VAXINTAIC provides an end-to-end system that transforms raw viral sequence data into ranked vaccine candidate insights through:
- Sequence acquisition and preprocessing
- Multiple sequence alignment and diversity analysis
- Epitope prediction and ranking
- Synthetic construct simulation (mRNA-level)
- Machine learning-based efficacy prediction
- Interactive dashboard visualization
External Sequence Data
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[01] Sequence Fetching
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[02] Alignment & Processing
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[03] Epitope Prediction
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[04] Epitope Ranking
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[05] Construct Design
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[06] Structural Modeling
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[07] AI Efficacy Prediction
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[08] Reports & Storage
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[Dashboard Visualization]
vaxintaic/
│
├── pipeline/ # Core computational pipeline
│ ├── 01_fetch_sequences.py
│ ├── 02_align_sequences.py
│ ├── 03_epitope_prediction.py
│ ├── 04_epitope_ranking.py
│ ├── 05_mrna_design.py
│ ├── 06_nanoparticle_model.py
│ ├── 07_efficacy_predictor.py
│ ├── 08_generate_report.py
│ ├── 09_diversity_analysis.py
│ ├── 10_immunogenicity_score.py
│ ├── 11_codon_adaptation.py
│ ├── 12_efficacy_predictor_v2.py
│ └── 13_generate_advanced_report.py
│
├── dashboard/ # Streamlit dashboard
│ ├── app.py
│ ├── part1_overview.py
│ ├── part2_epitope.py
│ ├── part3_diversity.py
│ └── part4_reports.py
│
├── data/ # Generated outputs
│ ├── sequences/
│ ├── alignments/
│ ├── epitopes/
│ ├── candidates/
│ ├── mrna/
│ ├── models/
│ ├── analysis/
│ └── reports/
│
├── config/ # Configuration files
├── docs/ # Images/screenshots
│
├── run_vaxintaic_full.py # Master pipeline controller
├── requirements.txt
├── README.md
└── .gitignore
git clone https://github.com/YOUR_USERNAME/vaxintaic.git
cd vaxintaicpython3 -m venv venv
source venv/bin/activatepip install -r requirements.txtpython run_vaxintaic_full.pyThis executes all pipeline stages sequentially:
- Sequence fetching
- Alignment
- Epitope prediction
- Ranking
- Construct design
- ML prediction
- Report generation
streamlit run dashboard/app.pyOpen in browser:
http://localhost:8501
- 🧭 Pipeline overview and metrics
- 📈 Construct performance analytics
- 🧫 Epitope visualization
- 🧬 Diversity and alignment insights
- 📄 Report and log viewer
- 🧠 JSON construct intelligence explorer
nano pipeline/03_epitope_prediction.pyKey logic:
- Sliding window peptide scanning
- Immunogenic scoring
nano pipeline/05_mrna_design.pyKey logic:
- Construct assembly
- Codon optimization (CAI, GC%)
nano pipeline/07_efficacy_predictor.pyFeatures used:
- GC content
- Codon adaptation index
- Stability index
- Immunogenicity
VAXINTAIC uses MySQL for structured storage.
Tracks pipeline runs:
timestamp_utc
num_sequences
construct_count
duration_secStores construct-level intelligence:
construct_id
prrsv_type
timestamp_utc
data (JSON)Pipeline Scripts
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CSV / FASTA Outputs
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MySQL Database
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Streamlit Dashboard
streamlit run dashboard/app.py --server.port 8090http://YOUR_SERVER_IP:8090https://prrsv-vaccine.aiconceptlimited.com.ng/
- Python
- Pandas / NumPy
- BioPython
- Scikit-learn
- Streamlit
- Plotly
- MySQL
This platform is intended for computational research, simulation, and educational purposes only.
Abubakar VAXINTAIC — AI for Vaccine Intelligence