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| == EMEN2 == === Thursday PM Practical === |
= EMEN2 = == Thursday PM Practical == |
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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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| == Installing EMEN2 == | |
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| === 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. |
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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. 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 10.6, we are using the Apple-provided Python: |
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| 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 [[EMEN2/Dependencies|install the dependencies]] and [[EMEN2/Install|emen2 from source]]. | |
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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. |
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 === If you compiled EMAN2 from source, rather than using our binary, you will need to: * Install * Berkeley DB * bsddb3 * Twisted * Mako Templates * Markdown * Matplotlib (optional, for plots) * PyQt4 (optional, for the EMDash GUI) * Download and install EMEN2 * 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: * 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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| I have prepared a tutorial environment based on some of our published data: | |
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| === Running EMEN2 === | [[attachment:emen2-demo.tar.gz|emen2-demo.tar.gz|&do=get]] |
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| This command will initialize the database and import the data for the workshop tutorial: | Note: this is just the metadata -- including the raw micrographs would have made this file hundreds of gigabytes. Untar the file: |
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| python -m emen2.db.clone -h $HOME/test_db -- --defs | tar -xvzf emen2-demo.tar.gz |
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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. | == 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. |
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 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
If you compiled EMAN2 from source, rather than using our binary, you will need to:
- Install
- Berkeley DB
- bsddb3
- Twisted
- Mako Templates
- Markdown
- Matplotlib (optional, for plots)
PyQt4 (optional, for the EMDash GUI)
- Download and install EMEN2
- 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
I have prepared a tutorial environment based on some of our published data:
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 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