Scientific programming

• Write Python scripts to automate repetitive tasks
• Manipulate molecular structures with RDKit and Biopython
• Build a complete docking pipeline from preparation to analysis
• Analyse results with pandas and produce tables
• Generate automated reports

Day 1 — Foundations and preparation

Detailed program — Day 1

Time	Content	Type
09:00 – 09:30	Welcome, introduction of participants and objectives	Introduction
09:30 – 10:45	Python basics: variables, loops, functions, modules	Theory
10:45 – 11:00	Break
11:00 – 12:30	Handling files and paths, reading PDB files	Practical work
12:30 – 14:00	Lunch
14:00 – 15:30	Introduction to RDKit: reading and writing molecules	Practical work
15:30 – 15:45	Break
15:45 – 17:15	Structure manipulation with Biopython	Practical work
17:15 – 17:45	Day summary and questions	Wrap-up

Day 2 — Grid, docking and validation

Detailed program — Day 2

Time	Content	Type
09:00 – 10:00	Principles of a reproducible pipeline	Theory
10:00 – 10:45	Writing the preparation script	Practical work
10:45 – 11:00	Break
11:00 – 12:30	Automating batch execution	Practical work
12:30 – 14:00	Lunch
14:00 – 15:30	Parsing output files and extracting scores	Practical work
15:30 – 15:45	Break
15:45 – 16:45	Building result tables with pandas	Practical work
16:45 – 17:30	Day summary and questions	Wrap-up

Day 3 — Consolidation and project

Detailed program — Day 3

Time	Content	Type
09:00 – 10:30	Generating charts and summary tables	Practical work
10:30 – 10:45	Break
10:45 – 12:30	Automating report generation	Practical work
12:30 – 14:00	Lunch
14:00 – 15:30	Versioning with Git: basics	Practical work
15:30 – 15:45	Break
15:45 – 16:45	Documenting and sharing a script	Practical work
16:45 – 17:30	Final assessment and closing	Wrap-up