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| title | chunk | source | category | tags | date_saved | instance |
|---|---|---|---|---|---|---|
| Cellular model | 2/2 | https://en.wikipedia.org/wiki/Cellular_model | reference | science, encyclopedia | 2026-05-05T14:02:05.293321+00:00 | kb-cron |
== Molecular level simulations == Cell Collective is a modeling software that enables one to house dynamical biological data, build computational models, stimulate, break and recreate models. The development is led by Tomas Helikar, a researcher within the field of computational biology. It is designed for biologists, students learning about computational biology, teachers focused on teaching life sciences, and researchers within the field of life science. The complexities of math and computer science are built into the backend and one can learn about the methods used for modeling biological species, but complex math equations, algorithms, programming are not required and hence won't impede model building. The mathematical framework behind Cell Collective is based on a common qualitative (discrete) modeling technique where the regulatory mechanism of each node is described with a logical function [for more comprehensive information on logical modeling, see ]. In the July 2012 issue of Cell, a team led by Markus Covert at Stanford published the most complete computational model of a cell to date. The model of the roughly 500-gene Mycoplasma genitalium contains 28 algorithmically-independent components incorporating work from over 900 sources. It accounts for interactions of the complete genome, transcriptome, proteome, and metabolome of the organism, marking a significant advancement for the field. Most attempts at modeling cell cycle processes have focused on the broad, complicated molecular interactions of many different chemicals, including several cyclin and cyclin-dependent kinase molecules as they correspond to the S, M, G1 and G2 phases of the cell cycle. In a 2014 published article in PLOS computational biology, collaborators at University of Oxford, Virginia Tech and Institut de Génétique et Développement de Rennes produced a simplified model of the cell cycle using only one cyclin/CDK interaction. This model showed the ability to control totally functional cell division through regulation and manipulation only the one interaction, and even allowed researchers to skip phases through varying the concentration of CDK. This model could help understand how the relatively simple interactions of one chemical translate to a cellular level model of cell division.
== Projects == Multiple projects are in progress.
CytoSolve - Commercial platform, possibly using MATLAB Synthecell - Experimental group Karyote - Indiana University - No longer active E-Cell Project - Last updated 2020 VCell - University of Connecticut Health Center - Simulation platform rather than a build a cell project Silicon Cell - No longer active WholeCell - Stanford University - No longer active MCell - National Center for Multiscale Modeling of Biological Systems (MMBioS) - Active as of 2023 Virtual Cell Challenge - competition to develop predictive models of single-cell transcriptional responses to CRISPR perturbations, hosted by Arc Institute and sponsored by Nvidia, 10x Genomics, and Ultima Genomics
== See also == Biological data visualization Biological Applications of Bifurcation Theory Molecular modeling software Membrane computing is the task of modeling specifically a cell membrane. Biochemical Switches in the Cell Cycle Masaru Tomita
== References ==