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== RBVI 2011 Renewal Ideas and Discussions ==
=== Table of Contents ===
 * [raw-attachment:fp3-TOC.docx Table of Contents]
=== Overview ===
 * [raw-attachment:Overview.docx Research Plan overview]
=== Technology Research and Development Projects ===
==== TR&D !#1: Chimera Molecular Modeling Environment ====
 * [raw-attachment:TRD1.docx TR&D 1] ([raw-attachment:TRD1.pdf pdf])
==== TR&D !#2: Software for Interactive Analysis of Large Molecular Assemblies ====
  * [raw-attachment:TRD2.docx TR&D 2] ([raw-attachment:TRD2.pdf pdf])
==== TR&D !#3: Structure-Function Linkage Database ====
  * [raw-attachment:TRD3.docx TR&D 3] ([raw-attachment:TRD3.pdf pdf])
==== TR&D !#4: Integrated Analysis and Visualization of Biological Context ====
  * [raw-attachment:TRD4.docx TR&D 4] ([raw-attachment:TRD4.pdf pdf])

=== Driving Biomedical Projects ===
 * Do not edit any of the individual projects -- they have all been combined into a unified "DBP" section
 1. DBP !#1: Modeling Macromolecular Assemblies - Andrej Sali
  * [raw-attachment:DBP1.docx DBP1]
 1. DBP !#2: Enzyme Function Initiative - John Gerlt
  * [raw-attachment:DBP2.docx DBP2]
 1. DBP !#3: Parasitic Disease Pathways - Jim McKerrow
  * [raw-attachment:DBP3.docx DBP3]
 1. DBP !#4: HIV Accessory and Regulator Complexes - Nevan Krogan/Yifan Cheng
  * [raw-attachment:DBP4.docx DBP4] combined systems biology and cryoEM.
  * Original separate drafts [attachment:DBP_Cheng.docx cryoEM part] and [attachment:DBP4_Krogan.docx systems biology part].
 1. DBP !#5: 3D Architecture of Hair Cell Stereocilia - Manfred Auer
  * [raw-attachment:DBP5.docx DBP5] passed final review from Manfred.
 1. DBP !#6: Modeling Biological Assemblies from cryoEM Maps - Wah Chiu
  * [raw-attachment:DBP6.docx DBP6 final version]
 1. DBP !#7: Data Validation and Web Visualization at the EMDB and PDB - Berman/Chiu/Lawson/Westbrook/Dutta
  * [attachment:mapmodelVTFbullets.pdf EM validation task force summary] from Cathy Lawson
  * [raw-attachment:DBP7.docx DBP7 final version]
 1. DBP !#8: Network Visualization of Genome Assembly Experiments - DeRisi
  * [raw-attachment:DBP8.docx DBP8]
 * [raw-attachment:combinedDBPs.docx Combined DBPs (except for summary table)]
 * [raw-attachment:combinedDBPs.pdf same in PDF format]
 * [raw-attachment:DBPTable.docx DBP Table]

=== Collaboration and Service ===
 * Do not edit any of the individual projects -- they have all been combined into a unified "Collaborations" section
 1. Integrating Chimera into the NRAMM Automated Processing Pipeline
  * Investigators: Bridget Carragher and Clint Potter, Scripps Research Institute
  * Grant: NIH P41 RR017573
  * [attachment:Collaboration_NRAMM.docx Collaboration #1] from Clint Potter.
 1. Molecular animations
  * Investigators: Graham Johnson
  * [attachment:collab-GTJ.docx Collaboration #2]
 1. Protein Polymorphism
  * Investigators: Tom Alber and Paula Therese Lang, University of California, Berkeley
  * [attachment:collab-PTL.docx Collaboration #3]
 1. Pharmacogenetics of Membrane Transporters
  * Investigators: Kathleen Giacomini and Deanna Kroetz (UCSF)
  * [attachment:collab-PMT.docx Collaboration #4]
 1. Integration of Methods of Structural Analysis of Functional Site: Active Site Profiling
  * Investigator: Jacquelyn Fetrow, Wake Forrest University
  * Grant:
  * [raw-attachment:collab-JSF.docx Collaboration #5]
 1. Images and Analysis for the Virus Particle Explorer Database
  * Investigator: Vijay Reddy, Scripps Research Institute
  * Grant: NIH P41 RR012255
  * [attachment:Collaboration_Reddy.docx Collaboration #6]
 1. Pipeline for Identifying Pathogen-Host Mechanisms via Systems Biology
  * Investigators: Allan Kuckinsky, Agilent Foundation; Nevan Krogan, UCSF
  * Grant: Agilent (no grant number)
  * [raw-attachment:collab7.docx Collaboration #7]
 1. MMTK Integration with UCSF Chimera
  * Investigator: Jean-Didier Maréchal and Victor Munoz, Universitat Autònoma de Barcelona
  * Grant: Spanish Ministry of Science and Innovation, grants CSD2007-00006 and CTQ2008-06866-C02-01
  * [attachment:collab-JDM.doc Collaboration #8]
 1. National Resource for Network Biology
  * Investigators: Trey Ideker, Gary Bader, Alex Pico, and Bruce Conklin
  * Grant: NIH P41 RR031228
  * [raw-attachment:collab9.doc Collaboration #9]
 1. Visualization Vault, Web Services, and Remote User Support
  * Investigators: Ferrin and RBVI staff
  * [raw-attachment:collabService.doc Collaboration #10]
 * [raw-attachment:combinedCollabs.docx Complete Collaboration and Service section (except for summary table)]
 * [raw-attachment:combinedCollabs.pdf same in PDF format]
 * [raw-attachment:CollabTable.docx Collaboration and Service Table]

=== Training, Dissemination, Administration ===
 * [raw-attachment:combinedTDA.docx Combined Training, Dissemination, and Administration (needs references section formatted)]

=== Letters of Support ===
 * [raw-attachment:lettersIntro.docx Intro page for Letters section]
 * [raw-attachment:lettersCombined.pdf Combined letters file]

=== Appendix ===
 * [wiki:Grant/appendix Items for inclusion on Appendix CD-ROM]

=== Documents ===
 * [raw-attachment:renewalOverview.pdf Overview of P41 requirements and deliverables]
 * [raw-attachment:RBVIrenewal.pdf 2006 RBVI Grant]

=== Action items (partial list) ===
 * Update these web pages:
  * www.cgl.ucsf.edu/Outreach/Dissemination/index.html