Download/Install

License:

• isodist is offered under the GNU General Public License (GPL)
• For more information about the GPL, visit their website
• Note: The original version of the code used in the Anal. Chem. paper used routines from Numerical Recipes in Fortran. Due to licensing issues we are unable to distribute the source code to those routines, and the slightly modified code available here uses routines that are available for distribution as source.

Disclaimer:

• The software is provided "as is" without warranty of any kind, express or implied, including but not limited to the warranties of merchantability, fitness for a particular purpose and noninfringement. In no event shall the authors or copyright holders be liable for any claim, damages or other liability, whether in an action of contract, tort or otherwise, arising from, out of or in connection with the software or the use or other dealings in the software.

Please cite the following paper when referencing isodist

Edit Sperling, Anne E. Bunner, Michael T. Sykes and James R. Williamson. Quantitative Analysis of Isotope Distributions in Proteomic Mass Spectrometry Using Least-Squares Fourier Transform Convolution. Analytical Chemistry, 80, pp. 4906-4917 (2008).

System Requirements

• isodist is written in Fortran 77, and any Unix-based machine with a Fortran compiler should be able to compile and run isodist
• We have successfully compiled and run isodist on Mac OS X (10.3.x, 10.4.x and 10.5.x) and 64 bit Linux machines
• You will need a Fortran compiler. If you aren't sure if your system has a Fortran compiler, please contact your local system administrator. For Mac OS X, a variety of Fortran compilers can be found here. isodist has been compiled with the g77 package available from that link.

Download the Source Code

• Please fill out the following form to download isodist
• If you would like to be informed of updates to the isodist software package, please check the appropriate box
• Download should start automatically. You will not be redirected to a new page, so please check your downloads folder. Please contact us with any issues.

Selected Binaries

For now, binaries are not distributed separately but are included in the main source distribution downloaded from the form above. Included versions are:

• Mac OS X Intel
• Mac OS X PPC
• x86_64 GNU/Linux 2.6.16

Version History

• April 28th, 2008 - First public release

Installation Instructions

1. If your browser did not do it for you, gunzip and un-tar the downloaded source code
   • gunzip isodist_release.tgz
   • tar -xvf isodist_release.tar
2. Change your working directory to the src/ subdirectory of the main isodist directory
   • cd isodist_release/src/
3. Edit the included Makefile, replacing "g77" with the name of your Fortran compiler.
4. Compile the program
   • make
5. (Optional) Install the executable into /usr/local/bin/
   • sudo make install
   • OR
   • make install (while logged in as the root user)

If you complete all of the above steps, the isodist executable (and only the executable) is installed into /usr/local/bin. It can run equally well from any directory of your choosing, including the account of a user without root access.

If the above installation does not work for you, it's likely that your Fortran compiler is incompatible with the included Makefile. Unfortunately we neither have access to all possible Fortran compilers nor the resources to test them all. f2c for example will require additional steps to convert the Fortran source code to C source code, as well as linking to the libf2c library.

Testing Your Isodist Install

Included with the distribution is a sample_data/ directory. Inside you will find a series of input files (something.in) relating to experiments demonstrated Analytical Chemistry paper. Within that directory you will find a peaks/ directory, and a reference_peaks/ directory. The former contains only input files, while the latter contains both input and expected output files. Simply run the sample input, and compare your results to those in reference_peaks/ Additionally, you may find it useful to compare generated .csv files to reference versions included.

Starting from the source directory...

1. Rehash the shell's path so that the executable can be located
   • rehash
2. Change to the test directory
• cd ../sample_data/
3. Run the samples (If you have installed isodist into /usr/local/bin/
   • isodist 13CIle.in
   • isodist 13CIle_bfix.in
   • isodist 15Npulse.in
   • isodist 2HLeu_13CIle.in
   • OR... if you did not install the executable into /usr/local/bin/, or you installed it somewhere else, you may need to specify the full path
   • ../src/isodist 13CIle.in
   • etc

Each command will cause a stream of output, including information about the fitting process and the final fitted parameters. Depending on the speed of your computer, it may take a few minutes to complete each command. lsIn addition, summary files are generated for each run. You should have the following 4 summary files after you have completed the 4 sample ".in" files. Please compare these to the four files of the same name in the reference_out/ subdirectory.

1. 13CIle.batch.csv
2. 13CIle_bfix.batch.csv
3. 15Npulse.batch.csv
4. 2HLeu_13CIle.batch.csv

Finally, there will be a peaks/ subdirectory which will contain a ".dat" and ".fit" file for each peak that has been fit. The ".dat" file is merely the data file, scaled by the charge so that the x-axis is mass rather than mass/charge, and the ".fit" file is the fitted spectrum. Use your favorite plotting program to compare the two. You can also compare the results to those in the reference_peaks/ subdirectory.

For more instructions on running isodist, please consult the documentation.