BioUML

Last updated
BioUML
Original author(s) Fedor A. Kolpakov
Developer(s) BioUML team
Initial release2002;22 years ago (2002)
Stable release
v. 2023.3 / September 2023;10 months ago (2023-09)
Written inJava
Available inEnglish
Type Bioinformatics
Website https://www.biouml.org/

BioUML (Biological Universal Modeling Language) [1] [2] is an open-source web-based software platform written in Java with support for JavaScript and R. The main field is systems biology and data analysis - visualization of biological data, modeling of biological systems, as well as access to bioinformatics databases [2] [3] . It was originally developed by Fedor Kolpakov in 2002 in collaboration between Biosoft.Ru and the Institute of Systems Biology in Novosibirsk, Russia. [3]

Contents

Available versions

The current release of BioUML is version 2023.3 released in September 2023. [4]

BioUML Server offers access to data and analysis methods installed server-side for BioUML clients (workbench and web edition) over the Internet.

BioUML Workbench is a Java application that can work standalone or as "thick client" for the BioUML server edition.

BioUML Web Edition is a web browser based "thin client" for the BioUML server edition and provides most of the functionality of the BioUML workbench. It utilizes AJAX and HTML5 <canvas> technology for interactive data editing and visual modeling.

The platform has been developed continuously since 2002 [4] and offers data analysis and visualizations for scientists involved in complex molecular biology research. The system allows for the formalized description of biological systems structure and function including tools required to make discoveries related to genomics, proteomics, transcriptomics and metabolomics. The BioUML platform is built in a modular architecture which has allowed for the relatively simple addition of new tools. This has allowed the integration of many 3rd party tools into the platform over the 7 years it has been available.[ citation needed ]

Application and usage

BioUML was used for visualization of data from Cyclonet's integrated database on cell cycle regulation and carcinogenesis in 2007 [5]

Next-generation sequencing (NGS) and other high throughput methods create huge data sets (called "big data") in the region of 100 terabytes upwards. BioUML can disseminate, analyze and produce visualizations and simulations. It allows for parameter fitting and supports several analysis techniques required to deal with large amounts of raw data. The management of large volumes of data, commonly referred to as 'big data,' poses technical challenges in terms of storage, delivery, and sharing due to the collaborative nature of research across multiple institutions. A typical genome data set might contain 500 terabytes of data which may need to be shared, often internationally using Internet2 technology. Proprietary data compression mechanisms have been created (by Valex LLC) for the NCBI Short Read Archive Project [6] that allow for the delivery of raw research data at speeds of up to 40 Gbit/s. To provide a full solution for such collaborative research, the makers of BioUML have developed a new hardware/software system in partnership with Valex LLC. This version of BioUML is called Bio datomics.

Related Research Articles

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References

  1. ↑ Kolpakov, Fedor; Akberdin, Ilya; Kashapov, Timur; Kiselev, llya; Kolmykov, Semyon; Kondrakhin, Yury; Kutumova, Elena; Mandrik, Nikita; Pintus, Sergey; Ryabova, Anna; Sharipov, Ruslan; Yevshin, Ivan; Kel, Alexander (2019-07-02). "BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data". Nucleic Acids Research. 47 (W1): W225–W233. doi:10.1093/nar/gkz440. ISSN   0305-1048. PMC   6602424 . PMID   31131402.
  2. 1 2 Kolpakov, Fedor; Akberdin, Ilya; Kiselev, Ilya; Kolmykov, Semyon; Kondrakhin, Yury; Kulyashov, Mikhail; Kutumova, Elena; Pintus, Sergey; Ryabova, Anna; Sharipov, Ruslan; Yevshin, Ivan; Zhatchenko, Sergey; Kel, Alexander (2022-05-10). "BioUML - towards a universal research platform". Nucleic Acids Research. 50 (W1): W124–W131 – via Oxford Academic.
  3. 1 2 Kolpakov, Fedor A (2002). "BioUML - framework for visual modeling and simulation of biological systems". ResearchGate. Retrieved 2024-07-21.{{cite web}}: CS1 maint: url-status (link)
  4. 1 2 "BioUML development history - BioUML platform". wiki.biouml.org. Retrieved 2024-07-21.
  5. ↑ Kolpakov, F; Poroikov, V; Sharipov, R; Kondrakhin, Y; Zakharov, A; Lagunin, A; Milanesi, L; Kel, A (2007). "CYCLONET--an integrated database on cell cycle regulation and carcinogenesis". Nucleic Acids Res. 35 (Database issue): D550–6. doi:10.1093/nar/gkl912. PMC   1899094 . PMID   17202170.
  6. ↑ "Galter Health Sciences Library & Learning Center | News".
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