Workshop Title: EMBO Workshop 2014

Venue of workshop: UCT, Cape Town, South Africa

Dates for the workshop: 28th September – 3rd October 2014

Workshop organisers: H3ABioNet, University of Cape Town

Trainers and support staff:  Click here

Syllabus and Tools: Click here

Prerequisites: List of software installed on the Window’s laptops used by trainees

Logistics information: A list of the information we provide concerning logistics for the course (access restricted)

Workshop Materials: https://training.h3abionet.org/embo_workshop_2014/

Course Program:

 

SUNDAY 28TH SEPTEMBER

 

Participant arrival and check in at hotel

 

20.00-21.00

Dinner: Little Scotia guest house

MONDAY 29TH SEPTEMBER

09.00-09.15

Introduction to the course: Organisers

 

09.15-10.00

1:1 Introduction round: all participants

 

10.00-10.30

Session 1: Introduction to bioinformatics, protein modules and sequence alignment [practicals and presentations]: Aidan Budd

 

10.30-11.00

Coffee break

 

11.00-12.00

Session 1 (continued): Introduction to bioinformatics, protein modules and sequence alignment [practicals and presentations]: Aidan Budd

 

12.00-13.00

Lunch

 

13.00-14.00

Modular protein architecture and construction of cell regulatory systems [Keynote Lecture]: Toby Gibson

 

14.00-15.30

Session 2: Web resources describing results of PPI experiments: design of such databases, minimal information to describe PPIs [practicals and presentations]: Nicola Mulder

 

15.30-16.00

Coffee break

 

16.00-17.00

Session 2 (continued): Web resources describing results of PPI experiments: design of such databases, minimal information to describe PPIs [practicals and presentations]: Nicola Mulder

 

17.00-17.30

Modelling interactions of the HIV gp120 protein [presentation]: Natasha Wood

 

17.30-18.30

Free practical session: trainees working with their own data

 

18.30

Shuttle pickup from UCT/Bernard Fuller Building to Little Scotia

 

19.00-21.00

Dinner: Little Scotia guest house

TUESDAY 30TH SEPTEMBER

09.00-10.00

Session 2b: Introduction to protein structure with Chimera [practicals and presentations]: Scooter Morris and Aidan Budd

     
 

10.00-10.30

Session 3: The freaks of protein sequence (I): Repeats [practicals and presentations]: Miguel Andrade

 

10.30-11.00

Coffee break

 

11.00-12.00

Session 3 (continued): The freaks of protein sequence (II): Biased regions [practicals and presentations]: Miguel Andrade

 

12.00-13.00

Lunch

 

13.00-14.00

Medical data mining: linking diseases, drugs, and adverse reactions [Keynote Lecture]: Lars Juhl Jensen

 

14.00-15.30

Session 4: Protein families and domains, including repeats (PFAM, SMART, etc.) [practicals and presentations]: Marco Punta

 

15.30-16.00

Coffee break

 

16.00-17.00

Session 4 (continued): Protein families and domains, including repeats (PFAM, SMART, etc.) [practicals and presentations]: Marco Punta

 

17.00-17.30

A web-based protein interaction network visualizer [presentation]: Gustavo Galazar

 

17.30-19.00

DAS Game: all participants lead by Gustavo Salazar and Natasha Wood

 

19.00

Shuttle pickup from UCT/Bernard Fuller Building to Down South Restaurant, Rondebosch

 

19.30-21.00

Dinner: Down South Restaurant, Rondebosch (including one glass of wine each)

WEDNESDAY 1ST OCTOBER

09.00-10.30

Session 5: Biology and prediction of intrinsically unstructured peptide regions [practicals and presentations]: Zsuzsanna Dosztányi

 

10.30-11.00

Coffee break

 

11.00-12.30

Session 5 (continued): Biology and prediction of intrinsically unstructured peptide regions [practicals and presentations]: Zsuzsanna Dosztányi

 

12.30-15.00

Lunch AND poster session

 

15.00-16.00

Session 6: Linear motif biology, prediction, and cooperativity in cellular signalling [presentations and practicals]: Holger Dinkel and Toby Gibson

 

16.00-16.30

Coffee break

 

16.30-17.30

Session 6 (continued): Linear motif biology, prediction, and cooperativity in cellular signalling [presentations and practicals]: Holger Dinkel and Toby Gibson

 

17.30-18.30

Dinner: Pizzas ordered into the venue i.e. UCT Health Science Campus (including wine)

 

18.30-21.00

Networking event (Cape Unseminar in Bioinformatics): all course participants and local bioinformaticians

 

21.15

Shuttle pickup from UCT/Bernard Fuller Building to Little Scotia

THURSDAY 2ND OCTOBER

09.00-10.30

Session 6 (continued): Using Jalview & Multiple Sequence Alignments to investigate short linear motif biology [presentations and practicals]: Holger Dinkel and Toby Gibson

 

10.30-11.00

Coffee break

 

11.00-12.00

Session 6 (continued): Automated access of online tools using REST interfaces [presentations and practicals]: Holger Dinkel and Toby Gibson

 

12.00-13.00

Lunch

 

13.00-14.00

From networks to structures and back again [Keynote Lecture]: John "Scooter" Morris

 

14.00-15.30

Session 7: STRING, networking, and PPIs [presentations and practicals]: Lars Juhl Jensen

 

15.30-16.00

Coffee break

 

16.00-17.30

Session 7 (continued): STRING, networking, and PPIs [presentations and practicals]: Lars Juhl Jensen

 

17.45

Shuttle pickup from UCT/Bernard Fuller Building to Little Scotia

 

18.45

Shuttle pickup from Little Scotia to Bihari Restaurant, Newlands

 

19.00-21.00

Gala Dinner: Bihari Restaurant, Newlands (including a glass of wine)

 

21.15

Shuttle pickup from Bihari Restaurant to Little Scotia

FRIDAY 3RD OCTOBER

09.00-10.30

Session 8: Exploring PPI networks using Cytoscape [presentations and practicals]: John "Scooter" Morris and Nadezhda T. Doncheva

 

10.30-11.00

Coffee break

 

11.00-12.30

Session 8 (continued): Exploring PPI networks using Cytoscape [presentations and practicals]: John "Scooter" Morris and Nadezhda T. Doncheva

 

12.30-14.00

Lunch

 

14.00-15.30

Session 8 (continued):Exploring PPI networks using Cytoscape [presentations and practicals]: John "Scooter" Morris and Nadezhda T. Doncheva

 

15.30-16.00

Coffee break

 

16.00-17.00

Session 8 (continued): Exploring PPI networks using Cytoscape [presentations and practicals]: John "Scooter" Morris and Nadezhda T. Doncheva

 

17.00-17.30

Wrap up and final Q and A session: all participants

 

17.45

Shuttle pickup from UCT/Bernard Fuller Building to Little Scotia

 

18.15-20.00

Dinner: Little Scotia guest house

SATURDAY 4TH OCTOBER

 

Participant departure and check out of hotel