Difference between revisions of "Delft Workshop 2017"

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== Preinstalling the software==
 
== Preinstalling the software==
  
We suggest students to install and test the software ''before'' departing for the workshop.  
+
We suggest students to download, install and test the software ''before'' departing for the workshop. Data should also be downloaded beforehand.
  
=== To work on own laptops ===
+
=== Downloading ''Dynamo ===
  
If you want to work with your own laptop, we advice you to preinstall Matlab on it.
+
Download the package in these google links  [https://drive.google.com/open?id=0B_T9apWxsZjMZ19CbS1JYzExRHc for linux] or  [https://drive.google.com/open?id=0B_T9apWxsZjMNFM5UXQzUEJBLUk Mac] respectively. After download (~4Gb), proceed to [[Installation | install and test]]
  
==== Free license for Matlab ====
+
=== Free license for Matlab ===
 +
 
 +
We advice you to preinstall Matlab on your laptop. This makes the work with ''Dynamo'' much easier
  
 
You can get [https://www.mathworks.com/programs/trials/trial_request.html a trial version of Matlab] and install it on your laptop. The license will be valid for 30 days.  After installing Matlab, you can [[Downloads | download]] the ''Dynamo'' version for your platform.
 
You can get [https://www.mathworks.com/programs/trials/trial_request.html a trial version of Matlab] and install it on your laptop. The license will be valid for 30 days.  After installing Matlab, you can [[Downloads | download]] the ''Dynamo'' version for your platform.
 
==== Standalone version ====
 
 
Dynamo can be used as a [[standalone]] (i.e., without Matlab ) in Linux and Mac systems.  Follow [https://drive.google.com/open?id=0B_T9apWxsZjMZ19CbS1JYzExRHc this google drive link for linux], or  [https://drive.google.com/open?id=0B_T9apWxsZjMNFM5UXQzUEJBLUk this one for mac].
 
  
 
=== To work on the servers of TU Delft ===
 
=== To work on the servers of TU Delft ===

Revision as of 18:48, 29 August 2017

A guide to use Dynamo during the TU Delft workshop for Cryo-EM. This covers the afternoon session of the 6th of September of 2017.

Preinstalling the software

We suggest students to download, install and test the software before departing for the workshop. Data should also be downloaded beforehand.

Downloading Dynamo

Download the package in these google links for linux or Mac respectively. After download (~4Gb), proceed to install and test

Free license for Matlab

We advice you to preinstall Matlab on your laptop. This makes the work with Dynamo much easier

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.

To work on the servers of TU Delft

Will be announced during the course.

Computer access

Will be announced during the course.

Opening a Linux terminal

We need to create a command terminal. Right click on the screen and select Open Terminal in the menu . A Linux command window will popup. Please create a folder for this course.

mkdir tomo
 cd  tomo 

Starting Dynamo

In the Linux terminal, open Matlab through:

matlab & 

it will take some secons. Then, in the Matlab window write:

 run /ISB2017/dynamo/dynamo_activate.m 

This will activate Dynamo in the current Matlab session.

Data

Program

Introduction to tomography and subtomogram averaging

45 minutes of presentation to introduce tomography, subtomogram averaging and Dynamo.

Tutorial 1: Getting started

on screen presentation/hands-on practical. The presentation will loosely the introductory materials in:

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

After the introduction of these general concepts, will follow together the basic hands-on tutorial of Dynamo.

Advanced getting started

After the coffee break at 16:00 participants will follow the advanced introduction on a reduced data set from a real tomogram.

Instructors

  1. Daniel Castaño-Díez, BioEM Lab, University of Basel
  2. Paula Pérez-Navarro, C-CINA, University of Basel
  3. Cynthia Taveneau, Institut Curie, Paris