EMEN2

Thursday PM Practical

EMEN2 is a comprehensive database and electronic notebook with a primary focus on TEM data. More generally it is a broad-purpose object oriented database which can be applied to a wide range of different problems.

Installing EMEN2

If you are using the EMAN2 binaries, the simplest way to install EMEN2 is to install it into that Python environment, as it already has several of the dependencies installed. To do this, you will need to use the "easy_install" script provided by that environment. On Linux, if you installed EMAN2 in your home directory, it will be "...." On Mac OS X, it will be the system default "easy_install" script.

First, install the remaining EMEN2 dependencies (Mac OS X example -- on Linux, use the EMAN2 easy_install, and 'sudo' is not required):

sudo easy_install mako
sudo easy_install twisted
sudo easy_install Markdown

Then install EMEN2 itself:

sudo easy_install emen2

If you are not using one of our EMAN2 binary packages:

• You will need to take care of installing Berkeley DB, bsddb3, and Matplotlib (optional) yourself.
• If you want to take advantage of some cryo-EM specific features, such as viewing MRC/DM3 images in your web browser, it is easiest if EMEN2 and EMAN2 can be loaded into the same Python environment.

• Additionally, for the EMDash GUI, you will also need PyQt4 available.

Additional information on dependencies and installation information: http://blake.bcm.edu/emanwiki/EMEN2/Dependencies http://blake.bcm.edu/emanwiki/EMEN2/Install

Running EMEN2

You can import the current database schema from NCMI and initialize a simple database with the command:

python -m emen2.db.clone -h $HOME/test_db -- --defs

This will prompt you to supply a root password for the database, and an administrator email for notifications and password recovery.

You can start the EMEN2 web server:

python -m emen2.web.server -h $HOME/test_db

...and connect with your web browser at http://localhost:8080