Exons:
Relevant bits of information for using the MUSC Shared Resource,
 the BioMolecular Computing Resource (BCR).

Exon_56 Sanger Centre Image 3.9 programs at MUSC.

This software written by John Sulston and modified extensively by Freidmann Wobus
 is really a suite of programs which utilize scanned gel images.

The programs are:

img3 
imconv
amstep2
amstep3
amstep4
amstep5
im3conv
imauto
imscan
imtransfer

 Setting up to run the main program im3 has two steps

 First create a project with the utility program
     imimport. imimport accepts three arguments, a project name,
     a gelname and an imagefile. for example type:

     imimport proja gel1 filename.tiff
    
     A project created by imimport  may be read by im3.

 Second type "source image39.sh".

 This sets various directories including on-line help
    which im3 needs to know about.

 Finally, typing "im3 &" will start im3.

 Here's an example of an image39.sh file:


____________________Cut between the lines and paste_____________________________________
#
#January 3, 2000
#Template startup file for Sanger Inst. IMAGE3.9 program
#IMTOP_DIR and FPCTOP_DIR must be customized for each user
#
setenv IMTOP_DIR /tmp_mnt/home/your_username/imdata
setenv IMHELP_DIR /tmp_mnt/usr/common/bcr/image/help
setenv IMCONVERT_CMD imconvert
setenv IMTRANSFER_CMD imtransfer
setenv FPCTOP_DIR /tmp_mnt/home/your_username/imdata
#
____________________Cut between the lines and paste_______________________________________

A major caveat: im3 works best at an SGI workstation. Exceed
and eXodus and MIX are not suitable for running im3. MACx is a
useful substitute but not as nice as working from an SGI workstation
 
     
 

The BCR at the Medical University of South Carolina
URL: http://bcr.musc.edu/
Last modified: March 19, 2001- ESH

e-mail to Starr comments about this page.