StarPep software & database

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Overview

StarPepDB is an integrated graph database holding bioactive peptides and metadata from a large variety of biological data sources. The collected data from such heterogeneous data sources are cleaned, standardized, and merged so that it can be released into the proposed organized collection. In addition to this outcome, this graph database is embedded in the software application named starPep toolbox, which allows querying, filtering, visualizing, and analyzing the integrated data taking advantage of network-based representations.

Research topic

System requirements

  • Hardware
    • Memory (RAM): A minimum of 4 GB is required, but we recommend 8GB or more.
    • Processors: We recommend a multi-core processor due to the fact that the software has been implemented to enable parallel processing of computationally intensive tasks.
    • Hard Disk: a minimum of 500 MB of free space is required for the database.
  • Software
    • Java SE Runtime Environment 8 on the target system.

Download

 

LINK File size DownloadS
starPepDB_v45k – Integrated graph database 12.7 MB 159
starPep toolbox v0.8 – User Guide 3.6 MB 161
starPep toolbox v0.8.3 – ZIP distribution 209.0 MB 160
starPep toolbox v0.8.3 – Windows installer 128.7 MB 147
starPep toolbox v0.8.3 – Linux installer 128.2 MB 137
starPep toolbox v0.8.3 – Mac OS X installer 128.3 MB 159

Screenshots

Publications

  • Aguilera-Mendoza, L., Marrero-Ponce, Y., Beltran, J. A., Tellez Ibarra, R., Guillen-Ramirez, H. A., & Brizuela, C. A.. Graph-Based data integration from bioactive peptide databases of pharmaceutical interest: towards an organized collection enabling visual network analysis. Bioinformatics, 2019 Nov 1;35(22):4739-4747. https://doi.org/10.1093/bioinformatics/btz260
  • Aguilera-Mendoza, L., Marrero-Ponce, Y., Garcia-Jacas C. R., Chavez, E., Beltran, J. A., Guillen-Ramirez, H. A., & Brizuela, C. A. Automatic construction of similarity networks for visual graph mining of bioactive peptides: an unsupervised learning approach. (submitted paper), 01 2020.

FAQs

  1. Is starPep toolbox compatible with Java 11?
    starPep toolbox does not yet support Java 11, and it will not work with any version of Java > 8.
  2. How do I configure starPep toolbox to run on Java 8?
    If you have multiple Java versions installed on your system, please find the etc/starPep.conf file in the installed directory and configure the jdkhome=”/path/to/jdk” accordingly. The symbol “#” at the beginint of the line means that it is commented out, please remove it.

Contact

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