CECAM analysing simulation data mini-workshop
Welcome to the website for this mini two day workshop which is part of an extended CECAM workshop at the Forschungszentrum Julich, Germany in October 2023.
As the use of biomolecular simulation grows, a corresponding boom in decentralised software development is taking place. This workshop focuses on Python-based tools for analysing biomolecular simulations and brings together software developers and users.
Unlike traditional workshops, there will be few talks; loosely drawing on the idea of an the majority of the workshop will be made up of tutorials and a HackDay. Participants will be encouraged to bring problems from their research and pitch their idea at the end of the first day. Teams will form to tackle the most popular ideas in a short HackDay, during which the software developers will be on hand to provide advice. No previous experience of a HackDay is required! We will make sure the teams are well balanced. Following a short presentation by each team, a prize will be award to the best project. The workshop will conclude with a short hands-on session where participants can tackle a problem of interest to them, taking advantage of the assembled expertise.
- Academics who develop and maintain open source python-based molecular simulation analysis frameworks
- Computational scientists, especially PhD students and postdoctoral researchers, who maybe use some of these frameworks but want to learn more, or who don’t know them but want to learn
- Demonstrate the power and utility of python-based frameworks for analysing molecular simulations
- Help attendees solve specific research-based analysis problems.
- Give the software developers feedback on how people use their python-based frameworks and what features would be useful
- Encourage more researchers to contribute to these open source frameworks
- Have fun (especially during the HackDay)
- Working knowledge of running bimolecular simulations (e.g. of proteins or DNA) using one of the main simulation codes (GROMACS/NAMD/AMBER/CHARMM/OpenMM/LAMMPS)
- Knowledge of the shell, basic python and preferably version control software (such as git). This mini-workshop is preceded by a Software Carpentry bootcamp that will teach these skills in an intensive two day course. If you don’t have these skills but wish to attend this workshop, please register for the bootcamp as well.
- A laptop. Installation instructions to follow. Generally Linux/Mac laptops are fine, Windows will be difficult.
- A problem from your research that you wish to solve. This has to fit with the theme of this workshop, i.e. analysing bimolecular simulation data. If you wish, you can pitch this problem for the HackDay.
To register for this mini-workshop (and any of the others in this extended workshop) please follow . The deadline is 27th July 2023. No registration fee required. After this date we will confirm whether you have been successful then you can arrange your own travel and accommodation.
- (ASU), main developer of
- (Max Planck Institute for Biophysical Chemistry), developer
- (Oxford University), contributor to
Wednesday 14 October 2023
- 0900 – 0930 Welcome and Introduction to the workshop
- 0930 – 1130 Talks by invited speakers
- 1130 – 1230 MDAnalysis tutorial
- 1230 – 1330 Lunch
- 1330 – 1400 MDAnalysis tutorial
- 1400 – 1530 pmx tutorial
- 1600 – 1700 Presentation of ideas for Hackday
- 1700 – 1730 Formation of Hackday teams
Thursday 15 October 2023
- 0900 – 1430 HackDay with experts on hand
- 1430 – 1500 Team presentations and Prize giving
- 1500 – 1630 Problem-solving / coding session
- 1630 – 1700 Close