Literature DB >> 33620773

Reproducibility in systems biology modelling.

Krishna Tiwari1,2, Sarubini Kananathan1, Matthew G Roberts1, Johannes P Meyer1, Mohammad Umer Sharif Shohan1, Ashley Xavier1, Matthieu Maire1, Ahmad Zyoud1, Jinghao Men1, Szeyi Ng1, Tung V N Nguyen1, Mihai Glont1, Henning Hermjakob1,3, Rahuman S Malik-Sheriff1.   

Abstract

Reproducibility of scientific results is a key element of science and credibility. The lack of reproducibility across many scientific fields has emerged as an important concern. In this piece, we assess mathematical model reproducibility and propose a scorecard for improving reproducibility in this field.
© 2021 The Authors. Published under the terms of the CC BY 4.0 license.

Entities:  

Year:  2021        PMID： 33620773     DOI： 10.15252/msb.20209982

Source DB:  PubMed          Journal:  Mol Syst Biol        ISSN： 1744-4292            Impact factor:   11.429


  17 in total

1.  BioUML-towards a universal research platform.

Authors:  Fedor Kolpakov; Ilya Akberdin; Ilya Kiselev; Semyon Kolmykov; Yury Kondrakhin; Mikhail Kulyashov; Elena Kutumova; Sergey Pintus; Anna Ryabova; Ruslan Sharipov; Ivan Yevshin; Sergey Zhatchenko; Alexander Kel
Journal:  Nucleic Acids Res       Date:  2022-05-10       Impact factor: 19.160

Review 2.  Boolean modelling as a logic-based dynamic approach in systems medicine.

Authors:  Ahmed Abdelmonem Hemedan; Anna Niarakis; Reinhard Schneider; Marek Ostaszewski
Journal:  Comput Struct Biotechnol J       Date:  2022-06-17       Impact factor: 6.155

3.  Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows.

Authors:  Olivia Eriksson; Upinder Singh Bhalla; Kim T Blackwell; Sharon M Crook; Daniel Keller; Andrei Kramer; Marja-Leena Linne; Ausra Saudargienė; Rebecca C Wade; Jeanette Hellgren Kotaleski
Journal:  Elife       Date:  2022-07-06       Impact factor: 8.713

4.  Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology.

Authors:  Anna Niarakis; Dagmar Waltemath; James Glazier; Falk Schreiber; Sarah M Keating; David Nickerson; Claudine Chaouiya; Anne Siegel; Vincent Noël; Henning Hermjakob; Tomáš Helikar; Sylvain Soliman; Laurence Calzone
Journal:  Brief Bioinform       Date:  2022-07-18       Impact factor: 13.994

Review 5.  Computational models in systems biology: standards, dissemination, and best practices.

Authors:  Luis Sordo Vieira; Reinhard C Laubenbacher
Journal:  Curr Opin Biotechnol       Date:  2022-02-23       Impact factor: 10.279

6.  GAMES: A Dynamic Model Development Workflow for Rigorous Characterization of Synthetic Genetic Systems.

Authors:  Kate E Dray; Joseph J Muldoon; Niall M Mangan; Neda Bagheri; Joshua N Leonard
Journal:  ACS Synth Biol       Date:  2022-01-13       Impact factor: 5.249

7.  An online notebook resource for reproducible inference, analysis and publication of gene regulatory networks.

Authors:  Marouen Ben Guebila; Deborah Weighill; Camila M Lopes-Ramos; Rebekka Burkholz; Romana T Pop; Kalyan Palepu; Mia Shapoval; Maud Fagny; Daniel Schlauch; Kimberly Glass; Michael Altenbuchinger; Marieke L Kuijjer; John Platig; John Quackenbush
Journal:  Nat Methods       Date:  2022-05       Impact factor: 47.990

8.  Countering reproducibility issues in mathematical models with software engineering techniques: A case study using a one-dimensional mathematical model of the atrioventricular node.

Authors:  Christopher Schölzel; Valeria Blesius; Gernot Ernst; Alexander Goesmann; Andreas Dominik
Journal:  PLoS One       Date:  2021-07-19       Impact factor: 3.240

9.  Characteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective.

Authors:  Christopher Schölzel; Valeria Blesius; Gernot Ernst; Andreas Dominik
Journal:  NPJ Syst Biol Appl       Date:  2021-06-03

Review 10.  Opening a debate on open-source modeling tools: Pouring fuel on fire versus extinguishing the flare of a healthy debate.

Authors:  Amin Rostami-Hodjegan; Frederic Y Bois
Journal:  CPT Pharmacometrics Syst Pharmacol       Date:  2021-05-01
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