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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. '''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.
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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:
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 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 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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Additional information on dependencies and installation information:
http://blake.bcm.edu/emanwiki/EMEN2/Dependencies
http://blake.bcm.edu/emanwiki/EMEN2/Install


=== Running EMEN2 ===

You can import the current database schema from NCMI and initialize a simple database with the command:
The procedure on Windows is similar; open the command prompt and run the EMAN2 Python,
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python -m emen2.db.clone -h $HOME/test_db -- --defs C:\EMAN2\Python\Scripts\easy_install emen2
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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. === ...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:

[[attachment:emen2-demo.tar.gz||&do=get]]

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.
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python -m emen2.web.server -h $HOME/test_db python -m emen2.web.server -h ~/testdb

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:

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

Ws2011/Emen2 (last edited 2011-03-12 21:54:54 by root)