Appion Home » History » Version 74
Amber Herold, 12/13/2010 11:43 AM
| 1 | 52 | Neil Voss | h1. Appion Main Page |
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| 2 | 11 | Amber Herold | |
| 3 | 59 | Neil Voss | !>http://lh5.google.com/vossman77/RzJbEE3GhuI/AAAAAAAAASY/SSaOA7FZKwI/nramm.jpg?imgdl=1!:http://nramm.scripps.edu |
| 4 | 56 | Neil Voss | |
| 5 | 52 | Neil Voss | h2. Overview |
| 6 | 1 | Eric Hou | |
| 7 | 52 | Neil Voss | Appion is a "pipeline" for semi-automated three-dimensional electron microscopy starting from raw images to complete three-dimensional models. |
| 8 | 32 | Amber Herold | |
| 9 | 52 | Neil Voss | 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. |
| 10 | 1 | Eric Hou | |
| 11 | 72 | Amber Herold | h2. Appion User Manual: |
| 12 | 70 | Amber Herold | |
| 13 | 73 | Amber Herold | The [[Appion_Manual|Appion Manual]] includes: |
| 14 | 74 | Amber Herold | * a description of Appion, |
| 15 | * version change logs, |
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| 16 | * upgrade instructions, |
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| 17 | * installation instructions and |
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| 18 | * daily usage instructions |
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| 19 | 64 | Amber Herold | |
| 20 | 1 | Eric Hou | |
| 21 | 52 | Neil Voss | h2. Publications: |
| 22 | 1 | Eric Hou | |
| 23 | 52 | Neil Voss | h3. Primary Publication to Cite: |
| 24 | 1 | Eric Hou | |
| 25 | 52 | Neil Voss | * 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. |
| 26 | 1 | Eric Hou | |
| 27 | h3. Additional References: |
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| 28 | 52 | Neil Voss | |
| 29 | 1 | Eric Hou | * 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. |
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| 31 | 57 | Neil Voss | * 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. |
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| 33 | 53 | Neil Voss | h2. Software Availability and Licensing Information |
| 34 | 52 | Neil Voss | |
| 35 | 53 | Neil Voss | Appion is released under the "Apache License, Version 2.0":http://www.apache.org/licenses/LICENSE-2.0 |
| 36 | 52 | Neil Voss | |
| 37 | 62 | Eric Hou | View an "myami code diagram":http://emg.nysbc.org/projects/appion/wiki/Myami_code_diagram base found in the "myami" repository. |
| 38 | 52 | Neil Voss | |
| 39 | h2. Youtube videos: |
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| 41 | * "An Introduction to Appion":http://www.youtube.com/watch?v=Wlxt_4yJKgA |
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| 42 | * "TiltPicker Demonstration":http://www.youtube.com/watch?v=z7BqGJczmjU |
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| 43 | 1 | Eric Hou | |
| 44 | h2. Citations |
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| 45 | |||
| 46 | View the entire collection of [[Appion citations]]. |
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| 47 | 69 | Amber Herold | |
| 48 | h2. Contact information: |
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| 49 | |||
| 50 | Please email _appion@scripps.edu_ with any questions. |