EMBO workshop 2020 - Revision history

Raffaele Coray at 13:23, 2 December 2024

2024-12-02T13:23:59Z

2020-08-25T14:19:24Z

Final exercise

2020-08-25T10:56:13Z

Homeworks

2020-08-25T10:54:16Z

2020-08-20T11:50:58Z

Start Dynamo inside a Matlab session

2020-08-20T11:50:45Z

Start Dynamo inside a Matlab session

2020-08-13T10:53:58Z

Interfacing with Other Tools

2020-08-13T09:54:21Z

Running Alignment Projects on the GPU during the workshop

2020-08-13T09:53:56Z

Running Alignment Projects on the GPU during the workshop

2020-08-13T09:49:29Z

← Older revision		Revision as of 13:23, 2 December 2024
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		+	[[Category:WalkthroughsSpecific]]
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	Dynamo is a [[https://www.sciencedirect.com/science/article/pii/S1047847711003650 flexible toolbox]] to help you solve problems in subtomogram averaging.		Dynamo is a [[https://www.sciencedirect.com/science/article/pii/S1047847711003650 flexible toolbox]] to help you solve problems in subtomogram averaging.

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 === Final exercise ===
-The main goal of this course is for you to be able to identifies strategies for setting up an appropriate approach for your problem. To this end, on the last day we suggest you  [[Getting a Structure from Multiple Tomograms of HIV Capsids | a problem data set to work with]].  The data for this exercise
+The main goal of this course is for you to be able to identify strategies for setting up an appropriate approach for your problem. To this end, on the last day we suggest you  [[Getting a Structure from Multiple Tomograms of HIV Capsids | a problem data set to work with]].  The data for this exercise
 can be found at:

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 Alister recently spent some time [[Integration with Warp and M  | 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
-=== Homeworks ===
+=== Final exercise ===
-The main goal of this course is for you to be able to identifies strategies for setting up an appropriate approach for your problem. To this end, on the last day we suggest you  [[Getting a Structure from Multiple Tomograms of HIV Capsids | a problem data set to work with]].
+The main goal of this course is for you to be able to identifies strategies for setting up an appropriate approach for your problem. To this end, on the last day we suggest you  [[Getting a Structure from Multiple Tomograms of HIV Capsids | a problem data set to work with]].  The data for this exercise
 Feel free to to use this part to articulate your final presentation on Friday.

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 ===PCA Based Classification===
 [[Walkthrough on PCA through the command line]]
 ==Day 3 ==
 === Fiducial based alignment and reconstruction ===
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 * [[Walkthrough on manual marker clicking  ]]
 === Creation of 3D scenes ===
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 * [[Walkthrough on placement of averages on table positions | Walkthrough ]]on depiction and manipulation of triangulations (synthetic data).
 = Running Alignment Projects on the GPU during the workshop =

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 Once you are inside your remote terminal, open a terminal (right click on the workspace) and start Matlab. You first need to load the module:
-<tt>module load MATLAB</tt>
+ <tt>module load MATLAB</tt>
 and then start Matlab itself:

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 once your Matlab session is up, you can load dynamo through:
-  <tt> run /g/XXX/loadDynamo.m</tt>
+  <tt>run /g/cryocourse/data/dynamo/activation</tt>
 == Own installation==

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 You can check the number of CPUs available to you in matlab with the following command
-  <nowiki>!lscpu | grep 'Core(s)'
+  <nowiki>!lscpu | grep 'Core(s)'</nowiki>
 You can then press the ''check'' button to check that your project inputs make sense, followed by the ''unfold'' button.

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 * cpu cores - 1
 * gpu identifiers - 0
-* parallelized averaging step - 0
+* parallelized averaging step - 8 (you may adjust this for your system depending on the number of CPUs available)
 You can then press the ''check'' button to check that your project inputs make sense, followed by the ''unfold'' button.
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 to launch the alignment project.
 = Submitting jobs For GPU computing=

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 The data can be found in
   <tt>/g/cryocourse/data/dynamo/t20s.mrc</tt>
 = 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.