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Molecular Biology Toolkit (MBT) A Java toolkit for molecular visualization John Moreland Apostol Gramda PI: Phil Bourne.

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Presentation on theme: "Molecular Biology Toolkit (MBT) A Java toolkit for molecular visualization John Moreland Apostol Gramda PI: Phil Bourne."— Presentation transcript:

1 Molecular Biology Toolkit (MBT) http://mbt.sdsc.edu A Java toolkit for molecular visualization John Moreland Apostol Gramda PI: Phil Bourne

2 S AN D IEGO S UPERCOMPUTER C ENTER University of California, San DiegoSDSC What is MBT? Java toolkit for developing custom molecular visualization applicationsJava toolkit for developing custom molecular visualization applications High-quality interactive 3D renderingHigh-quality interactive 3D rendering and more…and more…

3 S AN D IEGO S UPERCOMPUTER C ENTER University of California, San DiegoSDSC MBT Functionality ProvidesProvides –Data loading Local files (PDB, mmCIF, Fasta, etc)Local files (PDB, mmCIF, Fasta, etc) Compressed files (zip, gzip)Compressed files (zip, gzip) Remote (http, ftp, database, etc)Remote (http, ftp, database, etc) –Efficient data access Raw data (Structure)Raw data (Structure) Derived data (StructureMap)Derived data (StructureMap) –Vizualization (plug-in Viewers)

4 S AN D IEGO S UPERCOMPUTER C ENTER University of California, San DiegoSDSC MBT Architecture

5 S AN D IEGO S UPERCOMPUTER C ENTER University of California, San DiegoSDSC Loading data Local PDB fileLocal PDB file Structure structure = StructureFactory.load( new File( “data/1STN.pdb” ) ); Remote compressed mmCIF URLRemote compressed mmCIF URL Structure structure = StructureFactory.load( new URL( “http://mbt.sdsc.edu/data/5ebx.cif.gz” ) ); PDB ID CodePDB ID Code Structure structure = StructureFactory.load( “4hhb” );

6 S AN D IEGO S UPERCOMPUTER C ENTER University of California, San DiegoSDSC Accessing raw data The Structure ClassThe Structure Class int atomCount = structure.getStructureComponentCount( SturctureComponentRegistry.TYPE_ATOM ); for ( int i=0; i { "@context": "http://schema.org", "@type": "ImageObject", "contentUrl": "http://images.slideplayer.com/13/4070921/slides/slide_6.jpg", "name": "S AN D IEGO S UPERCOMPUTER C ENTER University of California, San DiegoSDSC Accessing raw data The Structure ClassThe Structure Class int atomCount = structure.getStructureComponentCount( SturctureComponentRegistry.TYPE_ATOM ); for ( int i=0; i

7 S AN D IEGO S UPERCOMPUTER C ENTER University of California, San DiegoSDSC Accessing derived data The StructureMap ClassThe StructureMap Class –Primary Structure Atom -> Residue -> Chain -> etc…Atom -> Residue -> Chain -> etc… –Secondary Structure From source data (conformations)From source data (conformations) Computed (eg: Kabsh & Sander)Computed (eg: Kabsh & Sander) –Bonds

8 S AN D IEGO S UPERCOMPUTER C ENTER University of California, San DiegoSDSC MBT StructureDocument A StructureDocument contains Structures and provides event propagation to all ViewersA StructureDocument contains Structures and provides event propagation to all Viewers Viewers view StructureDocument contentViewers view StructureDocument content

9 S AN D IEGO S UPERCOMPUTER C ENTER University of California, San DiegoSDSC MBT Viewers StructureViewerStructureViewer –3D primary and secondary structure display Sequence ViewerSequence Viewer –Residue display TreeViewerTreeViewer –Hierarchical display Others (MultSeq)Others (MultSeq)

10 S AN D IEGO S UPERCOMPUTER C ENTER University of California, San DiegoSDSC StructureViewer Primary StructurePrimary Structure –Balls & Sticks, CPK spheres, Bonds Secondary StructureSecondary Structure –Helix, Turn, Strand, Coil Backbone tracesBackbone traces

11 S AN D IEGO S UPERCOMPUTER C ENTER University of California, San DiegoSDSC 3D Geometry Engine General / Re-usable componentsGeneral / Re-usable components –Extrusion class supporting arbitrary cross-sections with “twist” and “scale” along path –Cached/shared sphere geometry –Cached/shared color attributes Consistent shape interconnectionsConsistent shape interconnections –Path continuity –Smooth shape-to-shape transitions

12 S AN D IEGO S UPERCOMPUTER C ENTER University of California, San DiegoSDSC Optimized for Large Molecules Loaders optimized for speed and small memory footprintLoaders optimized for speed and small memory footprint List and hierarchical data viewsList and hierarchical data views Sorts data where possible for O(logN) binary searchesSorts data where possible for O(logN) binary searches Display styles use “RangeMaps” to coalesce attribute referencesDisplay styles use “RangeMaps” to coalesce attribute references Style “interfaces” reduce storage of duplicate scalar valuesStyle “interfaces” reduce storage of duplicate scalar values

13 S AN D IEGO S UPERCOMPUTER C ENTER University of California, San DiegoSDSC MBT Demos Local 4hhb PDBLocal 4hhb PDB Remote 10mh Gzip mmCIFRemote 10mh Gzip mmCIF ExamplesExamples –Filters –StructureMapping –Styles

14 S AN D IEGO S UPERCOMPUTER C ENTER University of California, San DiegoSDSC MBT Status Now SupportsNow Supports –Derived Secondary Structures –Ligand map & display Working onWorking on –Style and authoring classes ContributorsContributors –Multiple Sequence Alignment viewer (PKR) –Kinase Database Loader (PKR) –Rasmol/Chime Scripting Engine (RIT)

15 S AN D IEGO S UPERCOMPUTER C ENTER University of California, San DiegoSDSC MBT Futures RNA/DNA chain “cartoons”RNA/DNA chain “cartoons” Surfaces (computed, imported)Surfaces (computed, imported) LOTS of GUI classesLOTS of GUI classes XML import/export (Data and Authored Documents)XML import/export (Data and Authored Documents)

16 S AN D IEGO S UPERCOMPUTER C ENTER University of California, San DiegoSDSC MBT Team Philip E. Bourne, PhD (UCSD) Project principle investigator Apostol Gramada (UCSD) Postdoc, toolkit co-developer John L. Moreland (SDSC) Project technical lead, toolkit co- developer

17 S AN D IEGO S UPERCOMPUTER C ENTER University of California, San DiegoSDSC MBT Collaborators Sasha Buzko (UCSD)Sasha Buzko (UCSD) –GUIs, Authoring, Data Structures Paul Craig, PhD (RIT)Paul Craig, PhD (RIT) –Biochemistry consulting, Scripting Douglas S. Greer, PhD (UCSD)Douglas S. Greer, PhD (UCSD) –Software design, OpenMMS toolkit John Tate, PhD (UCSD)John Tate, PhD (UCSD) –MBT prototype co-designer And many more!And many more!

18 S AN D IEGO S UPERCOMPUTER C ENTER University of California, San DiegoSDSC MBT Fundiing This project was funded as part of the NIH PPG grant number 1- P01-GM63208 and its NIGMS division.This project was funded as part of the NIH PPG grant number 1- P01-GM63208 and its NIGMS division.

19 S AN D IEGO S UPERCOMPUTER C ENTER University of California, San DiegoSDSC Questions? For more information, visit: http://mbt.sdsc.edu

20 S AN D IEGO S UPERCOMPUTER C ENTER University of California, San DiegoSDSC Sizes (bytes) Application: 5,460 SimpleViewer_signed.jar Toolkit: 487,208 mbt_0.0.4_bin_signed.jar Java/Java3D (one time): 10,244,264 JRE 1.4.1_02 2,703,177 Java3D 1.2.1_04

21 S AN D IEGO S UPERCOMPUTER C ENTER University of California, San DiegoSDSC MBT Overview A Java molecular visualization toolkit Local file & remote data loaders for PDB, mmCIF, Fasta, …Local file & remote data loaders for PDB, mmCIF, Fasta, … Coupled 2D/3D viewsCoupled 2D/3D views Rich & extensible APIRich & extensible API Portable & web- deployable JavaPortable & web- deployable Java


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