Appion Home » History » Version 61
Eric Hou, 06/15/2010 01:35 PM
| 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 | 53 | Neil Voss | h2. Contact information: |
| 12 | 34 | Amber Herold | |
| 13 | 55 | Neil Voss | Please email _appion@scripps.edu_ with any questions. |
| 14 | 1 | Eric Hou | |
| 15 | 52 | Neil Voss | h2. Software Installation: |
| 16 | 1 | Eric Hou | |
| 17 | 60 | Eric Hou | bq. see "Complete Installation":http://emg.nysbc.org/projects/appion/wiki/Complete_Installation |
| 18 | 1 | Eric Hou | |
| 19 | 52 | Neil Voss | h2. User Guide: |
| 20 | 1 | Eric Hou | |
| 21 | 61 | Eric Hou | bq. see "Appion User Guide":http://emg.nysbc.org/projects/appion/wiki/Appion_User_Guide |
| 22 | 1 | Eric Hou | |
| 23 | 52 | Neil Voss | h2. Publications: |
| 24 | 1 | Eric Hou | |
| 25 | 52 | Neil Voss | h3. Primary Publication to Cite: |
| 26 | 1 | Eric Hou | |
| 27 | 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. |
| 28 | 1 | Eric Hou | |
| 29 | h3. Additional References: |
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| 30 | 52 | Neil Voss | |
| 31 | 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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| 33 | 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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| 35 | 53 | Neil Voss | h2. Software Availability and Licensing Information |
| 36 | 52 | Neil Voss | |
| 37 | 53 | Neil Voss | Appion is released under the "Apache License, Version 2.0":http://www.apache.org/licenses/LICENSE-2.0 |
| 38 | 52 | Neil Voss | |
| 39 | 53 | Neil Voss | View an [[myami code diagram|overview of the Appion code]] base found in the "myami" repository. |
| 40 | 52 | Neil Voss | |
| 41 | h2. Youtube videos: |
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| 43 | * "An Introduction to Appion":http://www.youtube.com/watch?v=Wlxt_4yJKgA |
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| 44 | * "TiltPicker Demonstration":http://www.youtube.com/watch?v=z7BqGJczmjU |
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| 45 | 1 | Eric Hou | |
| 46 | 49 | Amber Herold | --- |