RECETOX — Research Center for Toxic Compounds in the Environment
RECETOX is engaged in research and education on managing the environmental and health risks associated with the chemicals around us. Based at Masaryk University in Brno, Czech Republic, we conduct cutting-edge environmental health research and develop diagnostic and preventive tools.
We study the human exposome — the totality of non-genetic factors influencing health over the life course — to understand how chemical exposures impact human health and to develop evidence-based solutions for risk assessment and policy-making.
Our work spans several key areas:
| Area | Description |
|---|---|
| Chemical Exposure Assessment | Mapping environmental chemicals and their transformations in human biospecimens |
| Biomarker Analysis | Targeted quantification of protein and chemical biomarkers using mass spectrometry |
| Exposomics & Metabolomics | High-resolution profiling of metabolites and environmental compounds |
| Data Services | Processing, analyzing, and interpreting complex spectrometric data |
| Population Studies | Cohort studies through CELSPAC and European collaborations |
RECETOX coordinates the EIRENE ERIC (European Research Infrastructure Consortium), a sustainable European infrastructure enabling advanced exposome research across Europe.
- Unite and harmonise European capacities for chemical-exposure and health studies
- Provide open-access infrastructure for developing new technologies
- Translate research results into public health actions
Learn more: https://eirene.eu
This organization hosts open-source software developed by RECETOX for environmental health research.
| Repository | Language | Description |
|---|---|---|
| recetox-aplcms | R | Feature detection from LC/MS spectra. Generates feature tables from mzML files with noise filtering and peak alignment. Available on Bioconda as r-recetox-aplcms. |
| epyraw | Python | Python wrapper for Thermo Fisher RawFileReader library. Read .raw mass spectrometry files in Python (Windows, Linux, macOS). Install via pip install epyraw. |
| mzmlr | R | Validate and read mzML files. Schema validation, spectrum/chromatogram extraction with lazy loading for memory efficiency. Available on CRAN. |
| MsBackendMzmlr | R | MsBackend implementation for the Spectra package using mzmlr. Memory-efficient on-disk access without requiring mzR. |
| recetox-xMSannotator | R | Custom adaptation of xMSannotator for annotated MS data processing. Complete rewrite following original program structure. |
| MSMetaEnhancer | Python | Tool for mass spectra metadata annotation via web services. |
| RIAssigner | Python | Retention index (RI) computation for GC-MS data. Supports .msp, .csv, and .tsv formats. |
| Repository | Language | Description |
|---|---|---|
| galaxytools | XML/Python/R | Galaxy tool wrappers for untargeted mass spectrometry analysis. Available at Galaxy UMSA. MIT licensed. |
| ei_spectra_predictions | - | Workflow for quantum chemistry-based prediction of electron ionization mass spectra for environmental chemicals. |
| Repository | Language | Description |
|---|---|---|
| fs-irods | Python | PyFilesystem2 extension for iRODS data management system. |
| specdatri_reporting | - | Scripts and GitHub Actions for gathering RECETOX impact metrics and reporting. |
| biobank-module | TypeScript | Biobank data handling module. Licensed under CC-BY-4.0. |
Our tools are distributed via multiple channels:
| Channel | Purpose |
|---|---|
| Bioconda / Biocontainers | Easy installation of R and Python packages |
| PyPI | Python packages (epyraw, RIAssigner) |
| CRAN | R packages (mzmlr) |
| Galaxy/UMSA | Web-based workflow execution at umsa.cerit-sc.cz |
| GitHub | Source code access and contribution |
RECETOX collaborates with:
- Academic institutions worldwide
- Industry partners for knowledge transfer
- Policy makers for evidence-based regulations
- European research infrastructure consortia
RECETOX Masaryk University, Kamenice 753/5, pavilion A29, 625 00 Brno, Czech Republic
- Website: https://www.recetox.muni.cz
- Email: See contact page
- EIRENE: https://eirene.eu
Most packages in this organization are released under permissive open-source licenses. See individual repositories for specific license terms.
This work is supported by:
- Masaryk University and the Ministry of Education, Youth and Sports of the Czech Republic
- European Union research and innovation programs
