Literature DB >> 35217296

Computational models in systems biology: standards, dissemination, and best practices.

Luis Sordo Vieira1, Reinhard C Laubenbacher2.   

Abstract

Mathematical and computational models are a key technology in systems biology. Progress in the field depends on the replicability and reproducibility of their properties and behavior. For this, an essential requirement is a set of clear standards for model specification and dissemination. This review covers existing standards, and it highlights the most important areas where further work is required. This includes the specification of agent-based models, an increasingly common modeling approach.
Copyright © 2022 Elsevier Ltd. All rights reserved.

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Year:  2022        PMID: 35217296      PMCID: PMC9177621          DOI: 10.1016/j.copbio.2022.102702

Source DB:  PubMed          Journal:  Curr Opin Biotechnol        ISSN: 0958-1669            Impact factor:   10.279


  26 in total

1.  A modular computational framework for medical digital twins.

Authors:  J Masison; J Beezley; Y Mei; Hal Ribeiro; A C Knapp; L Sordo Vieira; B Adhikari; Y Scindia; M Grauer; B Helba; W Schroeder; B Mehrad; R Laubenbacher
Journal:  Proc Natl Acad Sci U S A       Date:  2021-05-18       Impact factor: 11.205

2.  Reproducible Research Using Biomodels.

Authors:  Pedro Mendes
Journal:  Bull Math Biol       Date:  2018-09-06       Impact factor: 1.758

3.  Multi-scale modeling of tissues using CompuCell3D.

Authors:  Maciej H Swat; Gilberto L Thomas; Julio M Belmonte; Abbas Shirinifard; Dimitrij Hmeljak; James A Glazier
Journal:  Methods Cell Biol       Date:  2012       Impact factor: 1.441

4.  The Cell Collective: toward an open and collaborative approach to systems biology.

Authors:  Tomáš Helikar; Bryan Kowal; Sean McClenathan; Mitchell Bruckner; Thaine Rowley; Alex Madrahimov; Ben Wicks; Manish Shrestha; Kahani Limbu; Jim A Rogers
Journal:  BMC Syst Biol       Date:  2012-08-07

5.  SBML Level 3 Package: Flux Balance Constraints version 2.

Authors:  Brett G Olivier; Frank T Bergmann
Journal:  J Integr Bioinform       Date:  2018-03-09

6.  The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2.

Authors:  Michael Hucka; Frank T Bergmann; Claudine Chaouiya; Andreas Dräger; Stefan Hoops; Sarah M Keating; Matthias König; Nicolas Le Novère; Chris J Myers; Brett G Olivier; Sven Sahle; James C Schaff; Rahuman Sheriff; Lucian P Smith; Dagmar Waltemath; Darren J Wilkinson; Fengkai Zhang
Journal:  J Integr Bioinform       Date:  2019-06-20

7.  BioModels-15 years of sharing computational models in life science.

Authors:  Rahuman S Malik-Sheriff; Mihai Glont; Tung V N Nguyen; Krishna Tiwari; Matthew G Roberts; Ashley Xavier; Manh T Vu; Jinghao Men; Matthieu Maire; Sarubini Kananathan; Emma L Fairbanks; Johannes P Meyer; Chinmay Arankalle; Thawfeek M Varusai; Vincent Knight-Schrijver; Lu Li; Corina Dueñas-Roca; Gaurhari Dass; Sarah M Keating; Young M Park; Nicola Buso; Nicolas Rodriguez; Michael Hucka; Henning Hermjakob
Journal:  Nucleic Acids Res       Date:  2020-01-08       Impact factor: 16.971

Review 8.  Integrating machine learning and multiscale modeling-perspectives, challenges, and opportunities in the biological, biomedical, and behavioral sciences.

Authors:  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:  NPJ Digit Med       Date:  2019-11-25

Review 9.  SBML Level 3: an extensible format for the exchange and reuse of biological models.

Authors:  Sarah M Keating; Dagmar Waltemath; Matthias König; Fengkai Zhang; Andreas Dräger; Claudine Chaouiya; Frank T Bergmann; Andrew Finney; Colin S Gillespie; Tomáš Helikar; Stefan Hoops; Rahuman S Malik-Sheriff; Stuart L Moodie; Ion I Moraru; Chris J Myers; Aurélien Naldi; Brett G Olivier; Sven Sahle; James C Schaff; Lucian P Smith; Maciej J Swat; Denis Thieffry; Leandro Watanabe; Darren J Wilkinson; Michael L Blinov; Kimberly Begley; James R Faeder; Harold F Gómez; Thomas M Hamm; Yuichiro Inagaki; Wolfram Liebermeister; Allyson L Lister; Daniel Lucio; Eric Mjolsness; Carole J Proctor; Karthik Raman; Nicolas Rodriguez; Clifford A Shaffer; Bruce E Shapiro; Joerg Stelling; Neil Swainston; Naoki Tanimura; John Wagner; Martin Meier-Schellersheim; Herbert M Sauro; Bernhard Palsson; Hamid Bolouri; Hiroaki Kitano; Akira Funahashi; Henning Hermjakob; John C Doyle; Michael Hucka
Journal:  Mol Syst Biol       Date:  2020-08       Impact factor: 11.429

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  1 in total

1.  Risk Prediction of Ureaplasma urealyticum Affecting Sperm Quality Based on Mathematical Model and Cross-Sectional Study.

Authors:  Huang Liu; Kai Yang; Liping He; Shenghui Zhu; Tao Pang; Zhiyong Zhu; Yunyi Yao; Houbin Zheng; Qingqi Zeng; Xinzong Zhang
Journal:  Comput Math Methods Med       Date:  2022-05-25       Impact factor: 2.809

  1 in total

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