What is Appion » History » Revision 11
Revision 10 (Amber Herold, 06/16/2010 01:55 PM) → Revision 11/14 (Bridget Carragher, 01/03/2011 11:49 AM)
h1. What is Appion? Appion is a "pipeline" for single particle reconstruction. Appion is reconstruction integrated with Leginon data acquisition but can also be used stand-alone after uploading images (either digital or scanned micrographs) or stackes using a set of provided tools. Appion acquisition. It consists of a web based user interface linked to a set of python scripts that control several underlying integrated processing packages. These include EMAN, Spider, Frealighn, Imagic, XMIPP, findEM, findem, ACE, and Chimera. All data input and output is managed using a tightly integrated 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 look something like have the following: following appearance: !http://emg.nysbc.org/attachments/229/Picture_6.png! The user can select to proceed with any of the steps in the left hand menu options 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 and is built upon Leginon depend on the same basic architecture so architecture. If you can install either one or both together with almost no extra effort. You have installed Leginon before, you will need to perform find that the same basic three parts of Leginon system installation for either or both packages. also applies to Appion system. Following In fact, you will be performing a Leginon installation on your linux system during this basic installation, if Appion installation. If you want to run Leginon on the microscope, you will need to perform a few additional steps, and scope, follow the installation instructions can be found in the [[Leginon:Leginon_Manual|Leginon Manual]]. The four basic parts of Appion are act as : * *Processing server*- We provide either processing programs themselves or wrappers to processing packages generally in use used by the 3DEM community. * *Database server* - where all data and processing Instruction for setting up is tracked. provided. * *Web server* - We provide php and java scripts that you need to set up to serve as the graphical user interface to the command scripts and results. scripts. * *File server* - where the images and processed results (e.g. stacks, such as volume data, etc) data and all processing logs are stored. Installation instructions for all of these parts are included in the Appion installation instructions. In addition, Appion also needs: * *Processing *processing packages* - which are installed on the processing server and are not currently distributed as part of Appion. by us. All Fortunately, all 4 servers can run on the same machine. However, for an installation where high volume of data, processing and users is anticipated, If you have many users, it is recommended that you separate the first three parts of the system are installed onto into 3 separate computers. In such a case, you can divide the package requirement by the three server sides as well. ______ [[System Requirements|System Requirements >]] ______