KBase Narrative - SOMATA - Motivating Example

Cashman, Mikaela; Marsh, Alexis; Cottingham, Bob; Cohen, Myra

doi:10.25982/135473.103/1960315

Title: KBase Narrative - SOMATA - Motivating Example

Dataset
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Abstract

A systems view in the biological context is a useful approach to study complex and potentially interacting systems. In this narrative (accompanying an associated manuscript), we take a systems view of software tools themselves. Instead of using software as a single tool, we demonstrate how users can approach software with the same mindset as the organisms they study; as a complex system that can be optimized based on one’s environment and goals. We demonstrate this idea with an example KBase narrative showing how application parameters in KBase tools can change how a researcher perceives and interacts with bioinformatics tools while conducting a common experimental scenario. In this scenario we are trying to understand how different chemical compounds in a growth media change the metabolic pathways utilized in Escherichia coli.

Authors:

Cashman, Mikaela; Marsh, Alexis;

;

Oak Ridge National Laboratory ORNL; Oak Ridge National Laboratory
Iowa State University
Oak Ridge National Laboratory ORNL

Publication Date:: Fri Feb 17 04:00:00 UTC 2023

DOE Contract Number:: AC05-00OR22725; AC05-00OR22725

Research Org.:: U.S. Department of Energy Systems Biology Knowledgebase

Sponsoring Org.:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

OSTI Identifier:: 1960315

DOI:: https://doi.org/10.25982/135473.103/1960315

Citation Formats


                    Cashman, Mikaela, Marsh, Alexis, Cottingham, Bob, and Cohen, Myra. KBase Narrative - SOMATA - Motivating Example.  United States: N. p., 2023. 
        Web.  doi:10.25982/135473.103/1960315.

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                    Cashman, Mikaela, Marsh, Alexis, Cottingham, Bob, & Cohen, Myra. KBase Narrative - SOMATA - Motivating Example.  United States.  doi:https://doi.org/10.25982/135473.103/1960315

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                    Cashman, Mikaela, Marsh, Alexis, Cottingham, Bob, and Cohen, Myra. 2023.  
"KBase Narrative - SOMATA - Motivating Example".  United States.  doi:https://doi.org/10.25982/135473.103/1960315.  https://www.osti.gov/servlets/purl/1960315. Pub date:Fri Feb 17 04:00:00 UTC 2023

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@article{osti_1960315,

  title        = {KBase Narrative - SOMATA - Motivating Example},

  author       = {Cashman, Mikaela and Marsh, Alexis and Cottingham, Bob and Cohen, Myra},

  abstractNote = {A systems view in the biological context is a useful approach to study complex and potentially interacting systems. In this narrative (accompanying an associated manuscript), we take a systems view of software tools themselves. Instead of using software as a single tool, we demonstrate how users can approach software with the same mindset as the organisms they study; as a complex system that can be optimized based on one’s environment and goals. We demonstrate this idea with an example KBase narrative showing how application parameters in KBase tools can change how a researcher perceives and interacts with bioinformatics tools while conducting a common experimental scenario. In this scenario we are trying to understand how different chemical compounds in a growth media change the metabolic pathways utilized in Escherichia coli.},

  doi          = {10.25982/135473.103/1960315},

  journal      = {},

  number       = ,

  volume       = ,

  place        = {United States},

  year         = {Fri Feb 17 04:00:00 UTC 2023},

  month        = {Fri Feb 17 04:00:00 UTC 2023}

}

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DOI: https://doi.org/10.25982/135473.103/1960315

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