This repository contains all supporting scripts, notebooks, and structured input files used in the development and application of the SPECI and SPECI-AUTOCOPASI workflow, designed for automated chemical speciation and microkinetic modeling. It supports a Jupyter notebook-based interface and is tailored for reproducible research and extension by all other chemists.
To ensure full reproducibility of the environment used to run SPECI:
conda env create -f environment.ymlThis creates a new environment named speci-env (or as defined in the YAML file).
conda activate speci-envOnce the environment is activated:
jupyter notebookThen open and run the appropriate .ipynb file in the notebooks/ folder, or use the speci/ scripts directly depending on your workflow.
See read the doc for examples and detailed steps for how to use the different functions: https://speci.readthedocs.io/en/latest/index.html
The environment installs:
python >= 3.10jupyterlab/notebookpandas,numpy,matplotlibopenbabel(installed viaconda-forge, used for molecular handling)
See
environment.ymlfor full dependency list.
- 📁 Organizes
.ctinput files into clean example folders - 📊 Converts speciation data into structured
.csvformat - 🔎 Supports reaction sorting and automatic generation of input for downstream AUTOCOPASI use
- 🧠 Includes IIP (Intermediate Identification Protocol) implementation
This project uses Open Babel for chemical structure parsing and conversion. Open Babel is licensed under the GNU General Public License v2 (GPL-2.0). The Open Babel original code was not modified, it was called with the command line within this the SPECI script.
- You are free to use and modify this project, including Open Babel functionality, for research and educational purposes.
- If you redistribute modified versions of this repository (including scripts that directly use Open Babel), you must also:
- Make your full source code available
- Release it under GPLv2 or a compatible license
- Include the original Open Babel license text and attribution
This repository supports the methods presented in: Manting Mu et al., 2025 manuscript under preparation
If you use this software or any function originated from this software please cite it as below in your work.
Mu, M., Sommer, T., & García-Melchor, M. (2025). SPECI (Version 1.0.0) [Computer software]. https://doi.org/10.5281/zenodo.16823094
Manting Mu
For questions, bug reports, or suggestions, please open an issue, do not contact directly.
This project is distributed under the terms of the GNU General Public License v2.0, in compliance with Open Babel licensing. For full terms, see the LICENSE file or https://www.gnu.org/licenses/old-licenses/gpl-2.0.html.