VeVaPy, a Python Platform for Efficient Verification and Validation of Systems Biology Models with Demonstrations Using Hypothalamic-Pituitary-Adrenal Axis Models Article Swipe
Christopher Parker
,
Erik J. Nelson
,
Tongli Zhang
·
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.3390/e24121747
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.3390/e24121747
In order for mathematical models to make credible contributions, it is essential for them to be verified and validated. Currently, verification and validation (V&V) of these models does not meet the expectations of the system biology and systems pharmacology communities. Partially as a result of this shortfall, systemic V&V of existing models currently requires a lot of time and effort. In order to facilitate systemic V&V of chosen hypothalamic-pituitary-adrenal (HPA) axis models, we have developed a computational framework named VeVaPy—taking care to follow the recommended best practices regarding the development of mathematical models. VeVaPy includes four functional modules coded in Python, and the source code is publicly available. We demonstrate that VeVaPy can help us efficiently verify and validate the five HPA axis models we have chosen. Supplied with new and independent data, VeVaPy outputs objective V&V benchmarks for each model. We believe that VeVaPy will help future researchers with basic modeling and programming experience to efficiently verify and validate mathematical models from the fields of systems biology and systems pharmacology.
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- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.3390/e24121747
- https://www.mdpi.com/1099-4300/24/12/1747/pdf?version=1669726686
- OA Status
- gold
- Cited By
- 3
- References
- 60
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4311040694
All OpenAlex metadata
Raw OpenAlex JSON
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https://openalex.org/W4311040694Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.3390/e24121747Digital Object Identifier
- Title
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VeVaPy, a Python Platform for Efficient Verification and Validation of Systems Biology Models with Demonstrations Using Hypothalamic-Pituitary-Adrenal Axis ModelsWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2022Year of publication
- Publication date
-
2022-11-29Full publication date if available
- Authors
-
Christopher Parker, Erik J. Nelson, Tongli ZhangList of authors in order
- Landing page
-
https://doi.org/10.3390/e24121747Publisher landing page
- PDF URL
-
https://www.mdpi.com/1099-4300/24/12/1747/pdf?version=1669726686Direct link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
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https://www.mdpi.com/1099-4300/24/12/1747/pdf?version=1669726686Direct OA link when available
- Concepts
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Python (programming language), Computer science, Biology, Computational biology, Programming languageTop concepts (fields/topics) attached by OpenAlex
- Cited by
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3Total citation count in OpenAlex
- Citations by year (recent)
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2024: 2, 2023: 1Per-year citation counts (last 5 years)
- References (count)
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60Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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| referenced_works | https://openalex.org/W4236600748, https://openalex.org/W2800437807, https://openalex.org/W2004587382, https://openalex.org/W3014925868, https://openalex.org/W3168038426, https://openalex.org/W2129242603, https://openalex.org/W2129579709, https://openalex.org/W2015662215, https://openalex.org/W4237369438, https://openalex.org/W2150734066, https://openalex.org/W1474235225, https://openalex.org/W2535896286, https://openalex.org/W2015219993, https://openalex.org/W2055747883, https://openalex.org/W6831334664, https://openalex.org/W1971327350, https://openalex.org/W6607341338, https://openalex.org/W2191160519, https://openalex.org/W2058230185, https://openalex.org/W2089090494, https://openalex.org/W2068945449, https://openalex.org/W2082124768, https://openalex.org/W2103092138, https://openalex.org/W2546829433, https://openalex.org/W3016401445, https://openalex.org/W1991131705, https://openalex.org/W2129968987, https://openalex.org/W1983324998, https://openalex.org/W1498187975, https://openalex.org/W2914498899, https://openalex.org/W2047730840, https://openalex.org/W2020561965, https://openalex.org/W2048060485, https://openalex.org/W2560471521, https://openalex.org/W2485914614, https://openalex.org/W2793993424, https://openalex.org/W2406493898, https://openalex.org/W2413797628, https://openalex.org/W2810419619, https://openalex.org/W2913147596, https://openalex.org/W2899002317, https://openalex.org/W2570760970, https://openalex.org/W2036318837, https://openalex.org/W126033551, https://openalex.org/W2951092176, https://openalex.org/W2805610236, https://openalex.org/W2964148489, https://openalex.org/W2890494777, https://openalex.org/W3132502413, https://openalex.org/W3080314885, https://openalex.org/W2127479912, https://openalex.org/W2141133391, https://openalex.org/W6605108878, https://openalex.org/W2110458731, https://openalex.org/W2659701381, https://openalex.org/W2408020614, https://openalex.org/W4250116403, https://openalex.org/W181028834, https://openalex.org/W2040844633, https://openalex.org/W3106367734 |
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| corresponding_author_ids | https://openalex.org/A5003112405, https://openalex.org/A5050988947 |
| countries_distinct_count | 1 |
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| corresponding_institution_ids | https://openalex.org/I63135867 |
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| citation_normalized_percentile.is_in_top_10_percent | False |