WholeCellKB: model organism databases for comprehensive whole-cell models

Karr, Jonathan R.; Sanghvi, Jayodita C.; Macklin, Derek N.; Arora, Abhishek; Covert, Markus W.

doi:10.1093/nar/gks1108

Cited by 45 publications

(38 citation statements)

References 24 publications

(32 reference statements)

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“…The gene expression panel’s tooltips display gene names, descriptions, and instantaneous copy numbers (Figure 1c). Clicking on a gene in the translation panel (Figure 1f) opens a new tab which displays the gene’s entry in the WholeCellKB model organism database [10]. …”

Section: Resultsmentioning

confidence: 99%

WholeCellViz: data visualization for whole-cell models

2013

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BackgroundWhole-cell models promise to accelerate biomedical science and engineering. However, discovering new biology from whole-cell models and other high-throughput technologies requires novel tools for exploring and analyzing complex, high-dimensional data.ResultsWe developed WholeCellViz, a web-based software program for visually exploring and analyzing whole-cell simulations. WholeCellViz provides 14 animated visualizations, including metabolic and chromosome maps. These visualizations help researchers analyze model predictions by displaying predictions in their biological context. Furthermore, WholeCellViz enables researchers to compare predictions within and across simulations by allowing users to simultaneously display multiple visualizations.ConclusionWholeCellViz was designed to facilitate exploration, analysis, and communication of whole-cell model data. Taken together, WholeCellViz helps researchers use whole-cell model simulations to drive advances in biology and bioengineering.

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Section: Resultsmentioning

confidence: 99%

WholeCellViz: data visualization for whole-cell models

2013

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“…For example, Karr et al developed the WholeCellKB database [22] to organize the over 1,400 quantitative measurements used to build the M. genitalium WC model. These databases should be machine-readable so that they can be automatically queried and used to build models.…”

Section: Towards a Platform For Reproducible Modelingmentioning

confidence: 99%

Guidelines for Reproducibly Building and Simulating Systems Biology Models

Medley

Goldberg

Karr

2016

IEEE Trans. Biomed. Eng.

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Objective Reproducibility is the cornerstone of the scientific method. However, currently, many systems biology models cannot easily be reproduced. This paper presents methods that address this problem. Methods We analyzed the recent Mycoplasma genitalium whole-cell (WC) model to determine the requirements for reproducible modeling. Results We determined that reproducible modeling requires both repeatable model building and repeatable simulation. Conclusion New standards and simulation software tools are needed to enhance and verify the reproducibility of modeling. New standards are needed to explicitly document every data source and assumption, and new deterministic parallel simulation tools are needed to quickly simulate large, complex models. Significance We anticipate that these new standards and software will enable researchers to reproducibly build and simulate more complex models, including WC models.

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“…While efforts such as the BioCyc databases have sought to unify genomic and metabolic pathway information [27], separate databases contain functional parameters such as kinetic rates [28, 29] and expression levels [30]. To compile the data required to build the M. genitalium model, which we share via WholeCellKB [31], we had to download and synthesize parameters from these and other databases as well as the primary literature. For larger and more complex organisms, the sheer magnitude of data to collect, and the number of discrepancies to resolve, will present significant hurdles to parameterizing a model.…”

Section: Data Curationmentioning

confidence: 99%

The future of whole-cell modeling

Macklin

Ruggero

Covert

2014

Current Opinion in Biotechnology

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Integrated whole-cell modeling is poised to make a dramatic impact on molecular and systems biology, bioengineering, and medicine — once certain obstacles are overcome. From our group’s experience building a whole-cell model of Mycoplasma genitalium, we identified several significant challenges to building models of more complex cells. Here we review and discuss these challenges in seven areas: (1) experimental interrogation, (2) data curation, (3) model building and integration, (4) accelerated computation, (5) analysis and visualization, (6) model validation, and (7) collaboration and community development. Surmounting these challenges will require the cooperation of an interdisciplinary group of researchers to create increasingly sophisticated whole-cell models and make data, models, and simulations more accessible to the wider community.

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WholeCellKB: model organism databases for comprehensive whole-cell models

Cited by 45 publications

References 24 publications

WholeCellViz: data visualization for whole-cell models

WholeCellViz: data visualization for whole-cell models

Guidelines for Reproducibly Building and Simulating Systems Biology Models

The future of whole-cell modeling

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