15 papers · ranked by Valyu relevance
Anne E Carpenter, Thouis R Jones, Michael R Lamprecht, Colin Clarke + 8 more
'In Han Kang' 'Ola Friman' 'David A Guertin' 'Joo Han Chang' 'Robert A Lindquist' 'Jason Moffat' 'Polina Golland' 'David M Sabatini'] CellProfiler, the first free, open-source system for flexible and high-throughput cell image analysis is described.
Robert W Gregg, Panayiotis V Benos, Lenore Cowen
Cellular Potts Models (CPMs) are a popular method to simulate multiscale cellular behaviors because they retain some spatial information like cellular geometry but avoid the computational complexity of a full physics simulation. Their applications are general, but many researchers have focused on using these models to…
Thouis R Jones, In Han Kang, Douglas B Wheeler, Robert A Lindquist + 4 more
'Adam Papallo' 'David M Sabatini' 'Polina Golland' 'Anne E Carpenter'] Background Image-based screens can produce hundreds of measured features for each of hundreds of millions of individual cells in a single experiment. Results Here, we describe CellProfiler Analyst, open-source software for the interactive…
Asaf Liberman, Danny Kario, Matan Mussel, Jacob Brill + 3 more
'Kenneth Buetow' 'Sol Efroni' 'Uri Nevo'] The field of computer modeling and simulation of biological systems is rapidly advancing, backed by significant progress in the fields of experimentation techniques, computer hardware, and programming software. The result of a simulation may be delivered in several ways, from…
Gaelle Letort, Arnau Montagud, Gautier Stoll, Randy Heiland + 5 more
PhysiBoSS integrates these two software frameworks to obtain a detailed description of each cell’s behaviour and how an alteration in a cell can affect the whole population. There are three main parts in the PhysiBoSS structure: 1. BioFVM module handles the simulation of one or more diffusing environmental entities ().…
Alan Godoy, Pedro Tabacof, Fernando J. Von Zuben, Dante R. Chialvo
How can systems in which individuals’ inner workings are very similar to each other, as neural networks or ant colonies, produce so many qualitatively different behaviors, giving rise to roles and specialization? In this work, we bring new perspectives to this question by focusing on the underlying network that defines…
Federico Frascoli, Barry D. Hughes, Muhammad H. Zaman, Kerry A. Landman + 1 more
'Kerry A. Landman' 'Roeland MH. Merks'] Cell migration in healthy and diseased systems is a combination of single and collective cell motion. While single cell motion has received considerable attention, our understanding of collective cell motion remains elusive. A new computational framework for the migration of…
J. Vivas, D. Garzón-Alvarado, M. Cerrolaza
Background: Cell adhesion is a process that involves the interaction between the cell membrane and another surface, either a cell or a substrate. Unlike experimental tests, computer models can simulate processes and study the result of experiments in a shorter time and lower costs. One of the tools used to simulate…
Jamshaid A. Shahir, Natalie Stanley, Jeremy E. Purvis
With the growing number of single-cell datasets collected under more complex experimental conditions, there is an opportunity to leverage single-cell variability to reveal deeper insights into how cells respond to perturbations. Many existing approaches rely on discretizing the data into clusters for differential gene…
Ryan C Kennedy, Glen EP Ropella, C Anthony Hunt
Background Mechanistic explanations of cell-level phenomena typically adopt an observer perspective. Explanations developed from a cell’s perspective may offer new insights. Agent-based models lend themselves to model from an individual perspective, and existing agent-based models generally utilize a regular…
James M. Osborne, Alexander G. Fletcher, Joe M. Pitt-Francis, Philip K. Maini + 2 more
The coordinated behaviour of populations of cells plays a central role in tissue growth and renewal. Cells react to their microenvironment by modulating processes such as movement, growth and proliferation, and signalling. Alongside experimental studies, computational models offer a useful means by which to investigate…
Moriah Echlin, Boris Aguilar, Ilya Shmulevich, Alessandro Giuliani
Communication between cells enables the coordination that drives structural and functional complexity in biological systems. Both single and multicellular organisms have evolved diverse communication systems for a range of purposes, including synchronization of behavior, division of labor, and spatial organization.…
Elvira Toscano, Elena Cimmino, Angelo Boccia, Leandra Sepe + 1 more
'Giovanni Paolella'] In silico simulations are used to understand cell behaviour by means of different approaches and tools, which range from reproducing average population trends to building lattice-based models to, more recently, creating populations of individual cell agents whose mass, volume and morphology behave…
Scott Christley, Briana Lee, Xing Dai, Qing Nie
Background Simulation of sophisticated biological models requires considerable computational power. These models typically integrate together numerous biological phenomena such as spatially-explicit heterogeneous cells, cell-cell interactions, cell-environment interactions and intracellular gene networks. The recent…
Yousef Jamali, Mohammad Azimi, Mohammad R. K. Mofrad, Nick Monk
Understanding the biomechanical properties and the effect of biomechanical force on epithelial cells is key to understanding how epithelial cells form uniquely shaped structures in two or three-dimensional space. Nevertheless, with the limitations and challenges posed by biological experiments at this scale, it becomes…