EMBO workshop 2020

Dynamo is a [flexible toolbox] to help you solve problems in subtomogram averaging.

The goal of this workshop is to teach the principles of subtomogram averaging and show you some of the ways Dynamo can help you achieve that if you want subtomogram averaging to be a part of your research.

If at any time after the course you need help with Dynamo or subtomogram averaging generally, don't hesitate to ask on the [forum in Google Groups]

Instructors

Daniel Castaño-Diez - University of Basel

Alister Burt - Institut de Biologie Structurale

Computer setup

The house is intended to be completed with the remote access setup provided by the EMBL IT services. You are however welcome to follow it by installing Dynamo on your own laptop.

Own installation

If you prefer to install Dynamo on your laptop, please follow the instructions on Download. Please be aware that this setting will only work in Linux and Mac laptops; we don't have an updated Dynamo version in Windows. Matlab is not a prerequisite but we strongly recommend to use it if you have a licence (or feel motivated enough to use a free trial licence as provided by Mathworks).

Materials

Day 1

Basic principles

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.

• Complete the advanced starters guide (~2 hours)

The data can be found in

/g/cryocourse/data/dynamo/crop.rec 

the chimera path you need in the tutorial is

/g/easybuild/x86_64/CentOS/7/haswell/software/Chimera/1.13-foss-2017b-Python-2.7.14/bin/chimera

• Further work:
  • tutorial on the use command line operations for general purposes.
  • tutorial on the use of the command line to manage projects.

Day 2

Geometric Modelling

Short guided presentation:

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

• In the afternoon, we will focus on the extraction of particles from densely packed spherical geometry (~1 hour)
  

The data is available at

/g/cryocourse/data/dynamo/v17.rec

PCA Based Classification

Walkthrough on PCA through the command line

Day 3

Fiducial based alignment and reconstruction

These new features in Dynamo are at the testing stage.

• Walkthrough on GUI based tilt series alignment

• Walkthrough on command line based tilt series alignment

• Walkthrough on manual marker clicking

Interfacing with Other Tools

Dynamo is designed to allow maximum user flexibility and to encourage users to design their own solutions to the specific problems posed by their data.

Alister recently spent some time integrating Dynamo with Warp and M to be able to take advantage of Dynamo for tilt-series alignment and particle picking and plug the results into M's multi-particle refinement Integration with Warp and M

Creation of 3D scenes

Working on your own:

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

Further support material.

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

Template matching

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

The data can be found in

/g/cryocourse/data/dynamo/t20s.mrc

Submitting jobs For GPU computing

The following is applicable for subtomogram averaging projects setup to be run in the "gpu_standalone" mode under computing environment.

Once your project is unfolded, you should have an executable file

wizardTestProject.exe

The EMBL-HD cluster uses slurm for job submission and resource allocation.

To run this project as a job on their computing resources, we should first set up a submission script, here is an example

#!/bin/bash
#SBATCH -N 1                        # number of nodes
#SBATCH -n 1                        # number of cores
#SBATCH -o slurm.%N.%j.out          # STDOUT
#SBATCH -e slurm.%N.%j.err          # STDERR
#SBATCH --mail-type=END,FAIL        # notifications for job done & fail
#SBATCH --mail-user=alisterburt@gmail.com # send-to address
#SBATCH -p gpu						# select gpu usage
#SBATCH --gres=gpu:1				# number of gpus (if using gpus)


module load dynamo
./wizardTestProject.exe

Save this text file in the same directory as the executable file, then submit the job using sbatch

sbatch dynamo_test_gpu.sl 

This should then confirm that the job has been submitted

Submitted batch job 65146729 

Submitting jobs for CPU computing

The following is applicable for subtomogram averaging projects setup to be run in the "standalone" mode under computing environment.

Once your project is unfolded, you should have an executable file

wizardTestProject.exe

The EMBL-HD cluster uses slurm for job submission and resource allocation.

To run this project as a job on their computing resources, we should first set up a submission script, here is an example using 6 cores on 1 node

#!/bin/bash
#SBATCH -N 1                        # number of nodes
#SBATCH -n 6                        # number of cores
#SBATCH -o slurm.%N.%j.out          # STDOUT
#SBATCH -e slurm.%N.%j.err          # STDERR
#SBATCH --mail-type=END,FAIL        # notifications for job done & fail
#SBATCH --mail-user=alisterburt@gmail.com # send-to address


module load dynamo
./wizardTestProject.exe

Save this text file in the same directory as the executable file, then submit the job using sbatch

sbatch dynamo_test_cpu.sl 

This should then confirm that the job has been submitted

Submitted batch job 65146755