Past Events

This week of workshops is a hybrid event, in-person at Leeds University and online via Zoom. This is a bring your own device event, so if you are coming in person please bring a laptop (eduroam will be available for internet access). When registering you can select which workshops you will be attending (if you do not want or are not able to attend the whole week).

Programme

Monday 25 September, 9:30 am - 5 pm: Python

Prerequisites: None

What is Python? What is a Jupyter notebook? How do I use them? Are they useful for biomodelling? This workshop will introduce you to Python and Jupyter notebooks. You will learn both how to write Python scripts and Jupyter notebooks. This workshop assumes no background knowledge of python or programming. The morning will focus on learning the basics of programming and Python. The afternoon will focus on using that knowledge to write Jupyter notebooks, perform data analysis, and to pull it all together to learn how to use these tools for biomodelling.

Morning: Python 0-60mph

A rapid 0-60mph session that goes from the absolute beginning of how to program in Python, through to concepts such as loops, if statements, functions and modules. Material covered will be similar to Beginning Python and Intermediate Python, picking out the key concepts that form the foundation for the workshops later this week.

Afternoon: Jupyter for Data Analysis and Biomodelling

An introduction to Jupyter notebooks and a chance to explore and learn how to run interactive Python for data analysis. This will teach how to process and visualise data using Python modules in Jupyter, e.g. using pandas and seaborn. Material covered will be similar to Introduction to Data Analysis in Python, picking out the key concepts useful for biomodelling. We will finish with a quick introduction to BioSimSpace. This is a python module that makes it easy to set up, run and analyse biomolecular simulations in Jupyter notebooks.

Tuesday 26 September, 9:30 am - 12:30 pm: Alchemical Free Energy Calculations with BioSimSpace

Prerequisites: Python, knowledge of atomistic simulations.

This workshop will introduce non-specialists to the use of alchemical free energy methods to compute binding free energies. Brief lectures will introduce the key concepts of relative and absolute binding free energy calculations. Hands-on exercises will illustrate how the BioSimSpace software library may be used to perform such calculations with a variety of software implementations.

Tuesday 26 September, 2 pm - 5 pm: Docking

Prerequisites: None

This workshop will introduce docking of ligands to ensembles of protein structures.

Wednesday 27 September, 9:30 am - 5 pm: Amber

Prerequisites: None

This workshop will introduce running molecular dynamics simulations with AMBER. Includes setting up proteins and quality control.

Thursday 28 September, 9:30 am - 12:30 pm: CodeEntropy

Prerequisites: Python, Running molecular dynamics simulations, some knowledge of thermodynamics would help.

This workshop will look at the theory and practice of using the CCPBioSim supported CodeEntropy to calculate the entropy of biological systems using the multiscale cell correlation method.

Thursday 28 September, 2 pm - 5 pm and

Friday 29 September, 9:30 am - 3 pm: Open Force Field

Prerequisites: Python, knowledge of atomistic simulations.

The Open Force Field Initiative (https://openforcefield.org) is a network of academic and industry researchers working together to advance science and infrastructure required for building the next generation of small molecule and biomolecular force fields. In this workshop, you will learn how to use some of the core Open Force Field software infrastructure for assigning and using force fields, including i) the Open Force Field Toolkit, for developing and applying force fields based on direct chemical perception, ii) Open Force Field Interchange, a project for manipulating and converting molecular mechanics force fields, including setting up protein-ligand simulations and iii) Open Force Field BespokeFit, a software package for deriving system-specific force field parameters for your molecule.

Registration

Deadline: 1 September 2023.

Cost £0 - this includes all the workshops and lunches (for in-person attendees); travel and accommodation are not provided

Please click here to register!