The H3ABioNet recently co-organised a Scientific Communication Workshop from the 26th to the 27th of April 2021.
     
    The links below are the video recordings and resources that were used for the two days.
     

    Day 1 of Workshop: https://youtu.be/U2el7Zcyb-Y

    Day 2 of Workshop: https://youtu.be/XT8Lx8lR6-0

     

    Resources:

     
    1. Writing an effective abstract: Abstract document
    2. Communicating science exercise: Exercise document
    3. How to write good research manuscript: Manuscript document
    4. From trainee to tenure-track: Ten tips document
    5. How to give a “good” oral presentation: Oral presentation guidelines
    6. How to read, summarize, and critique a research article: Article critique document
    7. Opportunities for After Your Studies: Identifying Transferable Skills
    8. Personal Development Transferable Skills Profile and Action Plan: Transferable Skills Profile
    9. Transferable skills for a competitive edge: Transferable skills document


    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:

    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

     

    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.


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