Changes between Initial Version and Version 1 of ChIMP/Meetings

Timestamp:

Oct 15, 2009, 4:54:56 PM (17 years ago)

Author:

Scooter Morris

Comment:

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ChIMP/Meetings

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+= ChIMP Meetings (Joint Sali-Ferrin Lab Meetings) =
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+[[PageOutline]]
+
+== October 15, 2009 ==
+Attendees: Conrad, Scooter, yz, TomF, TomG, Keren, Elena, Dina
+
+=== Preliminary Progress ===
+ 1. SAXS: TomG & Dina
+  * Chimera interface to the SAXS module from IMP
+  * Can calculate and plot a SAXS profile for a PDB model
+  * Can overlay experimentally derived SAXS profile on the same plot
+  * Potential licensing issues with distributing this with Chimera
+  * Some potential UI enhancements:
+   * Re-use of a plot window to compare experimental profiles vs. changed model
+ 1. Opal: Conrad
+  * Web service framework (from SDSC)
+  * Easy to deploy web services -- can quickly wrap existing software (legacy command-line programs)
+  * Currently running 1.9 on the Plato cluster
+  * 2.0 is out, but not much change in functionality (primarily internal changes)
+  * Currently using Opal in Chimera for:
+   * Template lookup (interactive)
+   * BLAST pdb/nr
+    * Asynchronous -- can save in sessions, etc.
+  * Others
+   * GOElite
+  * Output is whatever the program outputs
+   * Files
+   * stdout, stderr
+
+=== Action Plan ===
+ 1. ~~Hire postdoc~~ - Done!
+ 1. Hire programmer
+  1. Write job description (yz, TomF)
+  1. Post through HR
+  1. Go through Craig's List?
+ 1. SAXS Interface
+  1. Work is known
+   * Share plot
+   * Use web services
+  1. Resolve license
+ 1. Bring yz up to speed
+  * Chimera
+  * IMP
+ 1. Develop an action plan for 
+  * !MultiFit Interface
+  * Protein Homology modeling/loop modeling
+
+
+=== Additional Projects ===
+ 1. Future/new projects
+  1. Coarse-grained models (beads)
+   * Fitting/optimization of coarse-grained models into density
+  1. Flexible fitting
+   * Refining data after manipulating structures within densities
+  1. Finding components within 2D micrographs
+   * Manipulate component in 3D, view on micrographs
+
+=== Issues ===
+ 1. Licensing issues with the SAXS module
+  * Ben is working with UCSF to get license approved
+   * Complicated: not all team members are only at UCSF, and some team members have left UCSF
+  * Goal is to release IMP as LGPL
+  * Would like to release IMP before releasing an IMP component (e.g. SAXS) separately as part of Chimera
+  * Tom thinks that the SAXS component for IMP should be included with Chimera download
+  * May need to think about incremental downloads
+
+== March 18, 2009 ==
+=== Introduction to IMP (Ben Webb) ===
+ 1. Aim of IMP:
+  * Use structural information from any source (experiment, physics, statistics)
+  * Information at different resolutions
+  * Generate models at low, high, or mixed resolution
+  * Obtain the set of all models that are consistent with the input data
+ 1. Satisfaction of spatial restraints
+  * Representation of a system
+  * Scoring function
+  * Optimization/sampling
+ 1. Example: nuclear pore complex
+  * Optimizing individual protein positions (500 proteins)
+  * Information:
+   * Low-resolution information
+   * Protein interactions
+ 1. Example: 26S proteasome
+  * Information:
+   * EM density map
+   * Some model information
+   * Gross (very low resolution) 
+ 1. Design
+  1. Small Kernel + modules
+   * Kernel provides some basic C++ classes, utility functions, and a set of abstract bases
+   * Modules provide the bulk of the functionality
+   * Sali lab provides the kernel and a basic set of modules
+  1. Kernel
+   * Encodes for:
+    * Representation
+     * Particle class provides data storage for the system
+     * Each Particle object is simply a hash of key/value pairs
+      * values can be integers, floats, strings, or pointers to Particles
+      * Keys can be added or removed at runtime
+      * Eash Particle is an independent hash
+     * Model object is a simple contains of Particles (plus Restraints and ScoreStates)
+     * e.g. a Model may contains particles with:
+      * x,y, z float attributes
+      * x,y,z and R float attributes
+      * particle 1 and particle2 pointer attributes (bonds)
+     * Particle access is usually through Decorators which:
+      * wrap Particles
+      * provide convenient interface
+      * add runtime checks
+      * provide a runtime class hierarchy
+     * e.g. a Particle with x,y,z keys can be wrapped by an XYZDecorator
+     * e.g. a Particle wrapped by a ResidueDecorator could provide residue information
+    * Scoring
+     * Most simply, the Restraint abstract class takes a set of Particles and returns:
+      * a score
+      * first derivatives w.r.t. Particle atttributes
+     * Known structural information is encoded as implementations of Restraint
+     * ScoreState class allows for derived system state information
+     * Building blocks
+      * UnaryFunction: return the score & derivative of the input w.r.t. some function
+      * PairScore: given two Particles, return some pairwise score & derivatives between them
+      * PairsRestraint: apply a PairScore to each of a list of Particle pais
+     * Example: combine Harmonic UnaryFunction with DistancePairScore to enforce a simple distance restraint
+   * Optimization
+    * Floating-point Particle attributes can be marked as 'optimizable'
+    * The Optimizer class
+     * Takes a Model as input
+     * Modifies the optimizable attributes to give the best score
+     * Yields the final Model state
+  1. IMP modules
+   * Modules provide useful functionality such as
+    * General purpose optimizers (e.g. conjugate gradients, steepest descent)
+    * Building block restraints
+    * Support for certain representations
+    * Special purpose optimizers (e.g. molecular dynamics, inference)
+    * Interfaces to other packages (e.g. import of homology-derived restraints from Modeller)
+    * Implementations of restraints for specific kinds of structural data (e.g. SAXS, EM, proteomics)
+    * Specific applications, e.g. docking
+   * Use defined interfaces in the IMP kernal
+   * Can be implemented in C++ or Python
+   * Live in their own IMP.foo namespace
+   * Can be part of IMP or maintained by other labs
+   * Can be released under any license compatible with IMP's (LGPL like)
+   * Wrapping
+    * Kernel and module C++ code wrapped by SWIG
+    * Resulting Python code very similar to the C++
+ 1. Compilation
+  * Type 'scons'
+  * Required dependencies: a C++ compiler, SWIG, boost
+  * Optional dependencies: Modeller, CGAL, our EM library
+  * Should work with reasonably recent version of g++, MSVC and boost
+ 1. Interfaces with Chimera
+  * Python frontend allows easy integration with other Python-based packages
+  * e.g. a Chimera extension can simply "import IMP"
+  * Alternatively
+   * can generate IMP inputs and run IMP in a separate process
+   * can read IMP outputs for visualization
+  * For loose integration in future, could use the same web server interface framework proposed for ModWeb, ModLoop, etc.
+
+=== Discussion ===
+ * Chimera is interactive, IMP is not necessarily
+ * Is there a benefit to monitoring an IMP run?
+  * Depends on the application
+   * NPC was very iterative
+  * Might definitely need user interaction during the optimization
+  * Biggest category is to have Chimera "check in" on results during optimization
+  * If you can visualize the current state of the system, you can change position with Chimera
+   * Guide be used to move things out of a local minimum
+ * Can Chimera be used to setup the constraints/restraints?
+  * Could use sequence conservation, etc.
+  * Chimera could be to prepare the information for an IMP job
+ * Chimera <--> IMP: Visualize IMP representation directly in Chimera (translator)
+  * Can IMP output an XML-based format?  Not yet, but it should be relatively straightforward
+
+== February 24, 2009 ==
+
+=== Introductions ===
+
+=== Background ===
+ * Goal: leverage work going on in each lab to "make something that is more than the sum of the independent parts"
+ * History: past attempts have never come together
+ * Tom and Andre started a renewed conversation to establish the collaboration
+
+=== Demo ===
+ * Chimera and model evaluation
+  * Using Render By Attribute to show Modbase error profile (using B-Factor)
+  * Question: How does "Render by Attribute" work when you don't have atoms or residues?
+   * Answer: Currently it doesn't.  Probably something to look at -- how to set up an equivalent mechanism for low-resolution structures?
+     * Perhaps we could use volume tracer pseudo-atoms (markers) with render-by-attribute?
+  * Question: Can you make worms transparent?
+   * Answer: You should be able to...
+  * Question: in molmap, could you set the threshold such that the volume within the mesh is a certain value.
+   * Answer: The underlying code would support that, but there is no UI, yet.  You can also report the volume as you adjust the threshold (which would be an adequate approach)
+  * Restraints
+   * One solution would be to extend the structure measurements tool (or use something similar)
+   * How would you visualize restraints involving multiple atoms?
+    * Structure/volume violations
+    * Chimera can detect several restraint violations already
+    * One solution might be to combine restraints and then plot the first derivative
+    * Chimera's new 2D plotting library might be used for constraints that are not spatially correlated.  
+    * Spatially correlated constraints could be plotted using "normal mode"-style arrows (currently can be done using bild).
+     * Getting an interface to do this interactively would be useful
+    * Can the tracer pseudo-atom XML file add new attributes?
+    * TODO: enhance markers (tracer pseudo-atoms) to support user-defined attributes.
+  * Ensembles
+   * EnsembleCluster
+    * Question: Can EnsembleCluster be used for points in space rather than molecules?
+    * Answer: Yes, if you read them in as atoms.  Might also be able to to use markers.
+    * TODO: enhance markers to be used by EnsembleMatch
+    * Suggestion: How to represent objects that represent structures, but are not atomic resolution?
+     * Maybe this is one area groups could work together to define standards
+     * Currently Chimera uses model, residue, atom as it's hierarchical nomenclature.  Would be useful to support additional nomenclature hierarchies that might represent lower resolution structures and other "weird" representations.
+  * Animations
+   * Continuing to enhance our command set
+   * No time-line based UI as of yet
+   * Tom's animation example...
+
+=== Specific Applications ===
+ * Multifit - Keren Lasker, Tom Goddard
+  * fit multiple proteins in EM maps with steric clash handling.
+  * Illustration [http://www.cgl.ucsf.edu/home/goddard/temp/1z5s/1z5s.html Chimera & MultiFit]
+  * Interface looks easily tractable, but there will need to be work to develop a general mechanism to support stand-alone runs without freezing Chimera
+ * SAXS - Dina Schneidman
+  * using small angle x-ray scattering as a modeling constraint
+  * want interactive 2-d plot of saxs curve and model display
+ * 2-d EM micrograph restraints - Javier Velazquez-Muriel
+  * use 2-d EM micrographs as modeling restraint
+  * can Chimera project simulated maps from models and correlate 2-d maps?
+ * ModWeb 
+=== Discussion ===
+ * What is the best way to interface between Chimera and other programs?
+ * One initial possibility would be to use readStdin, but use it "in reverse"
+  * Applications: MultiFit, projecting 3D models to 2D, SAXS 2-d plots.
+    * Our issues aren't with the simpler algorithms, the time consuming part is the user interface
+    * Where we need algorithmic help is in more complicated algorithms (e.g. MultiFit)
+  * TODO: improve 3D to 2D projection capabilities
+  * TODO: Andre and Tom -- discuss supplemental funding proposal
+ * Web server interface
+  * In the process of building Chimera infrastructure to support asynchronous requests to web servers, including saving and checking on session state.
+  * TODO: include Hau, Dina, and Karen with meeting with John Irwin to talk about web services implementation
+  * TODO: think about including Chimera<-->ModWeb functionality.  Include Ben and Ursula in John Irwin meeting?
+   * Key exchange would be the blocking point -- perhaps we could implement a Chimera interface that could be used to get the key automatically
+
+=== Moving Forward ===
+ * Meet every two weeks, but focus on a specific area and advertise the topic in advance.
+ * Keep content on wiki -- ChIMP project (Chimera-IMP)
+
+
+
+