MCell is available for Linux, OS X, and Windows. In the past, MCell was run exclusively from the command line. With the development of CellBlender, this is no longer necessary (although it can still be very useful). MCell, by itself, does not have a graphical user interface and cannot be run by double-clicking an icon. Also, there is no installer unlike many Windows applications.
Download the desired binary file for your system (e.g., MCell v. |release| for Linux x86) from the MMBioS web site.
Open the zipped Windows binary through the browser (shown here with Google Chrome).
Windows File Explorer should appear, displaying the MCell binary (mcell.exe) within the zipped file.
Drag and drop the binary to a new folder. For this example, we will create a new folder in the top level C directory called bin (i.e. C:\bin). To create a new directory, right click on the background in File Explorer, select New->Folder, type the name of the folder (e.g. bin), and hit Enter.
This step is optional but is highly recommended if you will be running MCell from the command line (i.e. without CellBlender). First, right click on Computer and select Properties.
In the new window, click the Advanced system settings button.
Then click the Environment Variables button in the System Properties
window. In the Environment Variables window, select the Path entry in
the list of System Variables, and hit the Edit button. At the end of
the list of Variable values, add ;C:\bin\. If you extracted MCell into
a directory besides "C:\bin\", use that instead. Also, be sure to use the
initial semicolon and the trailing backslash.
To run MCell in Windows without CellBlender, we are going to use PowerShell, which is included with Windows 7 and 8. Alternatively, you could use the Command Prompt, but we will not cover that here. To run PowerShell, hit the Windows key, type powershell, and hit Enter (Windows 8 pictured below).
Windows PowerShell will now appear on the screen. Type mcell.exe and hit Enter. If you see the following text on your screen, you have set up your PATH correctly.
The binary file that you download is a compressed file with a name that ends in
".gz". Open a terminal and navigate to where the file was downloaded (e.g. cd
/home/user/Downloads). Alternatively, you can do this through a GUI file
manager like Nautilus in Ubuntu, but we won't show that here.
Now, unzip the file by typing the following at the command line:
gunzip mcell-3.2.1_x86.gz
If this succeeds, the file will no longer have the ".gz" suffix.
Rename the file to something more convenient and make it executable, e.g.,
mv mcell-3.2.1_x86 mcell chmod a+x mcell
Depending on your preferences, you may want to put the resulting executable
binary in an appropriate place for yourself or all the users of the machine
(e.g., sudo mv mcell /usr/local/bin if you have root privileges). If you do
not have root privileges, then you can put it in your home directory (e.g.
mkdir /home/user/bin; mv mcell home/user/bin where user is your user
name). However, you need to make sure that the directory you put it in is
either in your PATH or that you add it to your PATH. You can add it to your
PATH by typing export PATH=$PATH:/home/user/bin (once again, user
should be your user name). To make this change permanent, add this command to
the .bash_profile file located in your home directory. If this file does
not exist, create it and add the line.
Verify that MCell is working by typing the following at the terminal:
mcell
If you have successfully put MCell in your PATH, you should see a startup message followed by an error that indicates no MDL (Model Description Language) file has been specified.
Startup Blender and go to the File->User Preferences menu.
In the User Preferences control panel choose the Addons tab.
Click the Install from File button at the bottom of the window.
Navigate to the unextracted zip file that you downloaded (cellblender_v1.0_RC.zip), select it, and click the Install from File button near the upper-right hand corner.
Note
If you need to install a newer version of CellBlender, the installation process is the same. The new version of CellBlender should cleanly install over the existing version.
Scroll down until you see Cell Modeling: CellBlender and select the checkbox to enable it.
Then, click Save User Settings to enable the addon permanently in Blender.