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 provides cryo-EM specific support for EMEN2, so it is recommended to install both systems into the same Python environment. The easiest way to do this is to use the EMAN2 binary release, as we have also included all additional EMEN2 dependencies in this package.

Note: Make sure that the PYTHONPATH environment variable is set to include the packages that come with EMAN2, e.g. by running the included "eman2.bashrc" script. On Linux, you will want ~/EMAN2/Python/lib in the path, and on OS X /Applications/EMAN2/extlib/site-packages.

On Linux, assuming EMAN2 is installed in your home directory:

~/EMAN2/Python/bin/python ~/EMAN2/Python/bin/easy_install emen2

On Mac OS X 10.6, we are using the Apple-provided Python:

sudo easy_install emen2

If you are using Mac OS X 10.5 or earlier you will need to install a more current Python (http://www.python.org) environment and install the dependencies and emen2 from source.

The procedure on Windows is similar; open the command prompt and run the EMAN2 Python,

C:\EMAN2\Python\Scripts\easy_install emen2

...installing from source

An adventure!

Shared EMEN2 and EMAN2 dependencies:

Berkeley DB
bsddb3
Matplotlib (optional, for plots)
PyQt4 (optional, for the EMDash GUI)

Additional EMEN2 dependencies:

Twisted
Mako Templates
Markdown

Please see the information in the EMEN2 wiki pages:

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

EMEN2 Tutorial Data

I have prepared a tutorial environment based on some of our published data:

emen2-demo.tar.gz

Note: this is just the metadata -- including the raw micrographs would have made this file hundreds of gigabytes.

Untar the file:

tar -xvzf emen2-demo.tar.gz

Running EMEN2

In this tutorial, we will use ~/testdb as our EMEN2 database environment

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

cd emen2-demo
python -m emen2.db.load -h ~/testdb

This will prompt you to supply a root password for the database, and an administrator email for notifications and password recovery. You can leave both empty (just hit enter) for the tutorial.

You can start the EMEN2 web server:

python -m emen2.web.server -h ~/testdb

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