Appion

h1. What is Appion?

Appion is a "pipeline" for single particle reconstruction integrated with Leginon data acquisition. It consists of a web based user interface linked to a set of python scripts that control several underlying processing packages. These include EMAN, Spider, findem, ACE, and Chimera. All data input and output is managed by MySQL databases. The ultimate goal is to have all control of the processing pipeline managed from the web based user interface and all output from the processing presented using web based viewing tools. These notes are provided as a rough guide to using the pipeline but are not guaranteed to be up to date or accurate.

Appion users usually start off at a web page that presents them with a range of options for processing, reconstruction, analysis. This may have the following appearance:

The user can select to proceed with any of the steps but some of these may be dependent on earlier steps. For example a stack cannot be made until particles have been selected. After any of the steps has been run the user can chose to view the results by clicking on the "completed" or "available" labels. 

Appion is built upon Leginon architecture.  If you have installed Leginon before, you will find that the same three parts of Leginon system installation also applies to Appion system.  In fact, you will be performing a Leginon installation on your linux system during this Appion installation.  If you want to run Leginon on the scope, follow the installation instructions found in the [[Leginon:Leginon_Manual|Leginon Manual]].

The four parts act as :

* *Processing server*- We provide either processing programs themselves or wrappers to processing packages used by 3DEM community.

* *Database server* - Instruction for setting up is provided.

* *Web server* - We provide php and java scripts you need to set up to serve as the graphical user interface to the command scripts.

* *File server* - where the images and processed results such as volume data and processing logs are stored.

In addition, Appion also needs:

* *processing packages* which are installed on the processing server and are not distributed by us.

Fortunately, all 4 servers can run on the same machine.  If you have many users, it is recommended that you separate the first three parts of the system into 3 computers.  In such a case, you can divide the package requirement by the three server sides as well.

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[[System Requirements|System Requirements >]]

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