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BioRemPP Web Service

Open-Access Scientific Platform for Bioremediation Functional Analysis

Version: 1.0.9-beta | Last Updated: 2026-03-07

Start Here

  • Quickstart Guide

    Get started in 3–5 minutes with a step-by-step tutorial

    Quickstart

  • Input Format

    Learn how to prepare your KO annotations by sample

    Input Format

  • Use Cases

    Explore 8 modules with 56 analytical use cases

    Use Cases Index

  • Methods Overview

    Understand the scientific methodology behind BioRemPP

    Methods

Additional Resources

Resource Description
Validation & Limitations Understanding scope and constraints
How to Cite Citation guidelines for publications
Terms of Use Usage policies and licensing
Contact Support and institutional contact

For Scientific Reviewers

If you are evaluating BioRemPP as a scientific web server, start with Use Cases → Module 1 (UC 1.1) and Methods Overview.

Overview

BioRemPP (Bioremediation Potential Profile) is an open-access scientific web service for exploratory, integrative functional analysis of bioremediation potential based on KEGG Orthology (KO) identifiers.

The platform integrates four curated databases with seven international regulatory frameworks to enable comprehensive assessment of functional capabilities relevant to environmental remediation contexts.

Key Features

  • Multi-database integration — BioRemPP, KEGG, HADEG, toxCSM
  • 56 analytical use cases across 8 specialized modules
  • 7 regulatory frameworks — IARC, EPA, ATSDR, WFD, PSL, EPC, CONAMA
  • Exportable results — CSV, Excel, JSON formats
  • No registration required — temporary cache with Job ID resume workflow

Research Tool Disclaimer

BioRemPP is designed for exploratory research and hypothesis generation. It is not validated for clinical diagnostics, regulatory compliance, or direct remediation decisions without independent experimental validation.

Target Audience

BioRemPP is designed for:

  • Bioinformatics researchers developing analytical pipelines for metagenomics and functional annotation
  • Environmental biologists conducting functional genomics research on bioremediation
  • Scientific reviewers evaluating integrative database platforms and bioremediation workflows
  • Graduate students exploring compound-centric functional analysis approaches

Inputs and Outputs

Inputs

BioRemPP accepts KEGG Orthology (KO) identifiers organized by sample.

Requirement Details
Format Plain text (.txt) with FASTA-like headers (>SampleName)
Content KO identifiers (one per line under each sample header)
Size limit 5 MB maximum
Preprocessing KO annotations must be generated upstream (eggNOG, KEGG KAAS, KOfamScan)

BioRemPP does not perform

Sequence assembly, gene calling, or functional annotation. Users must generate KO identifiers before submission.

Outputs

Category Description
Integrated tables Merged annotations from BioRemPP, HADEG, KEGG, and toxCSM
Interactive visualizations 8 modules with 56 Plotly-based analytical charts
Downloadable data CSV, Excel, and JSON export formats

Integrated Resources

  • BioRemPP Database v1.0

    Curated compound-centric mappings linking KO → genes → compounds → regulatory context

  • KEGG Database

    Metabolic pathway annotations and functional definitions (KEGG)

  • HADEG Database

    Hydrocarbon and xenobiotic degradation pathways (GitHub)

  • toxCSM Database

    Computational toxicity predictions with 50+ endpoints (toxCSM)

Regulatory Frameworks

Agency Scope
IARC International Agency for Research on Cancer
EPA United States Environmental Protection Agency
ATSDR Agency for Toxic Substances and Disease Registry
WFD Water Framework Directive (EU)
PSL Priority Substances List (Canada)
EPC European Parliament Commission
CONAMA National Environmental Council (Brazil)

High-Level Workflow

flowchart LR
    A[Upload KO Data] --> B[Validation]
    B --> C[Database Integration]
    C --> D[Modular Analysis]
    D --> E[Visualization & Export]
  1. Data submission — Upload plain-text files with KO identifiers by sample
  2. Validation — Format compliance, KO validation, structural constraints
  3. Database integration — Cascading joins across BioRemPP, KEGG, HADEG, toxCSM
  4. Modular analysis — Execute 56 use cases across 8 analytical modules
  5. Results — Interactive charts, tables, and downloadable exports

Data Policy & Privacy

Policy Implementation
No accounts No registration, authentication, or profiles
Temporary retention Data removed after limited retention window (default 4 hours)
No persistent storage Files processed in-memory only
No data sharing Uploaded content never shared externally
:material-https: Secure transport HTTPS/TLS encryption on production

Logging Policy

Only technical metadata is logged (IP, user-agent, errors). Uploaded content is never logged.

Reproducibility & Availability

Resource Link
Web Service https://bioinfo.imd.ufrn.br/biorempp/
Source Code github.com/BioRemPP/biorempp_web
Docker Image Available for local/institutional deployment
License Apache-2.0 (code) / CC BY 4.0 (database)

Limitations & Scope

Important Considerations

  • Research-only — Not validated for clinical, regulatory, or operational decisions
  • Database-dependent — Results constrained by integrated database coverage
  • KO-level resolution — Does not capture isoform or substrate specificity
  • Computational toxicity — toxCSM predictions require experimental validation
  • Presence/absence only — No quantitative expression or metabolic flux data

Citation

Web Service

BioRemPP Development Team (2026). BioRemPP: Bioremediation Potential Profile 
Web Service (v1.0.9-beta). Available at: https://bioinfo.imd.ufrn.br/biorempp/
BibTeX Format 
@misc{biorempp2025,
  title={BioRemPP: Bioremediation Potential Profile Web Service},
  author={BioRemPP Development Team},
  year={2025},
  url={https://bioinfo.imd.ufrn.br/biorempp/},
  note={Version 1.0.9-beta}
}

License Summary

Component License
Database Content CC BY 4.0
Source Code Apache 2.0
KEGG Academic free; commercial requires license
HADEG Open access (GitHub)
toxCSM Open access for academic research

Contact & Support

Get Help

Channel Details
Email biorempp@gmail.com
Bug Reports GitHub Issues
Response Time ~5 business days
Bug Report Template

When reporting issues, please include:

  1. BioRemPP version (from footer)
  2. Browser type and version
  3. Operating system
  4. Steps to reproduce
  5. Expected vs. observed behavior
  6. Example input file (if applicable)
  7. Screenshots or error messages

Acknowledgments

Institutional Support:

  • Federal University of Rio Grande do Norte (UFRN)
  • Graduate Program in Bioinformatics (PPg-Bioinfo)
  • Instituto Metrópole Digital (IMD)
  • Laboratory of Molecular Biology and Genomics (LBMG–UFRN)

Funding: CNPq, CAPES

We acknowledge the developers of KEGG, HADEG, toxCSM, and the open-source communities behind Python, Dash, Plotly, and Pandas.