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| 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. |
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. |
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| 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. | 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. |
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| sudo easy_install Markdown | sudo easy_install markdown |
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| 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. |
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). |
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