Computer & Information Sciences

Improving Reproducibility of Computational Models

Published August 2, 2021 Curated Collections

The reproducibility of the research is a crucial element to keep science moving forward. In July 2019, PLOS Computational Biology announced its intention to launch a pilot to support improved reproducibility of systems biology or physiology-based models for manuscripts submitted to the journal. This pilot offered expert technical peer review, specifically checking that submitted systems biology or physiology-based models run according to the results presented in the manuscript.

In this collection, take a closer look at a range of published articles from the pilot.

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PLOS Computational Biology Collection

PLOS Computational Biology Collection

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10.1371/journal.pcbi.1008573 CC BY 4.0

PLOS Computational Biology Coincident glutamatergic depolarizations enhance GABA_A receptor-dependent Cl^– influx in mature and suppress Cl^– efflux in immature neurons
January 19, 2021 Aniello Lombardi, Peter Jedlicka, Heiko J. Luhmann, Werner Kilb

The impact of GABAergic transmission on neuronal excitability depends on the Cl--gradient across membranes. However, the Cl--fluxes…
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10.1371/journal.pcbi.1008519 CC BY 4.0

PLOS Computational Biology Multi-scale modeling of macrophage—T cell interactions within the tumor microenvironment
December 23, 2020 Colin G. Cess, Stacey D. Finley

Within the tumor microenvironment, macrophages exist in an immunosuppressive state, preventing T cells from eliminating the tumor. Due to…
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10.1371/journal.pcbi.1008852 CC BY 4.0

PLOS Computational Biology Personalized computational model quantifies heterogeneity in postprandial responses to oral glucose challenge
March 31, 2021 Balázs Erdős, Bart van Sloun, Michiel E. Adriaens, Shauna D. O’Donovan, Dominique Langin, Arne Astrup, Ellen E. Blaak, Ilja C. W. Arts, Natal A. W. van Riel

Plasma glucose and insulin responses following an oral glucose challenge are representative of glucose tolerance and insulin resistance,…
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10.1371/journal.pcbi.1008635 CC BY 4.0

PLOS Computational Biology Building clone-consistent ecosystem models
February 8, 2021 Gerrit Ansmann, Tobias Bollenbach

Many ecological studies employ general models that can feature an arbitrary number of populations. A critical requirement imposed on such…
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10.1371/journal.pcbi.1009021 CC BY 4.0

PLOS Computational Biology MiMeNet: Exploring microbiome-metabolome relationships using neural networks
May 17, 2021 Derek Reiman, Brian T. Layden, Yang Dai

The advance in microbiome and metabolome studies has generated rich omics data revealing the involvement of the microbial community in…
PLOS Computational Biology Imputation of spatially-resolved transcriptomes by graph-regularized tensor completion
April 7, 2021 Zhuliu Li, Tianci Song, Jeongsik Yong, Rui Kuang

High-throughput spatial-transcriptomics RNA sequencing (sptRNA-seq) based on in-situ capturing technologies has recently been developed to…
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10.1371/journal.pcbi.1009019 CC BY 4.0

PLOS Computational Biology Ion dynamics at the energy-deprived tripartite synapse
June 18, 2021 Manu Kalia, Hil G. E. Meijer, Stephan A. van Gils, Michel J. A. M. van Putten, Christine R. Rose

The anatomical and functional organization of neurons and astrocytes at ‘tripartite synapses’ is essential for reliable neurotransmission,…
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10.1371/journal.pcbi.1008730 CC BY 4.0

PLOS Computational Biology DEXOM: Diversity-based enumeration of optimal context-specific metabolic networks
February 11, 2021 Pablo Rodríguez-Mier, Nathalie Poupin, Carlo de Blasio, Laurent Le Cam, Fabien Jourdan

The correct identification of metabolic activity in tissues or cells under different conditions can be extremely elusive due to mechanisms…
PLOS Computational Biology Post-lockdown abatement of COVID-19 by fast periodic switching
January 21, 2021 Michelangelo Bin, Peter Y. K. Cheung, Emanuele Crisostomi, Pietro Ferraro, Hugo Lhachemi, Roderick Murray-Smith, Connor Myant, Thomas Parisini, Robert Shorten, Sebastian Stein, Lewi Stone

COVID-19 abatement strategies have risks and uncertainties which could lead to repeating waves of infection. We show—as proof of concept…
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10.1371/journal.pcbi.1008880 CC BY 4.0

PLOS Computational Biology Orchestrating privacy-protected big data analyses of data from different resources with R and DataSHIELD
March 30, 2021 Yannick Marcon, Tom Bishop, Demetris Avraam, Xavier Escriba-Montagut, Patricia Ryser-Welch, Stuart Wheater, Paul Burton, Juan R. González

Combined analysis of multiple, large datasets is a common objective in the health- and biosciences. Existing methods tend to require…
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10.1371/journal.pcbi.1009098 CC BY 4.0

PLOS Computational Biology Projecting contact matrices in 177 geographical regions: An update and comparison with empirical data for the COVID-19 era
July 26, 2021 Kiesha Prem, Kevin van Zandvoort, Petra Klepac, Rosalind M. Eggo, Nicholas G. Davies, Centre for the Mathematical Modelling of Infectious Diseases COVID-19 Working Group , Alex R. Cook, Mark Jit

Mathematical models have played a key role in understanding the spread of directly-transmissible infectious diseases such as Coronavirus…
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10.1371/journal.pcbi.1009109 CC BY 4.0

PLOS Computational Biology Sperm migration in the genital tract—In silico experiments identify key factors for reproductive success
July 15, 2021 Jorin Diemer, Jens Hahn, Björn Goldenbogen, Karin Müller, Edda Klipp

Sperm migration in the female genital tract controls sperm selection and, therefore, reproductive success as male gametes are conditioned…
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10.1371/journal.pcbi.1008605 CC BY 4.0

PLOS Computational Biology Machine learning based CRISPR gRNA design for therapeutic exon skipping
January 8, 2021 Wilson Louie, Max W. Shen, Zakir Tahiry, Sophia Zhang, Daniel Worstell, Christopher A. Cassa, Richard I. Sherwood, David K. Gifford

Restoring gene function by the induced skipping of deleterious exons has been shown to be effective for treating genetic disorders.…
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10.1371/journal.pcbi.1008463 CC BY 4.0

PLOS Computational Biology Bursting in cerebellar stellate cells induced by pharmacological agents: Non-sequential spike adding
December 14, 2020 Saeed Farjami, Ryan P. D. Alexander, Derek Bowie, Anmar Khadra

Cerebellar stellate cells (CSCs) are spontaneously active, tonically firing (5-30 Hz), inhibitory interneurons that synapse onto Purkinje…
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10.1371/journal.pcbi.1008208 CC BY 4.0

PLOS Computational Biology MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics
January 28, 2021 Zachary B. Haiman, Daniel C. Zielinski, Yuko Koike, James T. Yurkovich, Bernhard O. Palsson

Mathematical models of metabolic networks utilize simulation to study system-level mechanisms and functions. Various approaches have been…
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10.1371/journal.pcbi.1008453 CC BY 4.0

PLOS Computational Biology DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier
November 18, 2020 Maxat Kulmanov, Robert Hoehndorf

Predicting the phenotypes resulting from molecular perturbations is one of the key challenges in genetics. Both forward and reverse…
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10.1371/journal.pcbi.1008702 CC BY 4.0

PLOS Computational Biology The impact of phenotypic heterogeneity of tumour cells on treatment and relapse dynamics
February 12, 2021 Michael Raatz, Saumil Shah, Guranda Chitadze, Monika Brüggemann, Arne Traulsen

Intratumour heterogeneity is increasingly recognized as a frequent problem for cancer treatment as it allows for the evolution of…
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10.1371/journal.pcbi.1008704 CC BY 4.0

PLOS Computational Biology A kinetic model of the central carbon metabolism for acrylic acid production in Escherichia coli
March 8, 2021 Alexandre Oliveira, Joana Rodrigues, Eugénio Campos Ferreira, Lígia Rodrigues, Oscar Dias

Acrylic acid is a value-added chemical used in industry to produce diapers, coatings, paints, and adhesives, among many others. Due to its…
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10.1371/journal.pcbi.1008787 CC BY 4.0

PLOS Computational Biology Neural modelling of the encoding of fast frequency modulation
March 3, 2021 Alejandro Tabas, Katharina von Kriegstein

Frequency modulation (FM) is a basic constituent of vocalisation in many animals as well as in humans. In human speech, short rising and…
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10.1371/journal.pcbi.1008460 CC BY 4.0

PLOS Computational Biology Proteostasis is adaptive: Balancing chaperone holdases against foldases
December 14, 2020 Adam MR de Graff, David E. Mosedale, Tilly Sharp, Ken A. Dill, David J. Grainger

Because a cell must adapt to different stresses and growth rates, its proteostasis system must too. How do cells detect and adjust…
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10.1371/journal.pcbi.1008143 CC BY 4.0

PLOS Computational Biology An electrodiffusive neuron-extracellular-glia model for exploring the genesis of slow potentials in the brain
July 16, 2021 Marte J. Sætra, Gaute T. Einevoll, Geir Halnes

Within the computational neuroscience community, there has been a focus on simulating the electrical activity of neurons, while other…
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10.1371/journal.pcbi.1008464 CC BY 4.0

PLOS Computational Biology Drug2ways: Reasoning over causal paths in biological networks for drug discovery
December 2, 2020 Daniel Rivas-Barragan, Sarah Mubeen, Francesc Guim Bernat, Martin Hofmann-Apitius, Daniel Domingo-Fernández

Elucidating the causal mechanisms responsible for disease can reveal potential therapeutic targets for pharmacological intervention and,…
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10.1371/journal.pcbi.1009134 CC BY 4.0

PLOS Computational Biology Internality and the internalisation of failure: Evidence from a novel task
July 6, 2021 Federico Mancinelli, Jonathan Roiser, Peter Dayan

A critical facet of adjusting one’s behaviour after succeeding or failing at a task is assigning responsibility for the ultimate outcome.…
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10.1371/journal.pcbi.1008421 CC BY 4.0

PLOS Computational Biology Mathematical modeling of hepatitis C RNA replication, exosome secretion and virus release
November 5, 2020 Carolin Zitzmann, Lars Kaderali, Alan S. Perelson

Hepatitis C virus (HCV) causes acute hepatitis C and can lead to life-threatening complications if it becomes chronic. The HCV genome is a…
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10.1371/journal.pcbi.1008094 CC BY 4.0

PLOS Computational Biology Pseudocell Tracer—A method for inferring dynamic trajectories using scRNAseq and its application to B cells undergoing immunoglobulin class switch recombination
May 3, 2021 Derek Reiman, Godhev Kumar Manakkat Vijay, Heping Xu, Andrew Sonin, Dianyu Chen, Nathan Salomonis, Harinder Singh, Aly A. Khan

Single cell RNA sequencing (scRNAseq) can be used to infer a temporal ordering of cellular states. Current methods for the inference of…
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10.1371/journal.pcbi.1008562 CC BY 4.0

PLOS Computational Biology A mathematical model of the role of aggregation in sonic hedgehog signalling
February 22, 2021 Daniel J. A. Derrick, Kathryn Wolton, Richard A. Currie, Marcus John Tindall

Effective regulation of the sonic hedgehog (Shh) signalling pathway is essential for normal development in a wide variety of species.…
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10.1371/journal.pcbi.1008085 CC BY 4.0

PLOS Computational Biology Remote homology search with hidden Potts models
November 30, 2020 Grey W. Wilburn, Sean R. Eddy

Most methods for biological sequence homology search and alignment work with primary sequence alone, neglecting higher-order correlations.…
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10.1371/journal.pcbi.1008466 CC BY 4.0

PLOS Computational Biology A mechanistic framework for a priori pharmacokinetic predictions of orally inhaled drugs
December 15, 2020 Niklas Hartung, Jens Markus Borghardt

The fate of orally inhaled drugs is determined by pulmonary pharmacokinetic processes such as particle deposition, pulmonary drug…
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10.1371/journal.pcbi.1008538 CC BY 4.0

PLOS Computational Biology Multiobjective optimization identifies cancer-selective combination therapies
December 28, 2020 Otto I. Pulkkinen, Prson Gautam, Ville Mustonen, Tero Aittokallio

Combinatorial therapies are required to treat patients with advanced cancers that have become resistant to monotherapies through rewiring…
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10.1371/journal.pcbi.1008003 CC BY 4.0

PLOS Computational Biology Biological network growth in complex environments: A computational framework
November 30, 2020 Torsten Johann Paul, Philip Kollmannsberger

Spatial biological networks are abundant on all scales of life, from single cells to ecosystems, and perform various important functions…
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10.1371/journal.pcbi.1008633 CC BY 4.0

PLOS Computational Biology Testing, tracing and isolation in compartmental models
March 4, 2021 Simone Sturniolo, William Waites, Tim Colbourn, David Manheim, Jasmina Panovska-Griffiths

Existing compartmental mathematical modelling methods for epidemics, such as SEIR models, cannot accurately represent effects of contact…
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10.1371/journal.pcbi.1007960 CC BY 4.0

PLOS Computational Biology Computational study on ratio-sensing in yeast galactose utilization pathway
December 4, 2020 Jiayin Hong, Bo Hua, Michael Springer, Chao Tang

Metabolic networks undergo gene expression regulation in response to external nutrient signals. In microbes, the synthesis of enzymes that…
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10.1371/journal.pcbi.1008319 CC BY 4.0

PLOS Computational Biology Predicting antimicrobial resistance using conserved genes
October 19, 2020 Marcus Nguyen, Robert Olson, Maulik Shukla, Margo VanOeffelen, James J. Davis

A growing number of studies are using machine learning models to accurately predict antimicrobial resistance (AMR) phenotypes from…

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Improving reproducibility of computational models

Read the initial pilot announcement for more details.