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View Code? Open in Web Editor NEWDemarcate bacteria species based on stable ecotype model
License: GNU General Public License v3.0
Demarcate bacteria species based on stable ecotype model
License: GNU General Public License v3.0
New Ecotype Simulation README INSTALLATION ================================================================================ Extract the contents of the archive to your hard drive: Windows: C:\ecosim\ POSIX (Linux, OSX, etc): ~/ecosim/ Create a Desktop shortcut to the shell script for your platform. Windows: C:\ecosim\ecosim.bat POSIX (Linux, OSX, etc): ~/ecosim/ecosim.sh REQUIREMENTS - EXECUTION ================================================================================ Java 7 JRE ------------------------------ A Java 7 Runtime Environment (JRE) is required to execute this program. You can download it here: http://www.oracle.com/technetwork/java/javase/downloads/index.html REQUIREMENTS - COMPILATION ================================================================================ To compile the Fortran programs, you will need to have a Fortran compiler installed. You can download and get installation instructions for the GNU Fortran compiler here: http://gcc.gnu.org/install/ To compile the Java portion of the program, you will need to have the Java 7 Development Kit (JDK) installed. You can download the JDK here: http://www.oracle.com/technetwork/java/javase/downloads/index.html You will also need to have Apache Ant installed for the compilation of the Java program. You can get installation instructions and download binaries here: http://ant.apache.org/manual/install.html Windows ============================== The Makefile was created to compile these programs in a POSIX environment with access to the GNU Make system. If you wish to compile these programs in a Windows environment using the provided Makefile, you will need to install GNU Make and GNU CoreUtils in addition to the other requirements. You can download the binaries here: http://gnuwin32.sourceforge.net/packages.html Cygwin is also an acceptable POSIX environment for Windows. You can get installation instructions, and download the binaries here: http://cygwin.com/install.html You will also need to have the Pthreads-w32 library installed. You can get installation instructions, and download the binaries here: http://sourceware.org/pthreads-win32/ BUILDING THE SOURCE ================================================================================ Make ------------------------------ To build the binary files and the jar file, issue the command: make To build the binary files and the jar file, and then copy them to the installation folder, issue the command: make install To clean the directory of all build files, issue the command: make clean To uninstall make uninstall TO RUN ==================================== make run CHANGES ==================================== -> combined es1 and es2 demarcation -> fixed sigma value NaN in Hillclimb.f90 -> changed bin level, added .700 binlevel. And the switch value is 5 -> sigma and omega fixed during demarcation, added 0.70 and 0.75 binlevel, modified output file, now output gui log
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