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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 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. |
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| First, install the remaining EMEN2 dependencies (Mac OS X example -- on Linux, use the EMAN2 easy_install, and 'sudo' is not required): | On Linux, assuming EMAN2 is installed in your home directory: |
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| sudo easy_install mako sudo easy_install twisted sudo easy_install markdown |
~/EMAN2/Python/bin/python ~/EMAN2/Python/bin/easy-install emen2 |
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| Then install EMEN2 itself: | On Mac OS X: |
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| 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, you will need to either install EMEN2 and EMAN2 into the same environment, or perform some careful configuration. |
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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. |
Additional information on dependencies and installation information: * http://blake.bcm.edu/emanwiki/EMEN2/Dependencies * http://blake.bcm.edu/emanwiki/EMEN2/Install |
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| Additional information on dependencies and installation information: http://blake.bcm.edu/emanwiki/EMEN2/Dependencies http://blake.bcm.edu/emanwiki/EMEN2/Install |
=== EMEN2 Tutorial Data === |
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| Untar the file: {{{ tar -xvzf emen2-demo.tar.gz cd emen2-demo }}} |
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| This command will initialize the database and import the data for the workshop tutorial: | 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. |
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| python -m emen2.db.clone -h $HOME/test_db -- --defs | cd emen2-demo python -m emen2.db.load -h ~/testdb |
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| This will prompt you to supply a root password for the database, and an administrator email for notifications and password recovery. | 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 as the default (just hit enter) for the tutorial. |
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.
On Linux, assuming EMAN2 is installed in your home directory:
~/EMAN2/Python/bin/python ~/EMAN2/Python/bin/easy-install emen2
On Mac OS X:
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, you will need to either install EMEN2 and EMAN2 into the same environment, or perform some careful configuration.
Additional information on dependencies and installation information:
EMEN2 Tutorial Data
Untar the file:
tar -xvzf emen2-demo.tar.gz cd emen2-demo
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 as the default (just hit enter) for the tutorial.
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