Appion: an integrated, database-driven pipeline to facilitate EM image processing

By Gabriel Lander, S. Stagg, Neil R. Voss, Anchi Cheng, D. Fellmann, Jim Pulokas, C. Yoshioka, Christopher Irving, Anke M. Mulder, Pick-Wei Lau and 3 more. 2009

888 citations recorded by the source corpus.

The use of cryo-EM and three-dimensional image reconstruction is becoming increasingly common. Our vision for this technique is to provide a straightforward manner in which users can proceed from raw data to a reliable 3D reconstruction through a pipeline that both facilitates management of the processing steps and makes the results at each step more transparent. Tightly integrated with a relational SQL database, Appion is a modular and transparent pipeline that extends existing software applications and procedures. The user manages and controls the software modules via web-based forms, and all results are similarly available using web-based viewers directly linked to the underlying database, enabling even naive users to quickly deduce the quality of their results. The Appion API was designed with the principle that applications should be compatible with a broad range of specimens and that libraries and routines are modular and extensible. Presented here is a description of the design and architecture of the working Appion pipeline prototype and some results of its use.

Subfields: Electrical and Electronic Engineering, Structural Biology, Surfaces, Coatings and Films

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Citations in the corpus

RELION: Implementation of a Bayesian approach to cryo-EM structure determination (2012, methodology): “Efforts to do so in APPION (Lander et al., 2009) and EMAN2 (Tang et al.”
A Next-Generation Cleaved, Soluble HIV-1 Env Trimer, BG505 SOSIP.664 gp140, Expresses Multiple Epitopes for Broadly Neutralizing but Not Non-Neutralizing Antibodies (2013, methodology): “Particles were picked automatically using DoG Picker and put into a particle stack using the Appion software package [74,75].”
Electron-Microscopy-Based Epitope Mapping Defines Specificities of Polyclonal Antibodies Elicited during HIV-1 BG505 Envelope Trimer Immunization (2018, methodology): “Images were collected on a 4kx4k TemCam F416 detector and transferred into the Appion database (Lander et al., 2009) for initial image processing.”
Transcriptome engineering with RNA-targeting Type VI-D CRISPR effectors (2018, neutral): “ID=KRE6P5E8Z COOT Emsley et al., 2010 https://www2.mrc-lmb.cam.ac.uk/personal/ pemsley/coot/ PHENIX Adams et al., 2010 http://www.phenix-online.org/ PyMOL Open-Source PyMOL 1.8.x http://www.pymol.org/ UCSF Chimera Pettersen et al., 2004 https://www.cgl.ucsf.edu/chimera/ Leginon Suloway et al., 2005 ”
High resolution microtubule structures reveal the structural transitions in αβ–tubulin upon GTP hydrolysis (2014, methodology): “Image processing was performed within the Appion processing environment (Lander et al., 2009).”
Recent developments in the CCP-EM software suite (2017, background): “There are clear conceptual similarities to other frameworks such as Appion (Lander et al., 2009), Scipion (de la Rosa-Trevı́n et al., 2016) and Focus (Biyani et al., 2017).”
Uncleaved prefusion-optimized gp140 trimers derived from analysis of HIV-1 envelope metastability (2016, positive): “12) using DoG Picker and put into a particle stack using the Appion software package 61 .”