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Course Overview
EMBO Practical Course on Computational analysis of protein-protein interactions: From sequences to networks.
Intended Audience
Course is open to any H3ABioNet members wanting learn more about th computational analysis of protein-protein interactions.
Keywords: Systems biology, Protein structure, Protein-protein interactions, Networks
Skill level of training: Intermediate
Language: English
Credential awarded: No credential awarded
Type of training: Face-to-face
Venue of the course: UCT, Cape Town, South Africa
Dates for the course: Every Tuesday and Thursday from 10:30 CAT to 14:30 CAT
Course organisers: Workshop organisers: H3ABioNet, University of Cape Town Trainers and support staff: • Aidan Budd - Session 1: Introduction to bioinformatics, protein modules and sequence alignment [practicals and presentations] • Toby Gibson - Session 1: Modular protein architecture and construction of cell regulatory systems [Keynote Lecture] • Nicola Mulder - Session 2: Web resources describing results of PPI experiments: design of such databases, minimal information to describe PPIs [practicals and presentations] • Nicola Mulder - Session 2 (continued): Web resources describing results of PPI experiments: design of such databases, minimal information to describe PPIs [practicals and presentations] • Natasha Wood - Session 2: Modelling interactions of the HIV gp120 protein [presentation] • Scooter Morris and Aidan Budd - Session 2b: Introduction to protein structure with Chimera [practicals and presentations] • Miguel Andrade - Session 3: The freaks of protein sequence (I): Repeats [practicals and presentations] • Lars Juhl Jensen: Medical data mining: linking diseases, drugs, and adverse reactions [Keynote Lecture] • Marco Punta - Session 4: Protein families and domains, including repeats (PFAM, SMART, etc.) [practicals and presentations] • Gustavo Galazar - Session 4: A web-based protein interaction network visualizer [presentation] • Zsuzsanna Dosztányi - Session 5: Biology and prediction of intrinsically unstructured peptide regions [practicals and presentations] • Holger Dinkel and Toby Gibson - Session 6: Linear motif biology, prediction, and cooperativity in cellular signalling [presentations and practicals] • Holger Dinkel and Toby Gibson - Session 6 (continued): Using Jalview & Multiple Sequence Alignments to investigate short linear motif biology [presentations and practicals] • Holger Dinkel and Toby Gibson - Session 6 (continued): Automated access of online tools using REST interfaces [presentations and practicals] • John "Scooter" Morris - From networks to structures and back again [Keynote Lecture]: • Lars Juhl Jensen - Session 7: STRING, networking, and PPIs [presentations and practicals] • John "Scooter" Morris and Nadezhda T. Doncheva - Session 8: Exploring PPI networks using Cytoscape [presentations and practicals]
Participation: Logistics information: A list of the information we provide concerning logistics for the course (access restricted) • Logistics mail Tuesday 26th August • Logistics mail Thursday 25th September
Course Sponsors: H3ABioNet Local Classrooms
Course objectives
 

Classroom applications

Registration for classrooms opens: Thu, 01/01/1970
Registration for classrooms closes: Thu, 01/01/1970
Link to classroom application form:
Notification date for successful classrooms: Thu, 01/01/1970
Maximum number of participants that may be accepted per classroom will be capped at 40

Participant applications

Registration for participants opens: Thu, 01/01/1970
Registration for participants closes: Thu, 01/01/1970
Participant registration link:
Syllabus and Tools

Workshop 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

Prerequisites

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


Course limitations

For more information, please visit

Training material availability

Training Materials Availability:

Training materials for this course are available as a single downloadable archive here: https://doi.org/10.25375/uct.19106720. Should you re-use any of these materials, please ensure that both the author/s of the material AND H3ABioNet are clearly credited.