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Bio-Logic Builder: A Non-Technical Tool for Building Dynamical, Qualitative Models (Bio-Logic Builder)

Helikar, Tomáš ; Kowal, Bryan ; Madrahimov, Alex ; Shrestha, Manish ; Pedersen, Jay ; Limbu, Kahani ; Thapa, Ishwor ; Rowley, Thaine ; Satalkar, Rahul ; Kochi, Naomi ; Konvalina, John ; Rogers, Jim A; De La Fuente, Alberto (Editor)

2012, Vol.7(10), p.e46417 [Tạp chí có phản biện]

E-ISSN: 1932-6203 ; DOI: 10.1371/journal.pone.0046417

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  • Nhan đề:
    Bio-Logic Builder: A Non-Technical Tool for Building Dynamical, Qualitative Models (Bio-Logic Builder)
  • Tác giả: Helikar, Tomáš ; Kowal, Bryan ; Madrahimov, Alex ; Shrestha, Manish ; Pedersen, Jay ; Limbu, Kahani ; Thapa, Ishwor ; Rowley, Thaine ; Satalkar, Rahul ; Kochi, Naomi ; Konvalina, John ; Rogers, Jim A
  • De La Fuente, Alberto (Editor)
  • Chủ đề: Research Article ; Biology ; Computer Science ; Computational Biology ; Computer Science
  • Là 1 phần của: 2012, Vol.7(10), p.e46417
  • Mô tả: Computational modeling of biological processes is a promising tool in biomedical research. While a large part of its potential lies in the ability to integrate it with laboratory research, modeling currently generally requires a high degree of training in mathematics and/or computer science. To help address this issue, we have developed a web-based tool, Bio-Logic Builder, that enables laboratory scientists to define mathematical representations (based on a discrete formalism) of biological regulatory mechanisms in a modular and non-technical fashion. As part of the user interface, generalized “bio-logic” modules have been defined to provide users with the building blocks for many biological processes. To build/modify computational models, experimentalists provide purely qualitative information about a particular regulatory mechanisms as is generally found in the laboratory. The Bio-Logic Builder subsequently converts the provided information into a mathematical representation described with Boolean expressions/rules. We used this tool to build a number of dynamical models, including a 130-protein large-scale model of signal transduction with over 800 interactions, influenza A replication cycle with 127 species and 200+ interactions, and mammalian and budding yeast cell cycles. We also show that any and all qualitative regulatory mechanisms can be built using this tool.
  • Ngôn ngữ: English
  • Số nhận dạng: E-ISSN: 1932-6203 ; DOI: 10.1371/journal.pone.0046417

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