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Savuka - A general purpose global analysis program

Savuka Overview

    Savuka is a global analysis package that allows the user to graphically view, model, simulate, manipulate and globally fit data.
The program is for the most part not geared toward any particular application and therefore should be suitable for most applications where the above features are needed.

    Savuka was initially written (for VAX/VMS) by David Lambright in the late 1980's while he was a graduate student in Steve Boxer's lab at Stanford.  In 1991 while I was a grad student in Dewey Holten's lab at Washington University in St.Louis I was running into the limitations of the PC's at the time in using my global analysis software (written in ASYST) so Dave kindly sent me Savuka and the permission to modify it to suit my needs.  In Dewey Holten's lab I made a number of changes to Savuka to suit our applications (femtosecond pump-probe experiments) and changed the manner in which the global least-squares fit was handled.  If you happen to not like the way the fitting routines work, the finger should point to me.  After leaving Dewey's lab, Savuka stayed dormant for two years, since both of us were doing other things and didn't have the need for it.  Upon joining Bob Matthews' lab at Penn State I made more additions and modifications to Savuka in order to handle many of the new applications and techniques that we wanted to implement. Among the changes was a port of Savuka to IBM-PC's and to Silicon Graphics workstations (Jiabin Luo was very helpful with this transition).  (On a side note, we just retired the last of our Silicon Graphics workstations.)

     Today, we routinely use it for analysis of time-correlated single-photon counting data, protein equilibrium unfolding titrations and also for global analysis of folding kinetics (raw chevron data).  The user can put in custom models as Fortran subroutines.  I often put in custom models for people if needed (most protein thermal and chemical denaturation models and a number of binding models are already included).  The only drawback for some people is that Savuka is very Unix-like.  It's interface is command-line oriented and it runs in a Unix environment.  I run Savuka under Cygwin (which is a Linux variant that runs under the Windows operating system) on my laptop and find it more convenient than having to switch between a Linux OS and a Windows OS.  I get the best of both worlds, since I often find myself wanting the Unix command line prompts under Windows.

     Savuka is written in Fortran and you will need the f2c translator to compile it.  The f2c translator library is included in the zip file below along with source code and executable and a separate file with instructions on how to install it.  If you just want to run the executable you would not need to install f2c - you can simply copy savuka.exe to /usr/local/bin and you should be good to go.  You should note that Savuka depends on pgplot (and the Windows interface GrWin) for its graphics engine.  Cygwin, pgplot and GrWin are freely available over the web.  Many thanks to the folks who provide these valuable tools!

Installation

    The most convenient way to use Savuka is on a Mac OS X or Linux computer.
To install on a Mac:
  • Install xcode and xcode command line tools (can be downloaded from the Apple developer tools on the app store)
  • Install Xquartz
  • Install macports
  • Once these are installed you should open a shell window and execute "sudo port selfupdate".
  • Install gfortran following instructions here.  
  • Install pgplots via "sudo port install pgplot"

  • Download latest version of Savuka from my Dropbox folder and copy to a directory in which you have read/write privilege.  Note: if the file is locked you might need to unlock it by clicking on the file and then on "Get info".  
  • Run "sudo make clean" from the command line and then "sudo make".  This will compile and build the savuka executable.
  • Copy the bashrc file to your default directory (the one you end up in when you launch a shell window).  Rename this file ".bashrc" using the command "mv bashrc .bashrc".  You will need to edit the .bashrc file so that the path directs to where your Savuka files are (there is a template for you to follow in the .bashrc file).  Launch a new shell window and start Savuka.  Enjoy.

Notes on installing Savuka on Windows can be found here. Please note that I have not used savuka on Windows in a few years so it is difficult for me to support Windows installations.


Examples

A tutorial illustrating a simple 3-state fit, the use of SVD with Savuka and some notes on processing data are available.  Some examples of batch scripts can be found here

Formalities (Copyright, License, Fees etc.)

        The philosophy behind Savuka is the same as Dave Lambright's original one: it's available to anyone who needs it provided they will not use it for commercial purposes.  You are at liberty to modify it to suit your needs, although for the sake of consistency I ask that you not distribute the source yourself.  If you make changes to the code that you think would be useful for all users please contact me so that we can include them in a version that I distribute (with appropriate credit to you).
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This is the latest version as of April 2, 2013. Enjoy!  2809k v. 1 Apr 2, 2013, 2:58 PM Osman Bilsel
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These are the instructions to follow if you just want to install the executable without installing the fortran compiler.   30k v. 1 Apr 2, 2013, 2:58 PM Osman Bilsel
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Installation instructions for Savuka the f2c utility sample bashrc are in this zip file  2525k v. 1 Jul 21, 2009, 12:31 PM Osman Bilsel
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This zip of the utilities has a new program: asc2ye.exe for making a ye-format Savuka file (i.e., y-format with errors).  2657k v. 1 Sep 7, 2011, 10:36 AM Osman Bilsel
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This is the same as savuka-03072011.zip except that it also has the installation files in addition to the source code and executable (e.g., documentation, bash files etc.).  12678k v. 2 Sep 7, 2011, 8:58 AM Osman Bilsel
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The memory space in this version of Savuka has been expanded to 16384*128.  2194k v. 2 Sep 7, 2011, 8:58 AM Osman Bilsel
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This version is a minor update. The N-point average function has the option of propagating the weight of the points being averaged or summed.  2027k v. 2 Sep 7, 2011, 8:58 AM Osman Bilsel
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Test version - just has the executable.  694k v. 2 Nov 3, 2011, 8:21 AM Osman Bilsel