2. Installing MCell and CellBlender

2.1. MCell Installation

2.1.1. MCell Overview

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.

2.1.2. Download MCell (All Platforms)

Download the desired binary file for your system (e.g., MCell v. 3.2.1 for Linux x86) from the MMBioS web site.

2.1.3. Installing MCell (Windows)

2.1.3.1. Extract MCell (Windows)

Open the zipped Windows binary through the browser (shown here with Google Chrome).

_images/download_mcell.png

Windows File Explorer should appear, displaying the MCell binary (mcell.exe) within the zipped file.

_images/mcell_zip.png

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.

_images/new_folder.png

2.1.3.2. Put MCell in a PATH Directory (Windows)

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.

_images/computer_properties.png

In the new window, click the Advanced system settings button.

_images/advanced_settings.png

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.

_images/edit_path.png

2.1.3.3. Test MCell (Windows)

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).

_images/power_shell_launch.png

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.

_images/power_shell_use.png

2.1.4. Installing MCell (Linux/OS X)

2.1.4.1. Extract MCell (Linux/OS X)

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.

2.1.4.2. Rename and Make Executable (Linux/OS X)

Rename the file to something more convenient and make it executable, e.g.,

mv mcell-3.2.1_x86 mcell
chmod a+x mcell

2.1.4.3. Put MCell in a PATH Directory (Linux/OS X)

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.

2.1.4.4. Test MCell (Linux/OS X)

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.

2.2. CellBlender Installation (All Platforms)

2.2.1. Installing CellBlender

Startup Blender and go to the File->User Preferences menu.

_images/user_prefs.png

In the User Preferences control panel choose the Addons tab.

_images/addons_tab.png

Click the Install from File button at the bottom of the window.

_images/install_from_file.png

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.

_images/install_from_file2.png

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.

2.2.2. Activating CellBlender in Blender

Scroll down until you see Cell Modeling: CellBlender and select the checkbox to enable it.

_images/enable_cellblender.png

Then, click Save User Settings to enable the addon permanently in Blender.