July 2018

Movement is fundamental to human and animal life, emerging through interaction of complex neural, muscular, and skeletal systems. OpenSim is open-source software that unites state-of-the-art models and methods from biology, neuroscience, mechanics, robotics, and computer science to create fast and accurate physics-based simulations of movement. OpenSim complements experiments by computing muscle forces and other quantities that are difficult to measure, and enables prediction of movements such as bipedal locomotion in human ancestors and neuromuscular adaptations to exoskeletons or orthopaedic surgeries. Seth et al.

Image Credit: Human model and simulation from Rajagopal et al. [1]; chimpanzee model from O'Neill et al. [2] and unpublished simulation results provided by M.C. O'Neill and B.R. Umberger.

1. Rajagopal A, Dembia CL, DeMers MS, Delp DD, Hicks JL, Delp SL. Full-body musculoskeletal model for muscle-driven simulation of human gait. IEEE Trans Biomed Eng. 2016; 63(10):2068-2079

2. O'Neill MC, Lee LF, Larson SG, Demes B, Stern JT Jr, Umberger BR. A three-dimensional musculoskeletal model of the chimpanzee (Pan troglodytes) pelvis and hind limb. J Exp Biol. 2013; 216(19):3709-3723.

Research Articles

The role of the encapsulated cargo in microcompartment assembly

Farzaneh Mohajerani, Michael F. Hagan

PLOS Computational Biology: published July 31, 2018 | https://doi.org/10.1371/journal.pcbi.1006351

Crowdsourcing image analysis for plant phenomics to generate ground truth data for machine learning

Naihui Zhou, Zachary D. Siegel, Scott Zarecor, Nigel Lee, Darwin A. Campbell, Carson M. Andorf, Dan Nettleton, Carolyn J. Lawrence-Dill, Baskar Ganapathysubramanian, Jonathan W. Kelly, Iddo Friedberg

PLOS Computational Biology: published July 30, 2018 | https://doi.org/10.1371/journal.pcbi.1006337

Inter-trial effects in visual pop-out search: Factorial comparison of Bayesian updating models

Fredrik Allenmark, Hermann J. Müller, Zhuanghua Shi

PLOS Computational Biology: published July 30, 2018 | https://doi.org/10.1371/journal.pcbi.1006328

Activation of the DNA-repair mechanism through NBS1 and MRE11 diffusion

Ida Friis, Ilia A. Solov’yov

PLOS Computational Biology: published July 27, 2018 | https://doi.org/10.1371/journal.pcbi.1006362

Bayesian comparison of explicit and implicit causal inference strategies in multisensory heading perception

Luigi Acerbi, Kalpana Dokka, Dora E. Angelaki, Wei Ji Ma

PLOS Computational Biology: published July 27, 2018 | https://doi.org/10.1371/journal.pcbi.1006110

PyPhi: A toolbox for integrated information theory

William G. P. Mayner, William Marshall, Larissa Albantakis, Graham Findlay, Robert Marchman, Giulio Tononi

PLOS Computational Biology: published July 26, 2018 | https://doi.org/10.1371/journal.pcbi.1006343

A model for hydrophobic protrusions on peripheral membrane proteins

Edvin Fuglebakk, Nathalie Reuter

PLOS Computational Biology: published July 26, 2018 | https://doi.org/10.1371/journal.pcbi.1006325

OpenSim: Simulating musculoskeletal dynamics and neuromuscular control to study human and animal movement

Ajay Seth, Jennifer L. Hicks, Thomas K. Uchida, Ayman Habib, Christopher L. Dembia, James J. Dunne, Carmichael F. Ong, Matthew S. DeMers, Apoorva Rajagopal, Matthew Millard, Samuel R. Hamner, Edith M. Arnold, Jennifer R. Yong, Shrinidhi K. Lakshmikanth, Michael A. Sherman, Joy P. Ku, Scott L. Delp

PLOS Computational Biology: published July 26, 2018 | https://doi.org/10.1371/journal.pcbi.1006223

An enormous potential for niche construction through bacterial cross-feeding in a homogeneous environment

Magdalena San Roman, Andreas Wagner

PLOS Computational Biology: published July 24, 2018 | https://doi.org/10.1371/journal.pcbi.1006340

Shared spatiotemporal category representations in biological and artificial deep neural networks

Michelle R. Greene, Bruce C. Hansen

PLOS Computational Biology: published July 24, 2018 | https://doi.org/10.1371/journal.pcbi.1006327

FusionPathway: Prediction of pathways and therapeutic targets associated with gene fusions in cancer

Chia-Chin Wu, Hannah C. Beird, Jianhua Zhang, P. Andrew Futreal

PLOS Computational Biology: published July 24, 2018 | https://doi.org/10.1371/journal.pcbi.1006266

Real-time decision-making during emergency disease outbreaks

William J. M. Probert, Chris P. Jewell, Marleen Werkman, Christopher J. Fonnesbeck, Yoshitaka Goto, Michael C. Runge, Satoshi Sekiguchi, Katriona Shea, Matt J. Keeling, Matthew J. Ferrari, Michael J. Tildesley

PLOS Computational Biology: published July 24, 2018 | https://doi.org/10.1371/journal.pcbi.1006202

A marginalized two-part Beta regression model for microbiome compositional data

Haitao Chai, Hongmei Jiang, Lu Lin, Lei Liu

PLOS Computational Biology: published July 23, 2018 | https://doi.org/10.1371/journal.pcbi.1006329

Punishment and inspection for governing the commons in a feedback-evolving game

Xiaojie Chen, Attila Szolnoki

PLOS Computational Biology: published July 20, 2018 | https://doi.org/10.1371/journal.pcbi.1006347

Exploration and stabilization of Ras1 mating zone: A mechanism with positive and negative feedbacks

Bita Khalili, Laura Merlini, Vincent Vincenzetti, Sophie G. Martin, Dimitrios Vavylonis

PLOS Computational Biology: published July 20, 2018 | https://doi.org/10.1371/journal.pcbi.1006317

The evolutionary dynamics of metabolic protocells

Ximo Pechuan, Raymond Puzio, Aviv Bergman

PLOS Computational Biology: published July 20, 2018 | https://doi.org/10.1371/journal.pcbi.1006265

A minimally invasive neurostimulation method for controlling abnormal synchronisation in the neuronal activity

Malbor Asllani, Paul Expert, Timoteo Carletti

PLOS Computational Biology: published July 19, 2018 | https://doi.org/10.1371/journal.pcbi.1006296

Correction of copy number induced false positives in CRISPR screens

Antoine de Weck, Javad Golji, Michael D. Jones, Joshua M. Korn, Eric Billy, E. Robert McDonald III, Tobias Schmelzle, Hans Bitter, Audrey Kauffmann

PLOS Computational Biology: published July 19, 2018 | https://doi.org/10.1371/journal.pcbi.1006279

Stochastic resonance enhances the rate of evidence accumulation during combined brain stimulation and perceptual decision-making

Onno van der Groen, Matthew F. Tang, Nicole Wenderoth, Jason B. Mattingley

PLOS Computational Biology: published July 18, 2018 | https://doi.org/10.1371/journal.pcbi.1006301

A biophysically detailed computational model of urinary bladder small DRG neuron soma

Darshan Mandge, Rohit Manchanda

PLOS Computational Biology: published July 18, 2018 | https://doi.org/10.1371/journal.pcbi.1006293

A quantitative physical model of the TMS-induced discharge artifacts in EEG

Dominik Freche, Jodie Naim-Feil, Avi Peled, Nava Levit-Binnun, Elisha Moses

PLOS Computational Biology: published July 17, 2018 | https://doi.org/10.1371/journal.pcbi.1006177

Cancerin: A computational pipeline to infer cancer-associated ceRNA interaction networks

Duc Do, Serdar Bozdag

PLOS Computational Biology: published July 16, 2018 | https://doi.org/10.1371/journal.pcbi.1006318

Interaction of the human erythrocyte Band 3 anion exchanger 1 (AE1, SLC4A1) with lipids and glycophorin A: Molecular organization of the Wright (Wr) blood group antigen

Antreas C. Kalli, Reinhart A. F. Reithmeier

PLOS Computational Biology: published July 16, 2018 | https://doi.org/10.1371/journal.pcbi.1006284

Microheterogeneity-induced conduction slowing and wavefront collisions govern macroscopic conduction behavior: A computational and experimental study

Tanmay A. Gokhale, Huda Asfour, Shravan Verma, Nenad Bursac, Craig S. Henriquez

PLOS Computational Biology: published July 16, 2018 | https://doi.org/10.1371/journal.pcbi.1006276

miRAW: A deep learning-based approach to predict microRNA targets by analyzing whole microRNA transcripts

Albert Pla, Xiangfu Zhong, Simon Rayner

PLOS Computational Biology: published July 13, 2018 | https://doi.org/10.1371/journal.pcbi.1006185

Modelling how responsiveness to interferon improves interferon-free treatment of hepatitis C virus infection

Vishnu Venugopal, Pranesh Padmanabhan, Rubesh Raja, Narendra M. Dixit

PLOS Computational Biology: published July 12, 2018 | https://doi.org/10.1371/journal.pcbi.1006335

Information-theoretic analysis of realistic odor plumes: What cues are useful for determining location?

Sebastian D. Boie, Erin G. Connor, Margaret McHugh, Katherine I. Nagel, G. Bard Ermentrout, John P. Crimaldi, Jonathan D. Victor

PLOS Computational Biology: published July 10, 2018 | https://doi.org/10.1371/journal.pcbi.1006275

Phase-lags in large scale brain synchronization: Methodological considerations and in-silico analysis

Spase Petkoski, J. Matias Palva, Viktor K. Jirsa

PLOS Computational Biology: published July 10, 2018 | https://doi.org/10.1371/journal.pcbi.1006160

Differential roles of sleep spindles and sleep slow oscillations in memory consolidation

Yina Wei, Giri P. Krishnan, Maxim Komarov, Maxim Bazhenov

PLOS Computational Biology: published July 9, 2018 | https://doi.org/10.1371/journal.pcbi.1006322

The importance of mechanical constraints for proper polarization and psuedo-cleavage furrow generation in the early Caenorhabditis elegans embryo

Betül Senay Aras, Y. C. Zhou, Adriana Dawes, Ching-Shan Chou

PLOS Computational Biology: published July 9, 2018 | https://doi.org/10.1371/journal.pcbi.1006294

Gain control with A-type potassium current: I_A as a switch between divisive and subtractive inhibition

Joshua H. Goldwyn, Bradley R. Slabe, Joseph B. Travers, David Terman

PLOS Computational Biology: published July 9, 2018 | https://doi.org/10.1371/journal.pcbi.1006292

Age-dependent Pavlovian biases influence motor decision-making

Xiuli Chen, Robb B. Rutledge, Harriet R. Brown, Raymond J. Dolan, Sven Bestmann, Joseph M. Galea

PLOS Computational Biology: published July 6, 2018 | https://doi.org/10.1371/journal.pcbi.1006304

Unsupervised clustering of temporal patterns in high-dimensional neuronal ensembles using a novel dissimilarity measure

Lukas Grossberger, Francesco P. Battaglia, Martin Vinck

PLOS Computational Biology: published July 6, 2018 | https://doi.org/10.1371/journal.pcbi.1006283

A local uPAR-plasmin-TGFβ1 positive feedback loop in a qualitative computational model of angiogenic sprouting explains the in vitro effect of fibrinogen variants

Sonja E. M. Boas, Joao Carvalho, Marloes van den Broek, Ester M. Weijers, Marie-José Goumans, Pieter Koolwijk, Roeland M. H. Merks

PLOS Computational Biology: published July 6, 2018 | https://doi.org/10.1371/journal.pcbi.1006239

Subgraphs of functional brain networks identify dynamical constraints of cognitive control

Ankit N. Khambhati, John D. Medaglia, Elisabeth A. Karuza, Sharon L. Thompson-Schill, Danielle S. Bassett

PLOS Computational Biology: published July 6, 2018 | https://doi.org/10.1371/journal.pcbi.1006234

Excitable neuronal assemblies with adaptation as a building block of brain circuits for velocity-controlled signal propagation

Hesam Setareh, Moritz Deger, Wulfram Gerstner

PLOS Computational Biology: published July 6, 2018 | https://doi.org/10.1371/journal.pcbi.1006216

A dual regulation mechanism of histidine kinase CheA identified by combining network-dynamics modeling and system-level input-output data

Bernardo A. Mello, Wenlin Pan, Gerald L. Hazelbauer, Yuhai Tu

PLOS Computational Biology: published July 2, 2018 | https://doi.org/10.1371/journal.pcbi.1006305

Cover

OpenSim: open-source simulation software enables movement research from comparative biology to assistive robotics

Research Articles

Related Articles

Related Articles