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index.qmd
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# Preface {.unnumbered}
Welcome to the _StarPep toolbox_ project GitHub repository. Here is where all the components of the project are developed, reviewed, and maintained.
## About the Software
[StarPep toolbox](http://mobiosd-hub.com/starpep/) is a software for studying the antimicrobial peptides' (AMPs) chemical space with molecular network-based representations and similarity searching models. This application aims to contribute to peptide drug repurposing, development, and optimization.
This tool was developed as a Java desktop application that integrates the functionalities of several open-source projects. The graphical user interface was built on top of the [NetBeans Platform](https://platform.netbeans.org/), using the Java SE Runtime Environment 8. The graph database structure was implemented with the [Neo4j](https://neo4j.com/) platform. Some visualization features and the calculation of network properties were based on [Gephi](https://gephi.org/). The sequence alignment algorithms were implemented using the [BioJava](https://biojava.org/) API.
The AMPs were collected from a large variety of biological data sources to be organized into an integrated graph database called
[starPepDB](https://doi.org/10.1093/bioinformatics/btz260), composed of 45.120 AMPs and their metadata. This integrated graph database is
embedded in StarPep toolbox to enable end-user querying, filtering, visualizing, and analyzing the AMPs taking advantage of network-based representations.
The main features of StarPep toolbox are listed below:
- **AMPs' chemical space filtering:** obtain a subset of AMPs from the StarPepDB using their metadata (function, target pathogen, biological origin, chemical modifications, original database, and cross-referenced entries to PDB, PubMed, and UniProt).
- **Molecular descriptors:** calculate molecular descriptors of the AMPs by applying statistical and aggregation operators on physicochemical amino acid properties (e.g., net charge, isoelectric point, molecular weight, etc.).
- **Network Science:** build different types of networks (metadata, chemical space, and half-space proximal) and calculate global/local properties, centrality metrics, communities, etc.
- **Similarity searching:** create multi-query similarity searching models that can lead to the repurposing of AMPs with novel functional activities.
## The Team
This project was developed by members and collaborators of the *Grupo de Medicina Molecular y Traslacional (MeM&T)* at Universidad San Francisco de Quito, which is lead by [Yovani Marrero-Ponce](https://orcid.org/0000-0003-2721-1142).
## Contributing
We encourage your participation as a contributor in this project considering your interest, availability, or skill requirements. Detailed information about ways of collaborating on this project can be found in our [contributing guidelines](https://github.com/Grupo-Medicina-Molecular-y-Traslacional/StarPep/blob/main/CONTRIBUTING.md).
## License
...
## Get in touch
If you want to report a problem or suggest an improvement, you should [open an issue](https://github.com/Grupo-Medicina-Molecular-y-Traslacional/StarPep/issues/new) at this Github repository, and we can follow your questions or suggestions. But, you can also contact Yovani by emailing [email protected].