PSIMEx Workshop: Interactions and Pathways
Support provided by Enfin and SLING
Is it right for me?
This workshop is specifically intended to give experimental and computational biologists training on how to optimally explore and use protein-protein interaction resources. We will also explore EBI's data resources related to pathways. Preference will be given to those actively involved in or commencing protein interaction and/or pathway-related projects.
The course consist of two parts: the first three days will provide the necessary knowledge and hands-on training to use protein-protein interaction and pathways resources and tools. We will concentrate on how to transfer this information to new users, therefore we will discuss best practice in training and training materials, as well as how to support those interested in training others on the resources covered during the course. The fourth and fifth days will be devoted to 'Train the Trainer' and you have to have attended the first part of the course to take part in this session.
What will I learn?
- Molecular interactions state of the art
- Making sense of interactions
- Pathways informatics: databases and tools
- Ontologies and Standards in Interactions and Pathways
What will it cover?
- Retrieving and exploring protein-protein interactions
- Predicting targets for pull-down experiments
- Network analysis
- MIMIx, GO, ChEBI and HUPO (PSI)
- Exchanging protein interaction data: The IMEx consortium
- Finding and exploring biological pathways- Reactome
| Time | Topic |
|---|---|
|
Day 1 - Monday 28th March 2011 PPI & Standards IntAct |
|
| 13:00 - 13:30 | Registration with Tea/Coffee |
| 13:30 - 13:40 | Welcome & Safety (Vicky Schneider) |
| 13:40 - 14:30 | Protein-Protein Interactions and Standards (Sandra Orchard) |
| 14:30 - 15:30 | IntAct (Samuel Kerrien) Tutorial |
| 15:30 - 16:00 | Tea/Coffee Break |
| 16:00 - 17:30 | IntAct Continues (Samuel Kerrien) Lecture Query Text |
| 18:30 - 21:00 | Dinner at Red Lion for those booked with accommodation |
| 21:00 | Transport - a 16 seater shuttle bus will transport you from the Red Lion, Hinxton to the The Holiday Inn (you will not all fit in it at once, it will do two collections). |
|
Day 2 - Tuesday 29th March 2011 Cytoscape, PPI Networks Ontologies |
|
| 08:45 | Transport - only for those staying at The Holiday Inn Whittlesford a 16 seater shuttle bus will transport you from the hotel to the EBI (you will not all fit in it at once, it will do two collections). |
| 09:15 - 11:00 | Visualising PPI Cytoscape (Nadezhda T. Doncheva) |
| 11:00 - 11:30 | Tea/Coffee Break |
| 11:30 - 13:00 | Mapping and visualisation of biological networks (Nadezhda T. Doncheva) |
| 13:00 - 13:30 | Lunch |
| 13:30 - 15:30 | Protein interaction networks with functional and structural information (Javier De Las Rivas) Tutorial |
| 15:30 - 16:00 | Tea/Coffee Break |
| 16:00 - 17:30 | Ontologies (Vicky Schneider) |
| 17:30 - 19:00 | Poster session with drinks (all) |
| 19:00 - 21:30 | Course Dinner at Red Lion for all course attendees and Trainers |
| 21:30 | Transport - only for those staying at The Holiday Inn Whittlesford a 16 seater shuttle bus will transport you from the hotel to the EBI (you will not all fit in it at once, it will do two collections). |
|
Day 3 - Wednesday 30th March 2011 Pathways your data |
|
| 08:45 | Transport - only for those staying at The Holiday Inn Whittlesford a 16 seater shuttle bus will transport you from the hotel to the EBI (you will not all fit in it at once, it will do two collections). |
| 09:15 - 11:00 | Reactome (Steve Jupe) Tutorial |
| 11:00 - 11:30 | Tea/Coffee Break |
| 11:30 - 13:00 | From network to pathway based analysis (Steve Jupe) Lecture 1 Lecture 2 |
| 13:00 - 13:30 | Lunch |
| 13:30 - 15:30 | Your data 1 to 1 (all) |
| 15:30 - 16:00 | Tea/Coffee Break |
| 16:00 - 17:30 | 1 to 1 continues (all) |
| 18:30 - 21:00 | Dinner at Red Lion for those booked with accommodation |
| 21:00 | Transport - a 16 seater shuttle bus will transport you from the Red Lion, Hinxton to the The Holiday Inn (you will not all fit in it at once, it will do two collections). |
|
Day 4 - Thursday 31st March 2011 You become the trainer |
|
| 08:45 | Transport - only for those staying at The Holiday Inn Whittlesford a 16 seater shuttle bus will transport you from the hotel to the EBI |
| 09:15 - 10:00 | Day expectations basic concepts |
| 10:00 - 11:00 | What we learned the previous days (Vicky Schneider and team) |
| 11:00 - 11:30 | Tea/Coffee Break |
| 11:30 - 13:00 | Group Activity 1 (Vicky Schneider and team) |
| 13:00 - 13:30 | Lunch |
| 13:30 - 14:30 | Group Activity 2 (Vicky Schneider and team) |
| 14:30 - 15:30 | Training best practice and learning from each other |
| 15:30 - 16:00 | Tea/Coffee Break |
| 16:00 - 17:30 | Session continues plus wrap up of the day (Vicky Schneider) |
| 18:30 - 21:00 | Dinner at Red Lion for those booked with accommodation |
| 21:00 | Transport - a 16 seater shuttle bus will transport you from the Red Lion, Hinxton to the The Holiday Inn |
|
Day 5 - Friday 1st April 2011 Defining your syllabus 1 to 1 |
|
| 08:45 | Transport - only for those staying at The Holiday Inn Whittlesford a 16 seater shuttle bus will transport you from the hotel to the EBI |
| 09:15 - 11:00 | Group and individual activities: defining your syllabus and our support to you (Vicky Schneider and team) |
| 11:00 - 11:30 | Tea/Coffee Break |
| 11:30 - 13:00 | Training 1 to 1 (various EBI trainers) |
| 13:00 - 13:30 | Lunch and farewell |
Registration Fees:
Registration with Accommodation Fee = £275.00
Please note that the registration with accommodation fee includes:
* All meals (breakfast, lunch, dinner and refreshment breaks)
* Accommodation for 3 nights (check in 28th March 2011, check out 31st March 2011), at the Holiday Inn, Duxford
* Transport to/from the accommodation to the EBI during the 3 days
* Course materials
* Use of EBI IT Training Room computer during the 3 day course
Registration NO Accommodation Fee = £150.00
Please note that the registration without accommodation fee includes:
* Meals at EBI (refreshments breaks and lunch, plus course dinner on Tuesday 28th March)
* Course materials
* Use of EBI IT Training Room computer during the 3 day course
EBI Industry Programme Members Registration Fee = £125.00
Please note that the EBI Industry Programme Member registration fee includes:
* All meals (breakfast, lunch, dinner and refreshment breaks)
* Accommodation for 3 nights (check in 28th March 2011, check out 31st March 2011), at the Holiday Inn, Duxford
* Transport to/from the accommodation to the EBI during the 3 days
* Course materials
* Use of EBI IT Training Room computer during the 3 day course
There is an additional £75 subsidised fee for anyone who wishes to attend the 'Train the Trainer' sessions on the Thursday and Friday morning. This includes accommodation for the 31st March. You can only attend the second session if you have attended the first.
All delegates will need to arrange their own travel to and from the course.
Registration Closed
The course materials can be found at the following URL:
/training/sites/ebi.ac.uk.training/files/materials/2011/psimex.zip