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= Ideas and discussions for the RBVI 2011 Site Visit =

== Scenarios ==
=== Scenario 1 ===
 * SFLD/Cytoscape/Chimera

=== Scenario 2 ===
 * Chimera/Volume Tools/Cytoscape(?)

== Ideas of what to show ==
=== TR&D 1 ===

=== TR&D 2 ===
 * Building a "composite model" and linking molecules, maps and sequences of components.
 * Chimera analysis web log.  Would be cool to demo WebGL embedded in Chimera log then shown on a smart phone or tablet as a way to facilitate hallway/lecture-hall/lunch collaborative work.

 ==== Biological Systems ====
 * [http://www.cgl.ucsf.edu/chimera/data/hiv-core-june2011/hivcore.html HIV Capsid] - Illustrates composite model building of HIV conical core particle.  Capsid protein interfaces highly conserved drug target (June 2011 PNAS [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3136285/?tool=pubmed paper])
 * [http://www.cgl.ucsf.edu/chimera/animations/hivrna/hivrna.mov HIV RNA] - Secondary structure of full HIV RNA, I made 3-d model and animation with Chimera script. Nature 2009 [http://www.ncbi.nlm.nih.gov/pubmed/19661910 paper]).
 * [http://www.cgl.ucsf.edu/home/goddard/temp/dengue2.mov Dengue virus] - Maturation of dengue virus involves major rearchitecting of capsid.  Chimera animation shows hypothetical model from Michael Rossmann lab.
 * [http://www.cgl.ucsf.edu/Research/auer/gut-sep2010/ Termite gut] - Segmentation tool demo.
 * Muscle filaments, myosin / actin / tropomyosin.  Another good "composite" model example.  Haven't done much with this system yet though.  Recent Roger Craig / Raul Padron [http://www.ncbi.nlm.nih.gov/pubmed/21705660 paper], PNAS July 2011

=== TR&D 3 ===

=== TR&D 4 ===
 * Incremental loading of networks
 * Fuzzy clusters
 * Invoking Cytoscape from Chimera
 * SFLDLoader2??