Schedule¶
Workshop Hours
Time: 09:00–17:00 daily (UTC+03:00, Addis Ababa, Ethiopia)
Coffee Breaks: 10:30–10:45 AM & 3:30–3:45 PM
Lunch: 12:30–2:00 PM
Day 1 — Foundations¶
Monday, December 8, 2025
Morning Session (9:00 AM - 12:30 PM)¶
| Time | Topic | Type |
|---|---|---|
| 09:00–09:30 | Welcome and Workshop Overview | Plenary |
| • Welcoming remarks and Introduction • Training objectives and expected outcomes • Overview of the week's schedule and resources | ||
| 09:30–10:30 | Malaria-Climate Link | Lecture |
| • Climate-sensitive transmission system • Vector life cycle components • Parasite development and EIP • Host and environmental factors • Modeling approaches • Lesson: Malaria-Climate Link | ||
| 10:30–10:45 | ☕ Coffee Break | |
| 10:45–11:15 | Use Case: Amhara Region Study | Lecture |
| • Regional climate characteristics (Belg and Kiremt seasons) • Case study overview (2013-2019) • Climate anomalies and impacts (El Niño, La Niña) • Spatial patterns and hotspots • Policy implications for early warning • Lesson: Use Case | ||
| 11:15–12:00 | VECTRI Overview | Lecture |
| • Model history and development • What VECTRI is and is not • Model structure and capabilities • Inputs, outputs, and applications • Lesson: VECTRI Introduction | ||
| 12:00–12:30 | VECTRI Model Components | Lecture |
| • Larval cycle and breeding site hydrology • Larval mortality (crowding, flushing) • Gonotrophic cycle • Sporogonic cycle • Vector survival • Indoor temperatures and host community • Lesson: VECTRI Model Components |
Afternoon Session (2:00 PM - 5:00 PM)¶
| Time | Topic | Type |
|---|---|---|
| 14:00–15:00 | VECTRI Model Theory & Code | Lecture |
| • Model architecture and design • Code structure and organization • Key modules and functions • Lesson: VECTRI Model Theory & Code | ||
| 15:00–15:15 | ☕ Coffee Break | |
| 15:15–16:30 | VECTRI Core Equations | Hands-on |
| • Parameter definitions and physical meanings • Larval development equations • Survival probabilities and crowding effects • Gonotrophic and sporogonic cycle rates • Adult survival (Martens II model) • Pond dynamics and hydrology • Host-vector interactions • Transmission metrics (EIR, HBR) • Lesson: VECTRI Equations | ||
| 16:30–17:00 | Q&A and Review | Discussion |
| • Review of Day 1 concepts • Questions and clarifications • Preparation for Day 2 |
Day 2 — Setup and Python Basics¶
Tuesday, December 9, 2025
Morning Session (9:00 AM - 12:30 PM)¶
| Time | Topic | Type |
|---|---|---|
| 09:00–09:30 | Environment Setup | Hands-on |
| • System requirements and prerequisites • Installing dependencies • Configuring development environment • Lesson: Setup | ||
| 09:30–10:30 | Basic Linux Commands | Hands-on |
| • Navigation and file operations • Viewing and searching files • Permissions and environment variables • Text editing basics • Process management • Shell scripting introduction • Lesson: Basic Linux Commands | ||
| 10:30–10:45 | ☕ Coffee Break | |
| 10:45–11:30 | Python Setup and Basics | Hands-on |
| • Python installation and environment setup • Virtual environments • Package management (pip, conda) • Lesson: Python Setup | ||
| 11:30–12:30 | Python Fundamentals | Hands-on |
| • Python syntax and data types • Control structures (loops, conditionals) • Functions and modules • File I/O operations • Lesson: Python Basics |
Afternoon Session (2:00 PM - 5:00 PM)¶
| Time | Topic | Type |
|---|---|---|
| 14:00–15:30 | NumPy for Scientific Computing | Hands-on |
| • NumPy arrays and operations • Array indexing and slicing • Mathematical operations • Array manipulation and reshaping • Lesson: NumPy | ||
| 15:30–15:45 | ☕ Coffee Break | |
| 15:45–17:00 | Practice Exercises | Hands-on |
| • NumPy exercises and examples • Working with climate data arrays • Data manipulation practice • Q&A and troubleshooting |
Day 3 — Advanced Python and Climate Data¶
Wednesday, December 10, 2025
Morning Session (9:00 AM - 12:30 PM)¶
| Time | Topic | Type |
|---|---|---|
| 09:00–10:00 | Pandas for Data Analysis | Hands-on |
| • DataFrames and Series • Data manipulation and cleaning • Time series operations • Grouping and aggregation • Lesson: Pandas | ||
| 10:00–10:45 | Matplotlib for Visualization | Hands-on |
| • Creating plots and figures • Customizing visualizations • Subplots and layouts • Saving figures • Lesson: Matplotlib | ||
| 10:45–11:00 | ☕ Coffee Break | |
| 11:00–12:30 | Xarray for NetCDF Data | Hands-on |
| • Working with multidimensional arrays • NetCDF file handling • Coordinate systems and dimensions • Data selection and indexing • Lesson: Xarray |
Afternoon Session (2:00 PM - 5:00 PM)¶
| Time | Topic | Type |
|---|---|---|
| 14:00–14:45 | GeoPandas for Spatial Data | Hands-on |
| • Working with geospatial data • Shapefile operations • Spatial joins and overlays • Coordinate reference systems • Lesson: GeoPandas | ||
| 14:45–15:30 | Cartopy for Mapping | Hands-on |
| • Creating maps and projections • Adding geographic features • Plotting spatial data • Customizing map appearance • Lesson: Cartopy | ||
| 15:30–15:45 | ☕ Coffee Break | |
| 15:45–17:00 | Climate Data Access and Download | Lecture/Hands-on |
| • Overview of climate data sources • Accessing ERA5, CHIRPS, and other datasets • Data download workflows • Understanding data formats and structures • Lesson: Climate Data Downloading |
Day 4 — VECTRI Setup and Running¶
Thursday, December 11, 2025
Morning Session (9:00 AM - 12:30 PM)¶
| Time | Topic | Type |
|---|---|---|
| 09:00–09:45 | VECTRI Data Processing and Inspecting | Hands-on |
| • Preparing input data files • Data format requirements • Quality control checks • Inspecting data structure • Lesson: VECTRI Data Processing | ||
| 09:45–10:30 | VECTRI Command Line Interface | Hands-on |
| • Command-line execution syntax • Input file specification • Output file naming and structure • Common command options • Lesson: VECTRI Command Line Tutorial | ||
| 10:30–10:45 | ☕ Coffee Break | |
| 10:45–12:00 | VECTRI Model Configuration | Hands-on |
| • Model parameter files and configuration options • Setting simulation period (2013-2019) • Spin-up period considerations (1-2 years recommended) • Spatial domain setup • Time-step settings • Output variable selection • Lesson: VECTRI Configuring Parameters | ||
| 12:00–12:30 | Running VECTRI Simulations | Demo |
| • Executing model runs • Monitoring simulation progress • Common errors and troubleshooting • Computational requirements and runtime • Lesson: VECTRI Hands-On Simulations |
Afternoon Session (2:00 PM - 5:00 PM)¶
| Time | Topic | Type |
|---|---|---|
| 14:00–15:30 | Lab 4: Amhara Case Study Simulation | Hands-on |
| • Run VECTRI for Amhara region (2013-2019) • Monitor simulation and check for errors • Extract EIR, HBR, and case outputs • Create district-level aggregated time series • Calculate monthly and seasonal averages • Prepare data for validation analysis | ||
| 15:30–15:45 | ☕ Coffee Break | |
| 15:45–17:00 | VECTRI Output Analysis | Hands-on |
| • Understanding model outputs: EIR, HBR, Simulated cases • Extracting and processing output variables • Temporal patterns: daily, monthly, seasonal aggregation • Spatial patterns: district-level and gridded outputs • Lesson: VECTRI Output Analysis |
Day 5 — Advanced Analysis and Early Warning¶
Friday, December 12, 2025
Morning Session (9:00 AM - 12:30 PM)¶
| Time | Topic | Type |
|---|---|---|
| 09:00–10:30 | Advanced Output Analysis and Visualizations | Hands-on |
| • Creating comprehensive visualizations • Spatial maps and time series • Monthly and seasonal analysis • Anomaly detection • Climate-disease lag analysis • Correlation analysis • Lesson: VECTRI Analyzing Outputs & Visualizations | ||
| 10:30–10:45 | ☕ Coffee Break | |
| 10:45–12:30 | Parameter Sensitivity Analysis | Hands-on |
| • Understanding parameter sensitivity • Running sensitivity experiments • Analyzing parameter impacts • Identifying key parameters • Lesson: VECTRI Parameter Sensitivity |
Afternoon Session (2:00 PM - 5:00 PM)¶
| Time | Topic | Type |
|---|---|---|
| 14:00–15:30 | Spatial and Temporal Analysis | Hands-on |
| • Creating seasonal composites (Belg and Kiremt seasons) • Analyzing interannual variability (2013-2019) • Climate anomaly analysis: Wet vs. dry years, Warm vs. cool periods • Identifying high-risk districts and time periods • Western highlands vs. eastern lowlands comparison • Mapping transmission hotspots • Visualizing spatio-temporal patterns | ||
| 15:30–15:45 | ☕ Coffee Break | |
| 15:45–16:30 | Early Warning System Concepts | Lecture |
| • Components of malaria early warning systems • Integrating climate forecasts (seasonal predictions) • Lead time requirements for interventions • Defining thresholds and triggers: EIR percentiles, Case-exceedance thresholds • District-specific warning criteria • Communicating risk levels to stakeholders • Linking predictions to interventions (ITN distribution, IRS campaigns) | ||
| 16:30–16:45 | Participant Presentations (Optional) | Presentations |
| • Groups present their analyses and findings • Prototype early warning products • Lessons learned and challenges encountered • Discussion and feedback from trainers and peers | ||
| 16:45–17:00 | Workshop Closing | Plenary |
| • Summary of key learning outcomes • Future research and operational directions • Follow-up support and resources • Training evaluation and feedback • Certificate distribution • Closing remarks |
Lesson Distribution Summary¶
| Day | Theme | Lessons | Focus |
|---|---|---|---|
| Day 1 | Foundations | 6 lessons | Theory, VECTRI introduction, model components |
| Day 2 | Setup and Python Basics | 5 lessons | Environment setup, Linux, Python fundamentals, NumPy |
| Day 3 | Advanced Python and Climate Data | 6 lessons | Data processing libraries, climate data access |
| Day 4 | VECTRI Setup and Running | 5 lessons | VECTRI configuration, execution, output analysis |
| Day 5 | Advanced Analysis | 2 lessons | Advanced visualizations, parameter sensitivity |
Daily Structure
- Morning sessions: Theory, concepts, and hands-on lessons
- Afternoon sessions: Hands-on lab work and practice exercises
- Pair work encouraged: Participants work in pairs during lab sessions
- Q&A time: Built into each session for questions and discussions
- Lesson links: Each topic includes links to corresponding lesson materials
Materials Provided
- All training materials in digital format
- Code and example scripts via GitHub repository
- Sample datasets for practice exercises
- Reference documentation and guides
Preparation
- Complete all prerequisites before Day 1
- Bring personal laptop (Linux preferred, WSL2 for Windows)
- Test Python and Linux environment in advance
- Download required software (see Prerequisites page)
Contact & Support¶
Questions before the workshop?
Email: yonas.mersha14@gmail.com
Technical setup issues?
Check the Setup and Prerequisites pages
