Tkinter Numeric PyOpenGL TSRI ViPEr INNOVATIONS • • • • • No constraining data types Optional data duplication Scriptable, flexible On-the-fly node editing Nodes are lightweight wrappers of computations • Small (< 13,000 lines of Python code) • Platform independent • A Python package NOT a program ! – Can be added to any program TSRI NetworkNode ‘myfile.dat’ Input Port Name: inPort1 Type: String N umber: 0 Required: True SingleConnection: False Output Port name: outPort1 Type: None Number: 0 ‘file1.dat’ [myfile.dat’, ‘file1.dat’] MyNode def doit(self, inPort1): out =[] for n in names: out.append( read(n)) self.outputData(outPort1=out) TSRI Interactive Customization of Molecular Visualizations TSRI Molecular surface of sliding window of amino acid TSRI DEMO TSRI Aknowledgements • • • • Sophie Coon (PMV) Daniel Stoffler PhD (ViPEr) National Institute of Health, RR08605 MGL laboratory TSRI