EMEN2

Thursday PM Practical

EMEN2 is a web-based electronic notebook and object oriented database. While it has so-far been used primarily for cyro-EM, it is completely flexible and can easily be adapted to other disciplines. We are gradually building connectivity between EMEN2 and EMAN2, as will be demonstrated.

Installing EMEN2

EMAN2 binaries provide several of the dependencies required for EMEN2. To do this, you will need to use the "easy_install" script provided with EMAN2. On Linux, if you installed EMAN2 in your home directory, it will be "...." On Mac OS X, just use the "easy_install" which comes with OS X.

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 compiled EMAN2 from source, rather than using our binary, you will need to:

• Install
  • Berkeley DB
  • bsddb3
  • Matplotlib (optional, for plots)

  • PyQt4 (optional, for the EMDash GUI)

• 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 (which will happen if you are using the EMAN2 binary).

Additional information on dependencies and installation information:

• http://blake.bcm.edu/emanwiki/EMEN2/Dependencies

• http://blake.bcm.edu/emanwiki/EMEN2/Install

Running EMEN2

This command will initialize the database and import the data for the workshop tutorial:

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