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Index by title

• 2010 ADWCreate an image uploader program from scratch
• 2 Way Viewer Shared
• Alignment SubStacks
• Appion citations
• Appion config advanced
• Appion CTF parameter definition
• Appion forum
• Appion Home
  • 2010 Appion Developer Workshop
    • 2010 ADWAdd a new option to a program
    • 2010 ADWCreate an alignment program from scratch
    • 2010 ADWOrganization of the PHP programs
    • 2010 ADWOrganization of the Python programs
  • Appion Manual
    • An Introduction to Appion
      • Authors
      • What is Appion
    • Appion User Guide
      • Administration Tools Guide
      • Appion and Leginon Database Tools
        • Administration
          • Applications
          • Goniometer
          • Groups
          • Instruments
          • Revert Settings
          • Users
        • Hole Template Viewer
        • Image Viewers
          • 2 Way Viewer
          • 3 Way Viewer
          • Common Features
          • Dual Viewer
          • Image Viewer
          • RCT viewer
        • LOI - Leginon Observer Interface
        • Project DB
          • Create a Project Processing Database
          • Create New Project
          • Edit Project Description
          • Edit Project Owners
          • Grid Management
          • Share a Project Session with another User
          • Unlink a Project Processing Database
          • Upload Images to a new Project Session
            • Image pair upload for rct
          • View a Summary of a Project Session
          • View Projects
        • Tomography Tool
        • User Management
          • Enable User Authentication
          • Logout
          • Modify Your Profile
          • New User Registration
          • Retrieve Forgotten Password
      • Appion output
      • Appion Processing
        • Ab Initio Reconstruction
          • EMAN Common Lines
          • IMAGIC Angular Reconstitution
          • OTR Volume
          • RCT Volume
        • Common Workflow
          • Quality Assessment
          • Random-Conical Tilt (RCT) Reconstruction workflow
          • Step by Step Guide
          • Trimer processing workflow
        • CryoSPARC
        • CTF Estimation
          • Ace 2 Estimation
          • Ace Estimation
            • Aceman
            • Ace script
          • CtfFind Estimation
          • Phase plate CTF Estimation
        • Direct Detector Frame Processing
          • Catch up DD frame alignment
          • GainDark correction of the raw frame with or without drift correction
        • Image Assessment
          • Multi Img Assessment
          • Run Image Rejector
          • Web Img Assessment
        • IMAGIC Multi Reference Alignment
        • Import Tools
          • EMDB to Model
          • PDB to Model
          • PDB tp Model
          • Upload Model
          • Upload More Images
            • Upload image grouping
          • Upload Particles
          • Upload Stack
          • Upload Template
        • Particle Alignment
          • Run Alignment
            • Ed's Iteration Alignment
            • Spider Reference-based Alignment
            • Spider Reference-free Alignment
            • Xmipp Maximum Likelihood Alignment
            • Xmipp Reference-based Maximum Likelihood Alignment
          • Run Feature Analysis
            • Spider Coran Classification
            • Xmipp Kerden Self-Organizing Map
            • Xmipp Rotational Kerden Self-Organizing Map
          • Run Particle Clustering
            • Hierarchical or K-means Clustering
        • Particle Selection
          • Dog Picking
          • Manual Picking
          • Random Conical Tilt Picking
            • Align and Edit Tilt Pairs
            • Auto Align Tilt Pairs
          • Template Picking
        • Processing Cluster Login
        • Refine Reconstruction
          • EMAN Refinement
          • Frealign Refinement
          • IMAGIC Refinement
          • Refinement Post-processing Procedures
          • SPIDER Refinement
        • Region Mask Creation
          • Crud Finding
          • Manual Masking
          • Maskiton
        • Repeat from other session
        • Stacks
          • More Stack Tools
            • Combine Stacks
            • Convert Stack into Particle Picks
            • Jumpers SubStack
            • View Stacks
              • Center Particles
              • Create Substack
              • Filter by MeanStdev
              • Sort Junk
          • Stack Creation
        • Synthetic Data
          • Synthetic Dataset Creation
        • Terminology
        • Tomography
          • Align Tilt-Series
          • Align tilt series
          • Create full tomogram
          • Create tomogram subvolume
            • Average tomogram subvolumes
          • Upload full tomogram
        • Upload Refinement
        • Xmipp 3 Clustering 2D Alignment
    • Complete Installation
      • Additional Database Server Setup after Web Server Installation
      • Changes to auto-installed appion for production usage
      • Create a Test Project
        • Create a Processing Database
        • Process Images
      • Database Server Installation
      • Download additional Software (CentOS Specific)
      • File Server Setup Considerations
      • Installation Troublshooting Guide
      • Installing Appion with an existing Leginon installation
      • Install using the auto-installation tool
      • Instructions for installing CentOS on your computer
      • Instructions for installing Fedora on your computer
      • Processing Server Installation
        • Compile FindEM
          • Install FindEM from source
        • Compile Radermacher
        • Configure appioncfg
        • Configure leginoncfg
        • Configure sinedoncfg
        • Download Appion Files
        • Explanation of Sample Names
        • Install Ace2
          • Compile Ace2 from source
        • Install Appion Packages
        • Install dosefgpu driftcorr
          • Install motioncor2 shared
        • Install EMAN
        • Install EM Hole Finder
        • Install External Packages
          • Install MotionCor2
        • Install Imod
        • Install Protomo
        • Install Protomo2
        • Install SIMPLE
        • Install SPIDER
        • Install supporting packages
        • Install UCSF Chimera
        • Install Xmipp
        • Perform system check
        • Test Appion
      • Security Considerations
      • Select Linux distribution to use
      • Setup Remote Processing
        • ClusterPhpSettings
        • Configure web server to submit jobs
        • Configure web server to submit job to local cluster
        • Install SSH module for PHP
        • Setup job submission server
        • Testing job submission
      • Web Server Installation
        • Check php information
        • Configure Operating System
        • Configure phpini
        • Differences between Linux flavors
        • Download Appion and Leginon Files
        • Install Apache Web Server
        • Install phpMyAdmin
        • Install Redux image server
        • Install SSH module for PHP webserver
        • Install the MRC PHP Extension
          • Troubleshooting Notes
        • Install the Web Interface
          • Install the Web Interface Advanced
        • Install Web Server Prerequisites
        • Potential Problems
        • Start NFS
    • Upgrade Instructions
      • Minor release update
      • Upgrade From 20x
      • Upgrade From 21x
      • Upgrade From 22-redux
      • Upgrade From 22x
      • Upgrade From 30 or above
        • New support package requirement for 33
    • Version Change Log
      • Version 32 Change Log
  • Developers guide
    • Adding refine python parts
    • Adding refine runjob
    • AMI Eclipse Quick Start Guide
      • Example config file
    • Appion Testing
    • Appion tricks
    • Cluster job overview
    • Coding Best Practices
      • Code Review Guide
        • Code development process
        • Purpose of Code Reviews
    • Common variables used
    • CSS notes
    • Error Handling
    • General Best Practices
    • Git
    • How to add an AppionLoop GUI page
    • How to add a launch page
    • How to add a new refinement method
    • How to test upload images with your own sandbox
    • Javascript notes
    • Myami code diagram
    • MySQL Notes
      • Mysql Nested Subqueries Problem
    • Object Oriented Programming
    • PHP notes
    • Python notes
    • Refine Refactor documentation
    • Setup Local Databases
    • Subversion
    • Test datasets at AMI
    • Useful shell commands
    • Using basicReportinc
• Brignole et al 2009
• CentOS6 installation
  • Install Free-Hand Test
    • FreeHand compile
• Centos installation shared
• Code Standards
• Configure appioncfg shared
• Configure leginoncfg 2 1
• Configure leginoncfg Shared
• Configure sinedoncfg 2 1
• Configure sinedoncfg shared
• Convert Mass into Volume
• Database Server Installation Shared
• Database Setup After Webserver initialization Shared
• DB Migration Process
• Default groups
• Default users
• Doc test notes
• Download additional Software (Fedora Specific)
• Download Appion Files Shared
  • Currrent myami release
• EMG Redmine Quick Start Guide
  • Issue Workflow Tutorial
  • Wiki Tips
• File Formats
• File Server Setup Considerations Shared
• Helical Image Processing
• Helical Image Processing (PHOELIX)
• Helical Processing
• HTML notes
• Image Viewers Shared
• Index of test scripts
• Install Appion and Leginon using the auto-installation tool share
  • Reconfigure the database
  • Regkey request
• Install Appion bin shared
• Install Appion Packages Shared
• Install Appion Packages Short Shared
• Install dosefgpu driftcorr shared
• Install EMAN2
• Install EPEL shared
• Install Grigorieff lab software
• Install myami-22 on guppy
• Install phpMyAdmin shared
• Install SSH module for PHP shared
• Install supporting packages Shared
  • Extra supporting package table
• Install Torque
• Install Torque Client
• Job submission vs direct Appion Script running from terminal
• Linux distribution recommendation
  • Link to ubuntu
• Make a New Stack
• Mount NFS on a Mac
• Myami on Ubuntu
• New support package requirement for 32
• Notes from Recon meeting
• Perform System Check Shared
• Potential job submission problems
• Processing Server External Packages Installation
  • External Package requirement of Appion scripts
  • Package executable alias name in Appion
    • Package alias table
• Processing Server Installation Shared
• Python Coding Standards
• Reconstruction Parameters
• Refinement Package Status
• Run Database Update Script
• Start redux with systemd
• Start with existing ANY Linux flavor OS
• Start with existing CentOS installation
• Testing auto-installation
• Test Appion Shared
• Test page
• Tomo alignment appiondata
• Tom Goddard visit February 2010
• Troubleshooting the Web Server Shared
• Upgrade from pre-20
• Use Cronus3 or Fly to view your web app
• Version200
• Version210
• Version220
• Version230
• Version300
• Version future
• Web Server Installation on CentOS 6
  • Current myami release checkout
• Web Server Installation Shared
• What does User Authentication do to myamiweb
• Wrapper Testing

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