Course overview: EMBO Practical Course on Computational analysis of protein-protein interactions: From sequences to networks.
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 / in person
Dates for the workshop: 28th September – 3rd October 2014
Venue of workshop: UCT, Cape Town, South Africa
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]
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 Program:
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SUNDAY 28TH SEPTEMBER |
Participant arrival and check in at hotel |
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20.00-21.00 |
Dinner: Little Scotia guest house |
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MONDAY 29TH SEPTEMBER |
09.00-09.15 |
Introduction to the course: Organisers |
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09.15-10.00 |
1:1 Introduction round: all participants |
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10.00-10.30 |
Session 1: Introduction to bioinformatics, protein modules and sequence alignment [practicals and presentations]: Aidan Budd |
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10.30-11.00 |
Coffee break |
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11.00-12.00 |
Session 1 (continued): Introduction to bioinformatics, protein modules and sequence alignment [practicals and presentations]: Aidan Budd |
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12.00-13.00 |
Lunch |
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13.00-14.00 |
Modular protein architecture and construction of cell regulatory systems [Keynote Lecture]: Toby Gibson |
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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 |
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15.30-16.00 |
Coffee break |
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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 |
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17.00-17.30 |
Modelling interactions of the HIV gp120 protein [presentation]: Natasha Wood |
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17.30-18.30 |
Free practical session: trainees working with their own data |
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18.30 |
Shuttle pickup from UCT/Bernard Fuller Building to Little Scotia |
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19.00-21.00 |
Dinner: Little Scotia guest house |
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TUESDAY 30TH SEPTEMBER |
09.00-10.00 |
Session 2b: Introduction to protein structure with Chimera [practicals and presentations]: Scooter Morris and Aidan Budd |
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10.00-10.30 |
Session 3: The freaks of protein sequence (I): Repeats [practicals and presentations]: Miguel Andrade |
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10.30-11.00 |
Coffee break |
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11.00-12.00 |
Session 3 (continued): The freaks of protein sequence (II): Biased regions [practicals and presentations]: Miguel Andrade |
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12.00-13.00 |
Lunch |
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13.00-14.00 |
Medical data mining: linking diseases, drugs, and adverse reactions [Keynote Lecture]: Lars Juhl Jensen |
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14.00-15.30 |
Session 4: Protein families and domains, including repeats (PFAM, SMART, etc.) [practicals and presentations]: Marco Punta |
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15.30-16.00 |
Coffee break |
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16.00-17.00 |
Session 4 (continued): Protein families and domains, including repeats (PFAM, SMART, etc.) [practicals and presentations]: Marco Punta |
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17.00-17.30 |
A web-based protein interaction network visualizer [presentation]: Gustavo Galazar |
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17.30-19.00 |
DAS Game: all participants lead by Gustavo Salazar and Natasha Wood |
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19.00 |
Shuttle pickup from UCT/Bernard Fuller Building to Down South Restaurant, Rondebosch |
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19.30-21.00 |
Dinner: Down South Restaurant, Rondebosch (including one glass of wine each) |
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WEDNESDAY 1ST OCTOBER |
09.00-10.30 |
Session 5: Biology and prediction of intrinsically unstructured peptide regions [practicals and presentations]: Zsuzsanna Dosztányi |
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10.30-11.00 |
Coffee break |
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11.00-12.30 |
Session 5 (continued): Biology and prediction of intrinsically unstructured peptide regions [practicals and presentations]: Zsuzsanna Dosztányi |
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12.30-15.00 |
Lunch AND poster session |
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15.00-16.00 |
Session 6: Linear motif biology, prediction, and cooperativity in cellular signalling [presentations and practicals]: Holger Dinkel and Toby Gibson |
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16.00-16.30 |
Coffee break |
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16.30-17.30 |
Session 6 (continued): Linear motif biology, prediction, and cooperativity in cellular signalling [presentations and practicals]: Holger Dinkel and Toby Gibson |
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17.30-18.30 |
Dinner: Pizzas ordered into the venue i.e. UCT Health Science Campus (including wine) |
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18.30-21.00 |
Networking event (Cape Unseminar in Bioinformatics): all course participants and local bioinformaticians |
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21.15 |
Shuttle pickup from UCT/Bernard Fuller Building to Little Scotia |
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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 |
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10.30-11.00 |
Coffee break |
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11.00-12.00 |
Session 6 (continued): Automated access of online tools using REST interfaces [presentations and practicals]: Holger Dinkel and Toby Gibson |
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12.00-13.00 |
Lunch |
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13.00-14.00 |
From networks to structures and back again [Keynote Lecture]: John "Scooter" Morris |
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14.00-15.30 |
Session 7: STRING, networking, and PPIs [presentations and practicals]: Lars Juhl Jensen |
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15.30-16.00 |
Coffee break |
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16.00-17.30 |
Session 7 (continued): STRING, networking, and PPIs [presentations and practicals]: Lars Juhl Jensen |
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17.45 |
Shuttle pickup from UCT/Bernard Fuller Building to Little Scotia |
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18.45 |
Shuttle pickup from Little Scotia to Bihari Restaurant, Newlands |
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19.00-21.00 |
Gala Dinner: Bihari Restaurant, Newlands (including a glass of wine) |
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21.15 |
Shuttle pickup from Bihari Restaurant to Little Scotia |
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FRIDAY 3RD OCTOBER |
09.00-10.30 |
Session 8: Exploring PPI networks using Cytoscape [presentations and practicals]: John "Scooter" Morris and Nadezhda T. Doncheva |
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10.30-11.00 |
Coffee break |
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11.00-12.30 |
Session 8 (continued): Exploring PPI networks using Cytoscape [presentations and practicals]: John "Scooter" Morris and Nadezhda T. Doncheva |
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12.30-14.00 |
Lunch |
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14.00-15.30 |
Session 8 (continued):Exploring PPI networks using Cytoscape [presentations and practicals]: John "Scooter" Morris and Nadezhda T. Doncheva |
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15.30-16.00 |
Coffee break |
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16.00-17.00 |
Session 8 (continued): Exploring PPI networks using Cytoscape [presentations and practicals]: John "Scooter" Morris and Nadezhda T. Doncheva |
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17.00-17.30 |
Wrap up and final Q and A session: all participants |
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17.45 |
Shuttle pickup from UCT/Bernard Fuller Building to Little Scotia |
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18.15-20.00 |
Dinner: Little Scotia guest house |
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SATURDAY 4TH OCTOBER |
Participant departure and check out of hotel |
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.
