Difference between revisions of "PSI Workshop 2023"
| Line 7: | Line 7: | ||
== Laptops == | == Laptops == | ||
| − | + | Participants will bring their own laptops to access a PSI server which will host the data. However, each participant should also instal in their laptop prior to the workshop: | |
| − | Participants will bring their own laptops to access the | ||
* Matlab (R2023a version), a licence free trial version is available. | * Matlab (R2023a version), a licence free trial version is available. | ||
* Dynamo | * Dynamo | ||
* Chimera | * Chimera | ||
| − | We will publish here the links to | + | We will publish here the links to these relevant versions of those packages. |
== Access to PSI resources== | == Access to PSI resources== | ||
| Line 19: | Line 18: | ||
= Time Schedule = | = Time Schedule = | ||
| − | * On the first day we will present the basic tools in the Dynamo environment | + | * 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: | * 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 | + | ** [https://doi.org/10.3389/fmolb.2018.00082''Protocols for Subtomogram Averaging of Membrane Proteins in the Dynamo Software Package''] Navarro PP, Stahlberg H and Castaño-Díez D (2018). Front. Mol. Biosci. 5:82. |
| + | ** [https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001318''Step-by-step guide to efficient subtomogram averaging of virus-like particles with Dynamo''] Scaramuzza S, Castaño-Díez D (2021). PLoS biology. 19(8):e3001318. | ||
| + | |||
| + | * On the third day participants are encouraged to make a flash presentation (3 mins, max. slides) describing their | ||
{| class="wikitable" | {| class="wikitable" | ||
Revision as of 09:17, 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 a PSI server which will host the data. However, each participant should also instal 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 these relevant versions of those packages.
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:
- Protocols for Subtomogram Averaging of Membrane Proteins in the Dynamo Software Package Navarro PP, Stahlberg H and Castaño-Díez D (2018). Front. Mol. Biosci. 5:82.
- Step-by-step guide to efficient subtomogram averaging of virus-like particles with Dynamo Scaramuzza S, Castaño-Díez D (2021). PLoS biology. 19(8):e3001318.
- On the third day participants are encouraged to make a flash presentation (3 mins, max. slides) describing their
| 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
} |
