Difference between revisions of "PSI Workshop 2023"
| Line 6: | Line 6: | ||
= Computing resources = | = Computing resources = | ||
| − | == Access == | + | == Laptops == |
| + | |||
| + | Participants will bring their own laptops to access the PSI resources. In addition, each participant should installed in their laptop prior to the workshop: | ||
| + | * Matlab (R2023a version), a licence free trial version is available. | ||
| + | * Dynamo | ||
| + | * Chimera | ||
| + | We will publish here the links to | ||
| + | |||
| + | == Access to PSI resources== | ||
We will publish here a brief guide describing the steps to follow to access the computing resources. | We will publish here a brief guide describing the steps to follow to access the computing resources. | ||
= Time Schedule = | = Time Schedule = | ||
| + | |||
| + | * On the first day we will present the basic tools in the Dynamo environment | ||
| + | * The second day will be devoted to a hands-on guide on two practical cases: | ||
| + | * On the third day participants are encouraged to make a flash presentation | ||
{| class="wikitable" | {| class="wikitable" | ||
| Line 18: | Line 30: | ||
| 0 || 09:00 - 10:00|| Research Talk | | 0 || 09:00 - 10:00|| Research Talk | ||
|- | |- | ||
| − | | 1 || 10:00 - | + | | 1 || 10:00 - 10:45|| General introduction: Hands on |
|- | |- | ||
| 2 || 11:00 - 12:30 || [[Starters guide | Starters Guide: subtomogram averaging]] | | 2 || 11:00 - 12:30 || [[Starters guide | Starters Guide: subtomogram averaging]] | ||
| Line 38: | Line 50: | ||
! Module !! Time !! Subject | ! Module !! Time !! Subject | ||
|- | |- | ||
| − | | 4 || | + | | 4 || 15:15 - 15:45 || [[Walkthrough for template matching | Template Matching]] |
|- | |- | ||
| − | | 5 || | + | | 5 || 15:45 - 16:15 || [[Walkthrough on PCA through the command line | Principal Component Analysis ]] |
|- | |- | ||
| − | | 6a || | + | | 6a || 16:15 - 16:45 || [[Walkthrough on manual marker clicking | Alignment of tilt series: Manual]] |
|- | |- | ||
| − | | 6b || | + | | 6b || 16: || [[Walkthrough_on_GUI_based_tilt_series_alignment | Alignment of tilt series: GUI ]] |
|- | |- | ||
| 6c || Example || [[Walkthrough_on_command_line_based_tilt_series_alignment | Alignment of tilt series: command line]] | | 6c || Example || [[Walkthrough_on_command_line_based_tilt_series_alignment | Alignment of tilt series: command line]] | ||
| + | |||
| + | |} | ||
| + | |||
| + | {| class="wikitable" | ||
| + | |+ Day 2: Practical cases | ||
|- | |- | ||
| − | | 7 || | + | ! Module !! Time !! Subject |
| − | + | |- | |
| + | | 7 || 09:00 - 11:00 || [[Advanced starters guide | Complete walkthroug]] | ||
| + | } | ||
Revision as of 09:14, 3 August 2023
Workshop
The PSI Dynamo workshop will take place from August the 16th to August the 18th in the Paul Scherrer Institute.
The workshop provides hands-on training in all practical aspects of tomography and sub-tomogram averaging using our software Dynamo, encompassing all stages of the pipeline: alignment and reconstruction of tilt series, tomogram visualization and archiving, particle selection and extraction, and subtomogram alignment, averaging, refinement and classification. No previous experience is required. Computing infrastructure will be provided in place, and we welcome participants to bring their own data sets to work on them during this four-day course.
Computing resources
Laptops
Participants will bring their own laptops to access the PSI resources. In addition, each participant should installed in their laptop prior to the workshop:
- Matlab (R2023a version), a licence free trial version is available.
- Dynamo
- Chimera
We will publish here the links to
Access to PSI resources
We will publish here a brief guide describing the steps to follow to access the computing resources.
Time Schedule
- On the first day we will present the basic tools in the Dynamo environment
- The second day will be devoted to a hands-on guide on two practical cases:
- On the third day participants are encouraged to make a flash presentation
| Module | Time | Subject |
|---|---|---|
| 0 | 09:00 - 10:00 | Research Talk |
| 1 | 10:00 - 10:45 | General introduction: Hands on |
| 2 | 11:00 - 12:30 | Starters Guide: subtomogram averaging |
| 3 | 13:30 - 14:00 | General modelling |
| 3a | 14:00 - 14:30 | Models: Filaments |
| 3b | 14:30 - 14:45 | Models: Vesicles |
| 3c | 14:45 - 15:00 | Models: Surfaces |
| Module | Time | Subject |
|---|---|---|
| 4 | 15:15 - 15:45 | Template Matching |
| 5 | 15:45 - 16:15 | Principal Component Analysis |
| 6a | 16:15 - 16:45 | Alignment of tilt series: Manual |
| 6b | 16: | Alignment of tilt series: GUI |
| 6c | Example | Alignment of tilt series: command line |
| Module | Time | Subject |
|---|---|---|
| 7 | 09:00 - 11:00 | Complete walkthroug
} |
