BioPack Parameter Estimation Demonstration

This document provide instructions to install the JigCell BioPack parameter estimator softare, along with a walkthrough demonstating its basic use. In the future, the parameter estimator will be fully integrated with JigCell.

At this time, BioPack is only supported under Linux.

Requirements

  1. Lahey Fortran 90 Express compiler version 6.1
  2. Bash
  3. Java Developement Kit 1.4.2 or greater
  4. Linux and standard developement utilities (i.e., GNU make)
  5. The latest version of the GNU tools (UNIX). The specific tools used are cut, find, grep, make, tar, and xargs. WARNING: Do not use the GNU jar program, java compiler, or java runtime. Building the Jikes compiler is optional and additionally requires gcc and strip.

Instructions

  1. Download the "jigcell" and "biopack," "odrpack," and "tests" directories from the svn repository (such as "svn checkout http://jigcell.biol.vt.edu/svn/jigcell"
  2. Create a new directory in your home directory called "JigCell." Put jigcell, biopack, odrpack, and tests in your home directory as: ~/JigCell/jigcell, ~/JigCell/biopack, ~/JigCell/odrpack, and ~/JigCell/tests
  3. Build and Install JigCell.
    1. Go to JigCell/jigcell.
    2. Edit Makefile.config to set the path for JDK_DIR. Note: Paths containing non-alphanumeric characters may need to be quoted depending on your shell.
    3. [optional] Run "make jikes" to produce the Jikes compiler (you must be root to do this).
    4. Edit Makefile.config to select either the jikes or javac compiler.
    5. Run "make distro". This will take several minutes! Deprecation warnings and some (non-fatal) errors building the documentation are normal. Such errors will not interrupt the make process.
  4. Install jigcell.
    1. Go to JigCell/jigcell/www.
    2. Run "java -jar install.jar" to start the installation program.
    3. Follow the on screen installation instructions and choose to install JigCell into ~/JigCell
    4. Go to ~/JigCell/xpp and rename xppaut_linux to xppaut.
  5. Create a new Directory called ~/Biopack/lib/modules.
  6. Add to your path : "." and "JigCell/biopack/bin"
  7. Set the environment variable BIOPACK_DEVEL=~/JigCell with a command like (if you are in Bash): export BIOPACK_DEVEL=~/JigCell;.
  8. Set the environment variable BIOPACK_ROOT=~/JigCell/biopack
  9. Add ~/JigCell/biopack/bin to your PATH.
  10. Change directories to ~/JigCell/biopack/third_party_src then type "make"
  11. Change directories to ~/JigCell/biopack/src then type "make"
  12. Change directories to ~/JigCell/tests/biopack
    1. Open "Makefile" in your favorite editor and change the CLASSPATH to point to ~/JigCell/jigcell
    2. Save the Makefile then type make.
  13. Start a new terminal window. In that terminal window, change directory to ~JigCell/facilitator. Run "./fac_linux".
  14. Start a new terminal window. In that terminal window, change directory to ~JigCell. Run "./wrappedxppserver.sh".
  15. Start a new terminal window. These steps must be performed from this window:
    1. Go to the directory ~/JigCell/tests/biopack/files
    2. Edit pe_test_practice_read.sh. Change the CLASSPATH line so that the first path is ~/JigCell/jigcell/.
    3. Edit setup.pl to provide information for your machine.
    4. Do ". /usr/local/lf9561/bash_setup" to prepare the FORTRAN compiler. (This assumes you installed the FORTRAN compiler to /usr/local, adjust this path if necessary.)
    5. Run pe_test_practice_read.sh with the following command: ./pe_test_practice_read.sh 6
  16.  Note the last lines in the output, as these are the parameter values that you might wish to copy as indicated below.
  17.  Copy pe_test004*.* from JigCell/tests/biopack to ~/JigCell
  18. From ~/JigCell, run "runmanager.sh". Now do one of the following:
    1. Open pe_test004.run from the menu "File|Open Run File"
    2. Modify the basal parameter set with the new parameters from when you ran ./pe_test_practice_read.sh.
    or
    1. Open pe_test004_with_modifications.run from the menu "File|Open Run File" (this has already incorporated the new parameter values).
    2. You can try making and ploting some runs by clicking on the "plot" column for any of the rows in the spreadsheet.
  19. From ~/JigCell, run "comparator.sh". Do one of the following:
    1. Click on the "Experiment" tab, and from the "File|Open" menu open pe_test004.dat.
    2. Click on the "Model" tab, and from the "File|Open" menu open pe_test004.mss.
    3. Click on the "Objectives" tab, and from the "File|Open" menu open pe_test004.obs
    or
    1. Click on the "Experiment" tab, and from the "File|Open" menu open pe_test004.dat.
    2. Click on the "Model" tab, and from the "File|Open" menu open pe_test004_with_modifications.mss.
    3. Click on the "Objectives" tab, and from the "File|Open" menu open pe_test004.obs
  20. Run and view the results.