Workshop on BioExcel Software Tools

11 Feb 2026, 08:30 → 12 Feb 2026, 14:00 Europe/Ljubljana

This 1.5-day organized workshop within Adriatic Edition of Bioexcel offers a hands-on introduction to modern computational tools and workflows in biomolecular simulations. Participants (primarily from Italy, Croatia and Slovenia) will explore key software frameworks such as BioExcel Building Blocks (BioBB) for setting up reproducible molecular dynamics workflows, and gain practical experience with protein MD setup and automatic ligand parameterization. Further two topics of the workshop cover integrative modelling with HADDOCK, including a tutorial on antibody–antigen complex modelling and alchemical free energy calculations, followed by a PMX-based practical on ligand modifications.

 

Through a combination of lectures and guided tutorials, the workshop provides both theoretical grounding and practical skills best suited for PhD students and young researchers in computational biology and molecular modelling. 

 

Prerequisites: 

• working knowledge of Linux,
• basic familiarity with molecular modeling software.

 

Date: 11-12 February 2026

Location: Ljubljana, Slovenia

Venue: National Institute of Chemistry, Ljubljana, Slovenia

Room: Grand Lecture Hall, National Institute of Chemistry (Map)

Format: On-site

Fee: 70€ (to be paid after application is accepted; fee includes workshop participation, three coffee breaks and two lunches)

Topics: see Contribution list

 

Participation: 40 applicants will be selected for on-site participation. Applicants from Croatia, Italy and Slovenia will be prioritized for on-site participation. We can only accept participants from EuroHPC Joint Undertaking member institutions. In our selection, we will account for geographical and gender distribution. A letter of motivation needs to be handed in when registering (see form). Participants will need to bring a laptop for participating for the tutorial session and refresh their Linux skills. We recommend reviewing this introduction to the UNIX shell.

 

Registration starts:  5 November 2025

Registration extended to: 20 December 2025

Acceptance: 22 December 2025

Payment deadline: 10 February 2026

 

 

 

 

Travel_and_accomodation.pdf

Wednesday 11 February

08:30 → 09:15 Registration

09:15 → 09:30 Opening

09:30 → 10:30 Lecture: BioExcel Building Blocks (BioBB), a software library for interoperable biomolecular simulation workflows

Speaker: Adam Hospital

10:30 → 11:00 Break

11:00 → 13:00 Practicals: Protein MD setup & Automatic Ligand Parameterization using BioExcel Building Blocks

Speaker: Adam Hospital

13:00 → 14:00 Lunch

14:00 → 15:00 Lecture: Integrative modelling with HADDOCK

Speaker: Alexandre Bonvin

15:00 → 15:30 Break

15:30 → 17:00 Practical: HADDOCK tutorial on antibody-antigen modelling

Speaker: Alexandre Bonvin

19:30 → 22:00 Social dinner (optional, TBD)

Thursday 12 February

10:00 → 11:00 Lecture: Introduction to alchemical free energy calculations

Speaker: Bert de Groot

11:00 → 11:30 Break

11:30 → 13:00 Practical: Tutorial on ligand modifications with PMX

Speaker: Bert de Groot

13:00 → 14:00 Lunch