Difference between revisions of "EMBO workshop 2021"
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== Dynamic of the course == | == Dynamic of the course == | ||
| − | |||
The course is divided on different modules, described in the time schedule below. Each module is structured in three stages: | The course is divided on different modules, described in the time schedule below. Each module is structured in three stages: | ||
| Line 16: | Line 15: | ||
; Common discussion | ; Common discussion | ||
: on the last 5 minutes of the module, we come back to the general breakout room for discussion of problems found. | : on the last 5 minutes of the module, we come back to the general breakout room for discussion of problems found. | ||
| + | |||
| + | === Data location === | ||
| + | Each module has one or several walkthroughs. The data of the walkthroughs is sometimes synthetic and created on the fly, and sometimes a data set is necessary. In such cases, the text of walkthrough will point to an on-line location where the data can be downloaded. <br /> | ||
| + | During this course, the data will be also available in the filesystem, you will not need to download it. | ||
== Time schedule == | == Time schedule == | ||
| Line 95: | Line 98: | ||
=== Manual alignment of tilt series === | === Manual alignment of tilt series === | ||
We will click manually on the gold beads of our test tilt series | We will click manually on the gold beads of our test tilt series | ||
| + | [[Walkthrough on manual marker clicking ]] | ||
=== Automated alignment of tilt series through the GUI === | === Automated alignment of tilt series through the GUI === | ||
| + | [[Walkthrough on GUI based tilt series alignment ]] | ||
=== Automated alignment of tilt series through the command line === | === Automated alignment of tilt series through the command line === | ||
| + | [[Walkthrough on command line based tilt series alignment ]] | ||
== Models == | == Models == | ||
=== Catalogues === | === Catalogues === | ||
=== Helical models === | === Helical models === | ||
| + | [http://{{SERVERNAME}}/w/doc/misc/modelFilament.pdf tutorial ] | ||
=== Vesicle and surface models === | === Vesicle and surface models === | ||
| + | [http://{{SERVERNAME}}/w/doc/misc/modelMembrane.pdf tutorial on] membrane modeling with <tt> dmslice </tt> | ||
=== Reusing models === | === Reusing models === | ||
| + | Reusing model workflows ([[Walkthrough model worfklow reuse| walkthrough]]) | ||
== Template matching == | == Template matching == | ||
| + | [[Walkthrough for template matching | walkthrough]] for automated identification of proteosomes on a real tomogram through template matching. (~1 hour) <br /> | ||
| + | The data can be found in | ||
| + | <tt>/g/cryocourse/data/dynamo/t20s.mrc</tt> | ||
== Subtomogram averaging == | == Subtomogram averaging == | ||
=== Introduction === | === Introduction === | ||
=== Advanced starters guide === | === Advanced starters guide === | ||
| + | |||
=== Seed oversampling === | === Seed oversampling === | ||
| + | |||
| + | [[Walkthrough for lattices on vesicles| from densely packed spherical geometry ]] (~1 hour) <br /> | ||
| + | The data is available at | ||
| + | <tt>/g/cryocourse/data/dynamo/v17.rec</tt> | ||
| + | |||
=== High resolution pipeline === | === High resolution pipeline === | ||
Not a tutorial per se: this is a presentation on a set of tools to interconnect Dynamo, M and other software. | Not a tutorial per se: this is a presentation on a set of tools to interconnect Dynamo, M and other software. | ||
Revision as of 13:09, 24 June 2021
These tutorials takes place virtually on the 11th and 13th of September of 2021 (14-18:30), as a part of the EMBO workshop for Image processing in cryoEM
Contents
Tutorials
Connection
Please refer to your course material to access your credentials.
Dynamic of the course
The course is divided on different modules, described in the time schedule below. Each module is structured in three stages:
- Demostration
- all students are connected to the main room; goals of the module will be explained by an instructor.
- Individual work
- students go the breakout rooms they have been assigned and perform the tasks of the walkthrough in the tutorial.
- an instructor will be assigned to each breakout room.
- Common discussion
- on the last 5 minutes of the module, we come back to the general breakout room for discussion of problems found.
Data location
Each module has one or several walkthroughs. The data of the walkthroughs is sometimes synthetic and created on the fly, and sometimes a data set is necessary. In such cases, the text of walkthrough will point to an on-line location where the data can be downloaded.
During this course, the data will be also available in the filesystem, you will not need to download it.
Time schedule
This time schedule is temptative
Day 1: tomography
| day | 'time |
| 14:00 | Introduction |
| 14:30 | tilt series alignment: manual |
| 15:00 | tilt series alignment (GUI) |
| 15:30 | tilt series alignment (command line) |
| 16:00 | Break |
| 16:30 | models: catalogue system |
| 17:00 | models: helical symmetry |
| 17:30 | models: vesicles and surfaces |
| 18:00 | Template matching |
Day 2: Subtomogram averaging
| 'time | subject |
| 14:00 | Introduction |
| 14:30 | Getting started: synthetic thermosomes |
| 15:30 | Advanced tutorial: FHV |
| 16:00 | Break |
| 16:30 | FHV: continuation |
| 17:00 | Seed oversampling |
| 18:00 | High resolution pipelines |
| 18:20 | Closing remarks |
Contents
Alignment of tilt series
Data location: t.b.d.
Manual alignment of tilt series
We will click manually on the gold beads of our test tilt series Walkthrough on manual marker clicking
Automated alignment of tilt series through the GUI
Walkthrough on GUI based tilt series alignment
Automated alignment of tilt series through the command line
Walkthrough on command line based tilt series alignment
Models
Catalogues
Helical models
Vesicle and surface models
tutorial on membrane modeling with dmslice
Reusing models
Reusing model workflows ( walkthrough)
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
Subtomogram averaging
Introduction
Advanced starters guide
Seed oversampling
from densely packed spherical geometry (~1 hour)
The data is available at
/g/cryocourse/data/dynamo/v17.rec
High resolution pipeline
Not a tutorial per se: this is a presentation on a set of tools to interconnect Dynamo, M and other software.
