Appion

h1. Appion Main Page

!>http://lh5.google.com/vossman77/RzJbEE3GhuI/AAAAAAAAASY/SSaOA7FZKwI/nramm.jpg?imgdl=1!:http://nramm.scripps.edu

h2. Overview

Appion  is a "pipeline" for processing and analysis of EM images.  Appion is integrated with "Leginon":http//leginon.org data acquisition but can also be used stand-alone after uploading images (either digital or scanned micrographs) or particle stacks using a set of provided tools. Appion consists of a web based user interface linked to a set of python scripts that control several underlying integrated processing packages. All data input and output within Appion is managed using tightly integrated SQL databases. The goal is to have all control of the processing pipeline managed from a web based user interface and all output from the processing presented using web based viewing tools.  

The underlying packages integrated into Appion include "EMAN":http://blake.bcm.edu/eman, "Spider":http://www.wadsworth.org/spider_doc/spider/docs/spider.html, "Frealign":http://emlab.rose2.brandeis.edu/, "Imagic":http://imagescience.de/imagic/, "XMIPP":http://xmipp.cnb.csic.es/, "IMOD":http://bio3d.colorado.edu/imod/, "ProTomo":http://www.electrontomography.org/, "ACE":http://nramm.scripps.edu/software/ace/, "CTFFind and CTFTilt":http://emlab.rose2.brandeis.edu/, "findEM":http://nramm.scripps.edu/software/findem/, "DogPicker":http://nramm.scripps.edu/software/dogpicker/, "TiltPicker":http://nramm.scripps.edu/software/tiltpicker, "RMeasure":http://emlab.rose2.brandeis.edu/, "EM-BFACTOR":http://www.ual.es/~jjfdez/SW/embfactor.html, and "Chimera":http://www.cgl.ucsf.edu/chimera.  These packages must be acknowledged by appropriate citations when used within Appion. Appropriate citations are provided on the individual pages in Appion as well as "here":http://emg.nysbc.org/projects/appion/wiki/Appion_citations.  

Appion 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.

h2. Download Appion

Follow the Appion [[Complete_Installation|installation instructions]] to download and install Appion.  

If you download Appion we strongly encourage you "register as an Appion user":http://emg.nysbc.org/account/register.

This will allow us to keep you informed of new releases, bug fixes, and other useful information, and also allow us to keep track of the user base which is important to ensure future support of the software.

h2. Appion User Manual:

The *[[Appion_Manual|Appion Manual]]* includes:

* a [[An_Introduction_to_Appion|description of Appion]], 

* [[Version_Change_Log|version change logs]], 

* [[Upgrade_Instructions|upgrade instructions]], 

* [[Complete_Installation|installation instructions]] and  

* [[Appion_User_Guide|daily usage instructions]]

h2. Publications:

h3. Primary Publication to Cite:

* Lander, G.C.; Stagg, S.M., Voss, N.R., Cheng, A., Fellmann, D., Pulokas, J., Yoshioka, C., Irving, C., Mulder, A., Lau, P.W., _et al._ (2009). "Appion: an integrated, database-driven pipeline to facilitate EM image processing.". Journal of Structural Biology 166: 95-102. "PMID 19263523":http://www.ncbi.nlm.nih.gov/pubmed/19263523. 

h3. Additional References:

* Voss, N.R.; Lyumkis D, Cheng A, Lau PW, Mulder A, Lander GC, _et al._ (2010). "A toolbox for ab initio 3-D reconstructions in single-particle electron microscopy.". Journal of Structural Biology 169 (3): 389-98. "PMID 20018246":http://www.ncbi.nlm.nih.gov/pubmed/20018246.

* Stagg, S.M.; Lander GC, Quispe J, Voss NR, Cheng A, Bradlow H, Bradlow S, Carragher B, Potter CS (2008). "A test-bed for optimizing high-resolution single particle reconstructions". Journal of Structural Biology 163 (1): 29-39. "PMID 18534866":http://www.ncbi.nlm.nih.gov/pubmed/18534866.

h2. Software Availability and Licensing Information

Appion is released under the "Apache License, Version 2.0":http://www.apache.org/licenses/LICENSE-2.0

View an "myami code diagram":http://emg.nysbc.org/projects/appion/wiki/Myami_code_diagram base found in the "myami" repository.

h2. Youtube videos:

* "An Introduction to Appion":http://www.youtube.com/watch?v=Wlxt_4yJKgA

* "TiltPicker Demonstration":http://www.youtube.com/watch?v=z7BqGJczmjU

h2. Citations

View the entire collection of [[Appion citations]].

h2. Contact information:

Please email _appion@scripps.edu_ with any questions.

[[developers guide]]