= Welcome to the GAMMA Library =

''This site is a collaboration of Karl Young at UCSF and Brian Soher at Duke.''

''Recent work on GAMMA and this website is supported by a grant from the NIH.''

== GAMMA Overview : Software for simulating magnetic resonance phenomena. ==

GAMMA is written in C++ and some of GAMMA's API's have been exported to Python, using SWIG.

The original version of GAMMA was written by Scott A. Smith and Tilo Levante under the guidance of B.H. Meier and R.R. Ernst at the ETH in Zürich.

Some additional information about gamma can be retrieved from the following site:
  * Zurich : http://www.gamma.ethz.ch/index.html

Example of real-world applications of gamma, see:
  * http://nmr.magnet.fsu.edu/resources/index.html
  * http://www.magnet.fsu.edu/

== Obtaining and Building Gamma (and pyGamma) ==

[wiki:GammaBuildingLibrary Obtaining and Building the Gamma Library] - Learn how to get a copy of the source code and what to do with it once you get it.

If you're [PyGamma interested in PyGamma], we provide prebuilt binaries for
most platforms. We also have [PyGamma#BuildingPyGAMMA instructions on how to build PyGamma].

== Extending pyGamma ==

[wiki:ExtendingPygamma Extending Pygamma] can be a relatively simple process and is described here.


== Gamma - Updates and Changes ==

[wiki:CodeChangesToCompile Code Changes] - To get gamma to compile on gcc 4.3.3 (on Ubuntu 9.04), windows XP, visual studio 2008 express, and Mac OSX (gcc 4.0.1).

[wiki:GammaSwigIssues Swig Issues (and working code)] - Found while getting environment setup and testing the basic functionality of SWIG.  While using gcc 4.3.3/Ubuntu 9.04/Swig 1.3.9/python2.5 and 2.6

[wiki:GammaSwigImplementation Swig Implementation notes] - Including organization of code, some (potentially remaining) issues, and Makefile and visual-studio modifications.

[wiki:GammaTestingTools Gamma Testing Situation] - Tools and Environment setup for testing the gamma library.

[wiki:GammaMergerwithZurich Merging C++ code with that from Zurich (Matthais Ernst)] - Changes, Issues, etc.

[wiki:CodeCleanup Code Cleanup Notes] - Directories that have been deleted but can still be recovered.

== Performance Issues ==

==== Gamma vs. PyGamma ====

[wiki:GammaVsPyGamma Relative performance of PyGamma], the swigged versions of Gamma.

==== Speeding up Gamma and PyGamma ====

[wiki:GammaWithLapackAtlas Speeding up Gamma] with Lapack/Atlas, etc.


== To Do List ==

[wiki:GammaToDoList List of to-do-items] that are necessary, or just good, to implement for the gamma code base and project.

== Proper Citation in Papers and Presentations ==

Proper reference should be given, using the citation below, when GAMMA simulations are utilised in papers and/or presentations.

"Computer Simulations in Magnetic Resonance. An Object Oriented Programming Approach",
S.A. Smith, T.O. Levante, B.H. Meier, and R.R. Ernst, J. Magn. Reson., 106a.

== For more information about NMR on the web ==
  * http://www.cs.duke.edu/brd/Teaching/Previous/Bio/Readings/nmr-notes.html
  * http://web.mit.edu/speclab/www/facility.html

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