Literature DB >> 27576241

Moving Toward Model Reproducibility and Reusability.

Grace C Y Peng.   

Abstract

This paper provides a brief history of the U.S. funding initiatives associated with promoting multiscale modeling of the physiome since 2003. An effort led in the United States is the Interagency Modeling and Analysis Group (IMAG) Multiscale Modeling (MSM) Consortium. Though IMAG and the MSM Consortium have generated much interest in developing MSM models of the physiome, challenges associated with model and data sharing in biomedical, biological, and behavioral systems still exist. Since 2013, the IEEE EMBS Technical Committee on Computational Biology and the Physiome (CBaP TC) has supported discussions on promoting model reproducibility through publications. This special issue on model sharing and reproducibility is a realization of the CBaP TC discussions. Though open questions remain on how we can further facilitate model reproducibility, accessibility, and reuse by the worldwide community for different biomedical domain applications, this special issue provides a unique demonstration of both the challenges and opportunities for publishing reproducible computational models.

Entities:  

Mesh:

Year:  2016        PMID: 27576241      PMCID: PMC5258684          DOI: 10.1109/TBME.2016.2603418

Source DB:  PubMed          Journal:  IEEE Trans Biomed Eng        ISSN: 0018-9294            Impact factor:   4.538


  3 in total

Review 1.  Integration from proteins to organs: the Physiome Project.

Authors:  Peter J Hunter; Thomas K Borg
Journal:  Nat Rev Mol Cell Biol       Date:  2003-03       Impact factor: 94.444

2.  Editorial: What biomedical engineers can do to impact multiscale modeling (TBME Letters special issue on multiscale modeling and analysis in computational biology and medicine: part-2).

Authors:  Grace C Y Peng
Journal:  IEEE Trans Biomed Eng       Date:  2011-12       Impact factor: 4.538

3.  Reproducibility of research in biophysics.

Authors:  Les Loew; Dorothy Beckett; Edward H Egelman; Suzanne Scarlata
Journal:  Biophys J       Date:  2015-04-07       Impact factor: 4.033

  3 in total
  5 in total

1.  Perspectives on Sharing Models and Related Resources in Computational Biomechanics Research.

Authors:  Ahmet Erdemir; Peter J Hunter; Gerhard A Holzapfel; Leslie M Loew; John Middleton; Christopher R Jacobs; Perumal Nithiarasu; Rainlad Löhner; Guowei Wei; Beth A Winkelstein; Victor H Barocas; Farshid Guilak; Joy P Ku; Jennifer L Hicks; Scott L Delp; Michael Sacks; Jeffrey A Weiss; Gerard A Ateshian; Steve A Maas; Andrew D McCulloch; Grace C Y Peng
Journal:  J Biomech Eng       Date:  2018-02-01       Impact factor: 2.097

Review 2.  Hybrid modelling of biological systems: current progress and future prospects.

Authors:  Fei Liu; Monika Heiner; David Gilbert
Journal:  Brief Bioinform       Date:  2022-05-13       Impact factor: 13.994

3.  Multiscale modeling meets machine learning: What can we learn?

Authors:  Grace C Y Peng; Mark Alber; Adrian Buganza Tepole; William R Cannon; Suvranu De; Salvador Dura-Bernal; Krishna Garikipati; George Karniadakis; William W Lytton; Paris Perdikaris; Linda Petzold; Ellen Kuhl
Journal:  Arch Comput Methods Eng       Date:  2020-02-17       Impact factor: 7.302

4.  Tellurium notebooks-An environment for reproducible dynamical modeling in systems biology.

Authors:  J Kyle Medley; Kiri Choi; Matthias König; Lucian Smith; Stanley Gu; Joseph Hellerstein; Stuart C Sealfon; Herbert M Sauro
Journal:  PLoS Comput Biol       Date:  2018-06-15       Impact factor: 4.475

Review 5.  Credible practice of modeling and simulation in healthcare: ten rules from a multidisciplinary perspective.

Authors:  Ahmet Erdemir; Lealem Mulugeta; Joy P Ku; Andrew Drach; Marc Horner; Tina M Morrison; Grace C Y Peng; Rajanikanth Vadigepalli; William W Lytton; Jerry G Myers
Journal:  J Transl Med       Date:  2020-09-29       Impact factor: 5.531

  5 in total

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