EBI Affiliated Course - PSIMEx Workshop: Interactions and Pathways

Course Summary

Title: PSIMEx Workshop: Interactions and Pathways
Date: 28 March - 1 April 2011
Venue: EMBL-EBI, Hinxton, Nr Cambridge, CB10 1SD, UK
Organisers: Vicky Schneider, Sandra Orchard
Admin Support: Alison Barker
Registration Closes: 23th February 2011

Course Overwiew | Programme | Registration | Trainers

Co-Sponsored by ENFIN

Course Overview

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

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Draft Programme

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

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Course Participant Survey

Registration and Payment

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.

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Trainers

Nadezhda T. Doncheva - Max Planck Institute for Informatics, Germany

Javier De Las Rivas - Cancer Research Center (CiC-IBMCC, CSIC/USAL) Salamanca

Sandra Orchard - EMBL-EBI

Vicky Schneider - EMBL-EBI

Samuel Kerrien - EMBL-EBI

Steve Jupe - EMBL-EBI

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