San Diego Workshop 2018

This page describes the contents of the practical hands-on sessions of the Dynamo UCSD workshop (29th-30th January 2018).

Preinstalling the software

Participants are asked to bring their own laptops. We will reserve the first hour before the workshop to proceed to installation and troubleshooting on all the individual laptops. However, we strongly encourage participants to install and test the Dynamo software beforehand using the instructions below. Links to the Dynamo version that will be used during the workshop will be updated on the Friday, 26th of January.

We suggest students to download, install and test the software before departing for the workshop. Data should also be downloaded beforehand. Also note that you might need admin privileges to complete the steps below in some platforms. Make sure that you have access to admin credentials on your laptop.

You can use Dynamo with or without Matlab (standalone modus). Both options are fine to follow the contents of the workshop. We advice you to use it under Matlab, at the price of a slightly more complicated installation procedure.

Downloading Dynamo

Download the package in these google links for [ https://drive.google.com/open?id=1hdYLVsoqEQAbP7CdUxCpdUjrBtDAm1i2 Mac], Windows or Linux. After download (~4Gb), proceed to install and test

To install it, first create a folder in your filesystem in an arbitrary location of your choice:

mkdir <path to installation folder>

and untar the downloaded tarball into it:

tar -xf <tar file>  -C <path to installation folder>

For Windows platforms, we provide a zip file, that can be installed likewise.

Testing your standalone installation

We will first test if the package that you just downloaded and untarred/unzipped is functional on your system. This involves first activating Dynamo in a terminal, and then running it.

Activate shell in Mac/Linux

Activate your installation to work in standalone modus by typing in a Linux/MacOS shell the activation script:

 source <path to installation>/dynamo_activate_linux_shippedMCR.sh

or correspondingly for Mac:

 source <path to installation>/dynamo_activate_mac_shippedMCR.sh

Activate terminal in Windows

On a command prompt, type:

<path to installation>/dynamo_activate_windows.bat

Start Dynamo(all platforms )

From this point on, all platforms will work likewise. To test the activated installation, just type in the terminal:

dynamo

You should get the standalone Dynamo prompt in your terminal:

Dynamo >

It might take some time till it is operative (between seconds and minutes).

Free license for Matlab

If the standalone installation works, you don't need to install further elements in your system. You will be able to follow the contents of the workshop. However, we advice you to preinstall Matlab on your laptop. This makes the work with Dynamo much more comfortable.

You can get a trial version of Matlab and install it on your laptop. The license will be valid for 30 days. After installing Matlab, you can download the Dynamo version for your platform.

Testing your Matlab installation

Inside the Matlab shell type:

 run <path to installation>/dynamo_activate.m

Virtual machines

We recommend to use this device only as a last resource. If your system does not recognize the libraries provided in your package, you always have the option of installing a Virtual Machine in your system that emulates the Ubuntu distribution of linux. In this environment, Dynamo will run without errors, although the performance of the graphics system will be severely decreased.

Download an Ubuntu distribution

The version 16.04.3 of Ubuntu can be download as an iso file here

Download the virtual machine

A virtual machine can be downloaded here. A detailed walkthrough on the diverse steps can be found here

Instructions for Windows users

Windows is not the native development platform of Dynamo. We provide Windows versions of it (tested on Windows 7), but cannot guarantee that they'll work in other Windows systems.

The standalone for Windows will be uploaded in this google drive link .

Activating the Windows standalone

In DOS terminal write:

C:\ <path to the Dynamo installation>\dynamo_activate_windows.bat 

then open a Dynamo terminal by typing in the DOS

dynamo

If it doesn't work, type:

 set PATH=%PATH%;%MCR_ROOT%\runtime\win64

and then again

C:\ <path to the Dynamo installation>\dynamo_activate_windows.bat .

Preparing your Matlab in Windows

If the standalone fails, a Matlab trial version should be used. Please download it from Mathworks. In order to check if your system has all the libraries needed to run Dynamo, write in the Matlab shell

run <path to installation>/dynamo_activate.m

If the activation fails, you need to compile (i.e. 'mex') some files. These requieres to have a compiler on your system. Write

mex -setup

in the Matlab shell.

Installing a C++ compiler for windows

This will direct you to install a c++ compiler specific for the Matlab-Windows (MinGW-w64). You just need to follow the instructions on screen. Should take less than three minutes.

When the compiler is installed, run

mex -setup

to check that the system recognizes it. Then run dynamo_activate.m again.

Data

Downloading data beforehand may help avoiding waiting time during the workshop.

In Linux:

wget  https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/hiv/v17.rec
wget  https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/t20s/t20s.mrc
wget  https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/fhv/crop.rec 

Time schedule

Day 1:

09:00	Installation on individual laptops
10:10	Presentation Introduction to Dynamo and Subtomogram averaging Dynamo software.
10:45	Guided Hands-on Basics of Dynamo: formats and conventions.
12:00	Lunch
13:00	Hands on: Starters guide Basic tools applied on small sized synthetic data
14:30	Coffee
15:00	Hands on: Advanced starters guide Application on FHV viruses on mitochondrial membranes.
16:30	Demonstration Classification through PCA and MRA
17:00	End of presentations Participants are welcome to stay and work with own data with guidance of the instructors.

Day 2:

09:00	Geometrical modelling in Dynamo: surfaces and filaments Application on HIV viral capsids
10:30	Coffee
11:00	Classification and automated refinement
12:30	Lunch
13:30	Automated particle picking through template matching Application on GroEL solutions.
15:00	Coffee
15:30	Basics of creation of 3d scenes and movies. Application on FHV viruses on mitochondrial membranes.
16:45	Closing remarks
17:00	End of workshop Participants are welcome to stay and work with own data with guidance of the instructors.

General Introduction

Clicking particles in the Starters guide

Guided presentation:

• Basic Dynamo jargon

• tutorial on basic elements: help, data and metadata formats.
• tutorial on the basic concept in Dynamo alignment: the project.

Working on your own:

• Basic walkthrough: creating a catalogue, picking particles, launching a project.
• Advanced starters guide on a real tomogram. (~2 hours)
• Further work:
  • tutorial on the use command line operations for general purposes.
  • tutorial on the use of the command line to manage projects.

Geometric modeling

Geometric modeling for surfaces and filaments

Short guided presentation:

• tutorial on membrane modeling with dmslice
• Filament models with dtmslice
  • tutorial
  • walkthrough
• Reusing model workflows ( walkthrough)
• Further work: catalogue

Working on your own:

FHV tutorial on isolated membrane events (advanced starters guide)

HIV tutorial on densely packed slices

• In the afternoon, after the research talks, we will focus on the extraction of particles from densely packed spherical geometry on HIV viral capsides (~1 hour)

Template matching

Working on your own:

• We will follow this walkthrough for automated identification of proteosomes on a real tomogram through template matching. (~1 hour)

Template matching

Adaptive bandpass filtering

Working on your own:

• We will follow this walkthrough to create a small synthetic data set that illustrates the principles of adaptive bandpass filtering, a way of conducting a golden standard alignment procedure . (~40 mins)

Classification

Short guided presentation:

• PCA Basic concepts.
  advanced subboxing tutorial: combining with PCA and MRA tutorial
• Multirefererence Analysis
  Basic concepts.
  walkthrough (~10 min)
• Further work
  • Commandline operations with PCA

Creation of 3D scenes

Working on your own:

• Walkthrough on the FHV data set (~1hour)

Scene creation.

Further support material.

• Walkthrough on depiction and manipulation of triangulations (synthetic data).

Additional tools

Wednesday afternoon session.

• Subboxing

  motivation slide: extraction of vertices from icosahedral viruses

  Basic subboxing (tutoriall)

  advanced subboxing tutorial: combining with MRA tutorial

  suggested data set: prd1 Capsides (in the folder of isolated particles)

• Manual alignment.
• Exercises

Exercises

Exercises are scheduled for the last day. Nevertheless, feel free to start them any time during the workshop.

Organizers

• Elizabeth Villa, UCSD
• Daniel Castaño-Díez, BioEM Lab, University of Basel.

Instructors

• Jan Boehning, UCSD.
• Daniel Castaño-Díez, University of Basel.
• Paula Navarro, University of Basel.