Mentoring and Career Track Scheme (MCTS)
A hands-on introduction to Python programming, data analysis, and computational biology for wet lab biologists.
This workshop aims to:
- Broaden data analysis understanding in the institute
- Demystify computational methods
- Explain the logic behind methods, not just how to run tools
This is an introductory boost — not a comprehensive training program. The goal is to get you started, familiarize you with code, and help you understand the concepts behind common analyses.
You'll learn how to code by coding yourself, not in the classroom.
Week 1: Data Analysis Fundamentals (CGLab)
Format: 2-hour sessions daily, Monday–Thursday
Level: Complete beginners
Dates: April 27 – April 30
Time: 10:00–12:00
Format: 2-hour sessions daily, Monday–Thursday
Level: Complete beginners
Dates: May 4 – May 7
Time: 10:00–12:00
| Date | Room | Coordination | Topic | Material |
|---|---|---|---|---|
| Mon 27/4 — Day 1 | Orfanoudakis | Alexandros Pittis | Python Fundamentals | day1 |
| Tue 28/4 — Day 2 | Orfanoudakis | Alexandros Pittis | Plotting & Data Exploration | day2 |
| Wed 29/4 — Day 3 | Pagiatakis | Alexandros Pittis | Statistics & P-values | day3 |
| Thu 30/4 — Day 4 | Pagiatakis | Alexandros Pittis | Enrichment & Dimensionality Reduction | day4 |
🪵🔥 Thursday, April 30 (after Day 4, time TBD): BBQ 🍖🍗🥩🦴/🐙🦞🦪🦐 — everyone welcome!
| Date | Room | Coordination | Topic | Material |
|---|---|---|---|---|
| Mon 4/5 — Day 5 | Pagiatakis | Christos Andronis / Electra Tsaglioti (Bioinformatics Unit) | Bulk RNA-seq analysis | link |
| Tue 5/5 — Day 6 | Pagiatakis | Ethan Baird / Vaso Theodorou (Delidakis lab) | Single-cell RNA-seq analysis | link |
| Wed 6/5 — Day 7 | Pagiatakis | Orsalia Hazapis (Talianidis lab) | ATAC-seq | link |
| Thu 7/5 — Day 8 | Pagiatakis | Instructors | Bring your data |
Links are the same every day for each week.
Week 1 (Apr 27–30, 10:00 Athens)
Join Meeting
· Meeting ID: 850 1506 1426
· Passcode: 320451
Week 2 (May 4–7, 10:00 Athens)
Join Meeting
· Meeting ID: 824 1539 3379
· Passcode: 038331
- Maria Diamantaki — Froudarakis lab
- Yiannis Pyrris — CGLab
- Amalia Kapsetaki — CGLab
- Iordana Zirdeli — CGLab
- Kostis Paterakis — CGLab
- Athena Marouga — CGLab
- Eva Delidaki — CGLab
- Melina Doudali — CGLab
- Asterios Tsiftsis — CGLab
- Dimitris Papageorgiou — Pavlopoulos lab
- Ioannis Giannoulakis - Talianidis lab
- Despoina Georgiadou - Bioinformatics MSc programme
- Panagiota Meramveliotaki - Bioinformatics MSc programme
- No programming experience required
- Laptop with admin rights for software installation
- Install Python and tools — see docs/SETUP.md
- Go through the preparation notebooks — see precourse/ (Python basics, and an R introduction for Week 2)
All materials are in this repository:
- week1/ — Jupyter notebooks for Week 1 (4 days)
- precourse/ — Preparation notebooks (Python and R basics)
- data/ — Datasets used throughout the course
- docs/ — Setup instructions
Recommended: Python + Jupyter (VSCode optional) (see docs/SETUP.md)
Python packages (Week 1): numpy, pandas, matplotlib, seaborn, scipy, scikit-learn, umap-learn
R (Week 2): Some Week 2 sessions use R. Install R and RStudio Desktop — see docs/SETUP.md Step 5 for details.
Alternatives: Google Colab (browser-based, no installation) or IMBB JupyterHub (access provided during course, Python and R pre-installed).
- IMBB-FORTH lab members (MSc students, PhD students, Postdocs, Technicians) with no programming experience
Expected participants: Up to 40
Coordination: CGLab (Alexandros Pittis)
Contributing labs (tentative):
- Bioinformatics Unit (Andronis)
- Genome Integrity/Genomics Facility (Lavigne)
- Stem Cells (Delidakis)
- Chromatin & Cancer Epigenetics (Talianidis)
Python
- Python Graph Gallery — the biggest collection of Python chart examples
- Python lessons (in Greek) by Alexandros Kanterakis (ICS-FORTH)
- Pandas getting started tutorials — official pandas introduction
- Seaborn documentation
Genomics
- RNA-seq analysis with DESeq2 — the standard bulk RNA-seq tutorial
- Scanpy tutorials — single-cell RNA-seq in Python
- Single-cell best practices — comprehensive single-cell analysis guide
Course Coordinator: Alexandros Pittis alexandros.pittis@gmail.com · Comparative Genomics Lab @ IMBB-FORTH, Heraklion, Crete
This course will improve with your input. After each session, we welcome feedback on pace, clarity, and content.