Molecular Dynamics and Analysis using BRIDGE

Thursday 6 Dec 2018, 08:00 → 17:15 Africa/Johannesburg

Century City Convention Centre

Molecular Dynamics and analysis can be complicated for novitiates and researchers from neighbouring disciplines. Building upon the Galaxy Project platform, BRIDGE (Biomolecular Reaction & Interaction Dynamics Global Environment) is a web application that provides the ability to get started running molecular dynamics and analyses using curated workflows.

Target Audience: Are you keen to learn how to run a protein simulation using Molecular Dynamics?Computational chemists, biologists, protein scientists, crystallographers and anyone interested in running and analysing molecular dynamics simulations who is not familiar with the command line.

Prerequisites: Basic understanding of chemistry. A basic understanding of or keen interest in molecular dynamics.

Special requirements: Bring a laptop. Have access to the CHPC cluster. Register with BRIDGE. Install molecular viewer e.g. VMD.

README - BRIDGE Workshop

08:00 → 09:00 Registration

09:00 → 09:15 BRIDGE Overview: why MD and the value of this platform

why MD and the value of this platform

09:15 → 09:30 Logging into the platform

09:30 → 09:50 Setup of an example protein (cellulase) with CHARMM-GUI

09:50 → 10:05 Uploading datasets to BRIDGE

10:05 → 10:30 Running the MD workflow (Hands on)

10:30 → 11:00 Morning break

11:00 → 11:20 Workflows in BRIDGE: Explanation of the steps of an MD workflow

11:20 → 11:40 Creating your own history and workflow

11:40 → 12:00 Analysis: Run an analysis workflow and analyse data

12:00 → 12:15 Sharing data with collaborators

12:15 → 12:30 Analysis: complete the workflow (Hands on)

12:30 → 13:30 Lunch

13:30 → 13:50 Resources and Support for Galaxy and BRIDGE

13:50 → 15:00 Bring your own data – let’s see if this can work for you (Interactive)

15:00 → 15:30 Afternoon break

15:30 → 17:00 Q&A and testing with your own data sets (Interactive)

17:00 → 17:05 End of Workshop