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Related Concept Videos

Cell Lines01:16

Cell Lines

A cell line is a population of cells grown in vitro that can be subcultured over several generations. Normal cells cease to divide after a certain number of cell divisions, a process known as replicative senescence. This number, called the Hayflick limit, was conceptualized by Leonard Hayflick in 1961 when he observed that fetal cells grown in culture could only divide 40-60 times. This limit is due to the shortening of the telomeres during each round of cell division, preventing cell division...
Cell Diversity01:13

Cell Diversity

The concept of a cell started with microscopic observations of dead cork tissue by Robert Hooke in 1665. Hooke coined the term "cell" based on the resemblance of the small subdivisions in the cork to the rooms that monks inhabited, called cells. About ten years later, Antonie van Leeuwenhoek became the first person to observe the living and moving cells under a microscope. In the century that followed, the theory that cells represented the basic unit of life developed.
Multicellular organisms...
Cell Culture01:21

Cell Culture

Most vertebrate cells grow in vitro attached to a substrate as a monolayer, called adherent cultures. The flasks and plates used to grow cells are chemically treated to facilitate cell attachment. However, a few cell types, such as hematopoietic cells, can grow in a suspension. In contrast to adherent cultures, suspension cultures can grow in non-treated cultureware using magnetic stirrers or spinner flasks to agitate the culture media
Cell Specific Gene Expression01:58

Cell Specific Gene Expression

Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...
Cell Specific Gene Expression01:58

Cell Specific Gene Expression

Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...
Subcellular Fractionation01:32

Subcellular Fractionation

The homogenate obtained after cell lysis contains various membrane-bound organelles that can be further separated into pure fractions by subcellular fractionation. These isolates are used to study specific cellular components, analyze localized protein activity, and are even employed in diagnostics. Fractionation is typically achieved using centrifugation methods, the most common being density-gradient and differential centrifugation.
Differential Centrifugation
Differential centrifugation is...

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Analysis of Multidimensional Microscopy Data Using Cell-ACDC
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Analysis of Multidimensional Microscopy Data Using Cell-ACDC

Published on: November 7, 2025

WholeCellViz: data visualization for whole-cell models.

Ruby Lee1, Jonathan R Karr, Markus W Covert

  • 1Department of Bioengineering, Stanford University, Stanford, CA 94025, USA. mcovert@stanford.edu.

BMC Bioinformatics
|August 23, 2013
PubMed
Summary
This summary is machine-generated.

WholeCellViz is a new web-based software that visualizes whole-cell simulations. This tool aids researchers in exploring complex data, accelerating discoveries in biology and bioengineering.

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Area of Science:

  • Computational biology
  • Bioengineering
  • Systems biology

Background:

  • Whole-cell models are powerful tools for advancing biomedical science and engineering.
  • Analyzing complex, high-dimensional data from these models requires innovative visualization and analysis tools.

Purpose of the Study:

  • To develop a user-friendly, web-based software for exploring and analyzing whole-cell simulations.
  • To provide researchers with effective tools for biological discovery using whole-cell models.

Main Methods:

  • Development of WholeCellViz, a novel web-based software application.
  • Implementation of 14 distinct animated visualizations, including metabolic and chromosome maps.
  • Features enabling simultaneous display of multiple visualizations for comparative analysis.

Main Results:

  • WholeCellViz offers interactive visualizations that place simulation predictions within their biological context.
  • The software facilitates the analysis of model predictions by allowing researchers to explore data visually.
  • Users can compare simulation outcomes within and across different datasets simultaneously.

Conclusions:

  • WholeCellViz enhances the exploration, analysis, and communication of whole-cell model data.
  • The tool empowers researchers to leverage whole-cell simulations for significant advancements in biology and bioengineering.