Bioremediation Potential Profile — Scientific Web Application
BioRemPP is a scientific web service for bioremediation-oriented functional analysis. It integrates curated databases (BioRemPP, KEGG, HADEG, toxCSM) with international regulatory frameworks to assess functional potential for environmental remediation from KEGG Orthology (KO) annotations.
Live Application: https://bioinfo.imd.ufrn.br/biorempp/
docker run -p 8050:8050 biorempp/biorempp-web:latestOpen: http://localhost:8050
git clone https://github.com/BioRemPP/biorempp_web.git
cd biorempp_web
python -m venv venv && source venv/bin/activate
pip install -e ".[dev]"
python biorempp_app.pyFor detailed setup options, see Quickstart Guide.
Plain text file with KO identifiers organized by sample:
>Sample_1
K00001
K00002
>Sample_2
K00003
K00004
Limits: 100 samples, 500,000 KOs, 5 MB max file size.
Full specification: Input Format
BioRemPP provides 56 use cases across 8 thematic modules:
| Module | Focus |
|---|---|
| 1 | Comparative assessment (databases, samples, regulatory) |
| 2 | Exploratory analysis (functional potential ranking) |
| 3 | System structure (clustering, similarity, co-occurrence) |
| 4 | Functional and genetic profiling |
| 5 | Modeling interactions (samples, genes, compounds) |
| 6 | Hierarchical and flow-based functional analysis |
| 7 | Toxicological risk assessment |
| 8 | Assembly of functional consortia |
Complete catalog: Use Cases
| Database | Focus |
|---|---|
| BioRemPP | Compound-enzyme-agency mapping for bioremediation |
| KEGG | Xenobiotic metabolism and degradation pathways |
| HADEG | Aerobic hydrocarbon degradation enzymes |
| toxCSM | Computational toxicity predictions (31 endpoints) |
Regulatory frameworks: IARC, EPA, ATSDR, WFD, PSL, EPC, CONAMA.
Details: Data Sources | Database Schemas
| Section | Description |
|---|---|
| Getting Started | Quickstart, input format, example datasets |
| User Guide | Results interpretation, downloads, troubleshooting |
| Use Cases | Complete analytical catalog (56 use cases) |
| Methods | Data sources, mapping strategy, limitations |
| Configuration | Environment variables, Docker, deployment |
| API Reference | Technical documentation |
When using BioRemPP, please cite both the web service and the database:
Web Service:
Lima Silva, D. F., & Fassarella Agnez-Lima, L. (2026). BioRemPP: A Compound-Centric Web Server for Bioremediation Potential Profiling (1.0.0). Zenodo. https://doi.org/10.5281/zenodo.18919675
Database:
Lima Silva, D. F., & Fassarella Agnez-Lima, L. (2025–2026). BioRemPP Database: A Curated Compound-Centric Resource for Bioremediation Potential Profiling (1.0.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.18905195
Full citation guidelines: How to Cite
- Source Code: Apache License 2.0
- Database Content: CC BY 4.0
- Third-party: KEGG (academic license), HADEG (open access), toxCSM (open access)
Details: License | Terms of Use
BioRemPP is a research tool for hypothesis generation. Results represent genetic potential, not confirmed biological activity. Not intended for clinical, regulatory, or remediation decisions without experimental validation.
Complete limitations: Limitations and Scope
- Documentation: biorempp-web.readthedocs.io
- Issues: GitHub Issues
- Email: biorempp@gmail.com
BioRemPP v1.0.0 | Documentation | GitHub