Changes between Initial Version and Version 1 of 2016-09-22


Ignore:
Timestamp:
Sep 22, 2016, 4:09:32 PM (9 years ago)
Author:
Conrad Huang
Comment:

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  • 2016-09-22

    v1 v1  
     1= Attendees =
     2
     3  Elaine, Eric, Greg, Conrad, TomG, TomF, Scooter
     4
     5= Agenda =
     6  * Review action items from last meeting
     7  * Chimera 1.11.2 release
     8  * ChimeraX issues
     9    * Metadata for tools/bundles
     10      * Get toolshed/session-init funcs out of !__init!__?
     11  * Assign required site-visit functionality to people
     12  * Discussion of site visit scenarios
     13  * Continuation of 8-29 discussion
     14
     15= Discussion =
     16  * Previous action items:
     17    * ~~Conrad '''will''' make http reference in ChimeraX About panel into hyperlink
     18    * ~~Greg and TomG '''will''' investigate how "sym" command uses instancing and how it is reflected in x3d output
     19      * x3d output now honors sym instancing and produces much smaller output
     20  * Chimera 1.11.2 release
     21    * 1.11.2 will have a working !BlastProtein
     22    * Need to implement fix for blastpdb before 1.11.2
     23      - Fix by replacing Opal script for !BlastProtein service with shell script that displays error message and exit with status 1
     24      - 1.11.2 will use BlastProtein2 as service name
     25      - Major change in nr format deflines, with different results from preformatted NCBI blast database vs one built from NCBI fasta file
     26      - Make sure MDA and MAV are compatible with newest blast version
     27    * Check for Sierra problems with touchpad and scrolling
     28  * ChimeraX issues
     29    * Ribbon progress
     30      * Lots of stuff on Elaine's documentation page
     31      * Conrad ported some standalone helix code into ChimeraX but needs to complete it
     32    * Metadata for tools/bundles
     33      * Change in tool/bundle template
     34        * ~~Greg showed new classifier format
     35        * For UI purposes, there is no API for GUI options in open or save panel for bundles for now
     36        * For extra open/save arguments, register them in custom initialization function
     37      * ~~Get toolshed/session-init funcs out of !__init!__?
     38        * ~~Create a Bundle class and put Bundle API methods in instance with standard name in !__init!__
     39      * Steps in updating to new metadata
     40        1. Rename "tools" to "bundles", "gui.py" to "tool.py"
     41        2. Add support for new metadata format in toolshed
     42           - Including refactoring "fetch" code
     43        3. Migrate limited set of bundles to test new code
     44        4. Migrate remaining bundles
     45        5. Delete code for old metadata
     46      * New toolshed core functionality
     47        * New deliverables: selectors, command line options (low priority)
     48        * Make main startup code a bundle to be called from shim code
     49        * Undeletable bundles
     50      * New toolshed UI
     51        * Tabbed interface for installed bundles and all bundles
     52        * Both will provide interface to search/browse by deliverables (tools, commands, file formats, selectors, etc)
     53        * Perhaps a separate "Active Tools" tool
     54      * Toolshed "server"
     55        * Have instructions from Alex Pico for installing Cytoscape !AppStore
     56    * Matchmaker is working!
     57    * Interactive contact map for assemblies
     58    * IHM format support
     59      * Gaussian models
     60      * Issues with DOI links
     61    * OpenMM investigation
     62      * MDFF author is interested in using ChimeraX
     63  * Assign required site-visit functionality to people
     64    * Cytoscape and REST interface (Conrad, Scooter)
     65    * ~~Side view on !PyQt (Greg)
     66    * Toolshed (Conrad, Greg)
     67    * Ribbons (Conrad)
     68    * IHM cross-link distribution histograms (TomG)
     69    * Interface viewer (TomG)
     70    * IHM mmCIF support (TomG)
     71    * MAV (Eric)
     72    * blastpdb (Conrad)
     73    * Reach goals
     74      * String database (Scooter, Conrad)
     75      * Hydrogen bonds and contacts (Eric)
     76      * Link to NGL, !LiteMol (Scooter, Conrad, Greg)
     77      * Molprobity on Opal (Scooter)
     78      * Domains
     79        * Web service, Uniprot? (Eric)
     80        * Integration into hierarchy (Eric)
     81        * Interactive 2D graph (team)
     82      * Hierarchy browser
     83      * UI cleanup (team)
     84  * Site visit
     85    * Plan on three or four shorter DBP-based "vignettes" instead of two longer scenarios
     86    * Vignette with presenters:
     87      - '''Sali''' and IHM
     88      - van den Bedem and contact networks
     89      - ''Horwitz'' and optical microscopy
     90      - Krogan?
     91      - ''deRisi''?
     92      - Chiu?
     93    * Allot time for Chimera 1 if site visitors are not familiar with Chimera 1
     94  * Continuation of 8-29 discussion
     95
     96= Outstanding Action Items =
     97  * ~~Conrad will make http reference in ChimeraX About panel into hyperlink
     98  * ~~Greg and TomG will investigate how "sym" command uses instancing
     99  * Conrad will make sure that template tools directory is exempt from copyright updates