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David Borland edited this page Sep 26, 2017 · 6 revisions

Glossary of Terms

  • Cell Cycle: The process by which cells replicate their DNA to form two daughter cells. The cell cycle is central to nearly every facet of the life sciences.

  • Dataset: A collection of temporal data from live-cell imaging experiments, including multiple possible features collected for multiple possible species across multiple cells.

  • Species: A generic term used for the entities in the Stochastic Simulation Algorithm used to simulate cell-cycle progression. For our purposes, a species represents a particular protein.

  • Feature: A specific metric extracted from live-cell imaging experiments, e.g. Count, Intensity. There may be multiple features per species for each cell in the experimental dataset.

  • Source: A data source is either an experimental dataset, or a simulation. Each data source contain temporal information about molecular activity for a set of species across multiple cells.

  • Track: In the Data Browser, a track is a collection of individual cell traces, and the average trace, of a single feature for a single species.

  • Trace: A trace is a temporal sequence of molecular activity for a single cell, described by a single feature for a single species.

  • Model: A set of parameters indicating a) the expression levels of each species, b) any interactions between these species and each phase in the cell cycle, and c) any interactions between species for each phase in the cell cycle. A model can be simulated, producing a set of time sequences of molecular activities for a number of virtual simulated cells.

  • Interaction: For a computational model, an interaction is a one-way relationship between a species and another species or a phase. Interactions can be inhibiting or promoting. In the CCB user interface, these interactions are specified as exponents for the rate equations to be simulated. Negative exponents are inhibiting, and positive exponents are promoting.

  • Workspace: A pre-defined collection of experimental datasets and computational models that can be loaded and viewed simultaneously.

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