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Bio-logic builder: a non-technical tool for building dynamical, qualitative models.

ABSTRACT: 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.

SUBMITTER: Helikar T

PROVIDER: S-EPMC3474764 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Bio-logic builder: a non-technical tool for building dynamical, qualitative models.

Helikar Tomáš T Kowal Bryan B Madrahimov Alex A Shrestha Manish M Pedersen Jay J Limbu Kahani K Thapa Ishwor I Rowley Thaine T Satalkar Rahul R Kochi Naomi N Konvalina John J Rogers Jim A JA

PloS one 20121017 10

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 regu ...[more]

PMID: 23082121

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Project description:BackgroundLogic models are commonly used in evaluations to represent the causal processes through which interventions produce outcomes, yet significant debate is currently taking place over whether they can describe complex interventions which adapt to context. This paper assesses the logic models used in healthcare research from a complexity perspective. A typology of existing logic models is proposed, as well as a formal methodology for deriving more flexible and dynamic logic models.AnalysisVarious logic model types were tested as part of an evaluation of a complex Patient Experience Toolkit (PET) intervention, developed and implemented through action research across six hospital wards/departments in the English NHS. Three dominant types of logic model were identified, each with certain strengths but ultimately unable to accurately capture the dynamics of PET. Hence, a fourth logic model type was developed to express how success hinges on the adaption of PET to its delivery settings. Aspects of the Promoting Action on Research Implementation in Health Services (PARIHS) model were incorporated into a traditional logic model structure to create a dynamic "type 4" logic model that can accommodate complex interventions taking on a different form in different settings.ConclusionLogic models can be used to model complex interventions that adapt to context but more flexible and dynamic models are required. An implication of this is that how logic models are used in healthcare research may have to change. Using logic models to forge consensus among stakeholders and/or provide precise guidance across different settings will be inappropriate in the case of complex interventions that adapt to context. Instead, logic models for complex interventions may be targeted at facilitators to enable them to prospectively assess the settings they will be working in and to develop context-sensitive facilitation strategies. Researchers should be clear as to why they are using a logic model and experiment with different models to ensure they have the correct type.

Dataset Information

Bio-logic builder: a non-technical tool for building dynamical, qualitative models.

Publications

Bio-logic builder: a non-technical tool for building dynamical, qualitative models.

Similar Datasets

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