# refineGEMs

> Python software package

**Wikidata**: [Q123561349](https://www.wikidata.org/wiki/Q123561349)  
**Source**: https://4ort.xyz/entity/refinegems

## Summary
refineGEMs is a Python software package designed for refining genome-scale metabolic models. It is an open-source tool hosted on GitHub under the MIT License, with its latest stable version being 1.4.2 released on January 10, 2024.

## Key Facts
- refineGEMs is a Python package for refining genome-scale metabolic models.
- The software is licensed under the MIT License.
- The latest stable version is 1.4.2, released on January 10, 2024.
- refineGEMs depends on several Python libraries including biopython, Pandas, NumPy, SQLAlchemy, and others.
- The source code is hosted on GitHub at https://github.com/draeger-lab/refinegems.
- refineGEMs is classified as both a Python package and software.
- The project has been actively updated with 10 stable releases since its initial version 1.0.0 in May 2023.

## FAQs
### Q: What is refineGEMs used for?
A: refineGEMs is used for refining genome-scale metabolic models, which are computational representations of an organism's metabolic capabilities.

### Q: What programming language is refineGEMs written in?
A: refineGEMs is written in Python, a general-purpose programming language.

### Q: Where can I find the source code for refineGEMs?
A: The source code for refineGEMs is available on GitHub at https://github.com/draeger-lab/refinegems.

## Why It Matters
refineGEMs plays a crucial role in the field of systems biology by providing researchers with a tool to refine and improve genome-scale metabolic models. These models are essential for understanding cellular metabolism and predicting how organisms respond to genetic and environmental changes. By offering a Python-based solution, refineGEMs makes this complex computational task more accessible to the scientific community. The software's ability to integrate with other popular Python libraries like Pandas and NumPy allows for seamless data manipulation and analysis, streamlining the workflow for researchers working with large metabolic datasets. As metabolic modeling becomes increasingly important in fields such as drug discovery, metabolic engineering, and personalized medicine, tools like refineGEMs contribute significantly to advancing our understanding of biological systems and their applications in various scientific and industrial contexts.

## Notable For
- Being a specialized Python package for refining genome-scale metabolic models
- Offering 10 stable releases within its first year of development, demonstrating active maintenance and improvement
- Integrating with a wide range of Python libraries, enhancing its functionality and ease of use
- Being open-source under the MIT License, promoting accessibility and collaboration in the scientific community
- Providing a GitHub repository for source code access and version control

## Body
### Overview
refineGEMs is a Python software package specifically designed for refining genome-scale metabolic models (GEMs). These models are comprehensive representations of an organism's metabolic network, used to predict cellular behavior and understand metabolic processes.

### Technical Specifications
- **Programming Language**: Python
- **License**: MIT License
- **Latest Stable Version**: 1.4.2 (released January 10, 2024)
- **Source Code Repository**: https://github.com/draeger-lab/refinegems

### Dependencies
refineGEMs relies on several Python libraries to function:
- biopython
- importlib-resources
- Pandas
- NumPy
- MarkupSafe
- sortedcontainers
- ratelimit
- SQLAlchemy
- OLS Client

### Development History
The project has seen rapid development since its initial release:
- Version 1.0.0: May 5, 2023
- Version 1.0.1: May 9, 2023
- Version 1.1.0: July 6, 2023
- Version 1.2.0: August 9, 2023
- Version 1.2.1: August 10, 2023
- Version 1.2.2: August 16, 2023
- Version 1.3.0: August 21, 2023
- Version 1.4.0: November 8, 2023
- Version 1.4.1: November 9, 2023
- Version 1.4.2: January 10, 2024

### Classification
refineGEMs is classified as:
- A Python package
- Software
- An open-source project

### Accessibility
The software is available through:
- PyPI (Python Package Index) under the project name "refineGEMs"
- GitHub repository for source code access and community contributions

### Significance in Research
refineGEMs contributes to the field of systems biology by providing a tool for improving the accuracy and reliability of genome-scale metabolic models. These models are crucial for various applications, including:
- Understanding cellular metabolism
- Predicting organism responses to genetic modifications
- Designing metabolic engineering strategies
- Advancing personalized medicine approaches

By offering a Python-based solution, refineGEMs integrates well with the existing scientific Python ecosystem, making it a valuable tool for researchers working with metabolic data and models.

## References

1. [Source](https://pypi.org/project/refineGEMs)
2. [Release 1.0.0. 2023](https://github.com/draeger-lab/refinegems/releases/tag/v1.0.0)
3. [Release 1.0.1. 2023](https://github.com/draeger-lab/refinegems/releases/tag/v1.0.1)
4. [Release 1.1.0. 2023](https://github.com/draeger-lab/refinegems/releases/tag/v1.1.0)
5. [Release 1.2.0. 2023](https://github.com/draeger-lab/refinegems/releases/tag/v1.2.0)
6. [Release 1.2.1. 2023](https://github.com/draeger-lab/refinegems/releases/tag/v1.2.1)
7. [Release 1.2.2. 2023](https://github.com/draeger-lab/refinegems/releases/tag/v1.2.2)
8. [Release 1.3.0. 2023](https://github.com/draeger-lab/refinegems/releases/tag/v1.3.0)
9. [Release 1.4.0. 2023](https://github.com/draeger-lab/refinegems/releases/tag/v1.4.0)
10. [Release 1.4.1. 2023](https://github.com/draeger-lab/refinegems/releases/tag/v1.4.1)
11. [Release 1.4.2. 2024](https://github.com/draeger-lab/refinegems/releases/tag/v1.4.2)
12. [Release 1.5.0. 2024](https://github.com/draeger-lab/refinegems/releases/tag/v1.5.0)