Difference between revisions of "Glossary of ProcessDB terminology"
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'''Complex''' - A heteromultimer defined as two or more molecules bound together non-covalently. The ProcessDB icon for a complex is three spheres combined. | '''Complex''' - A heteromultimer defined as two or more molecules bound together non-covalently. The ProcessDB icon for a complex is three spheres combined. | ||
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+ | '''Database pane''' | ||
'''Experiment''' - An experiment is a time line of perturbations or investigator-initiated changes carried out in a laboratory or clinic using isolated biological molecules, living cells, tissues, organs or organisms. ProcessDB applies these perturbations to a model so that the modeler can compare model solutions directly with experimental data. The ProcessDB icon for an experiment is a small blue notebook with the word "Lab" on the front. | '''Experiment''' - An experiment is a time line of perturbations or investigator-initiated changes carried out in a laboratory or clinic using isolated biological molecules, living cells, tissues, organs or organisms. ProcessDB applies these perturbations to a model so that the modeler can compare model solutions directly with experimental data. The ProcessDB icon for an experiment is a small blue notebook with the word "Lab" on the front. | ||
− | '''Molecule''' - A biological or pharmaceutical assembly of covalently bonded atoms identified by a name. You are free to use all the molecules | + | '''Molecule''' - A biological or pharmaceutical assembly of covalently bonded atoms identified by a name. You are free to use all the molecules named by other ProcessDB users or you may create your own named molecules. The ProcessDB icon for a molecule is three spherical atoms connected by straight lines. It looks like a ball-and-stick model of a water molecule. If everyone in your workgroup uses the same molecule names, you will be able to compare and combine different models with a single click. |
'''Model''' - A model or model diagram defines the ''structure'' of your biological working hypothesis or theory. It consists of three kinds of processes: 1) biochemical reactions, 2) binding, and 3) transport. The ProcessDB icon for a model is a white cube of connected states. | '''Model''' - A model or model diagram defines the ''structure'' of your biological working hypothesis or theory. It consists of three kinds of processes: 1) biochemical reactions, 2) binding, and 3) transport. The ProcessDB icon for a model is a white cube of connected states. | ||
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'''Model Of Experiments (MOE)''' - A model of experiments is an MR combined with one or more experiments. The ProcessDB icon for a model of experiments is a green cube of connected states. | '''Model Of Experiments (MOE)''' - A model of experiments is an MR combined with one or more experiments. The ProcessDB icon for a model of experiments is a green cube of connected states. | ||
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+ | '''Model Tree Structure Pane''' | ||
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+ | '''MR Pane''' | ||
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+ | '''Parameter Set''' | ||
'''Place''' - A place is a defined physiological location where one or more molecules or complexes can reside. See '''State'''. The ProcessDB icon for a place looks like a dented pillow or and orange red blood cell. | '''Place''' - A place is a defined physiological location where one or more molecules or complexes can reside. See '''State'''. The ProcessDB icon for a place looks like a dented pillow or and orange red blood cell. | ||
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'''State''' - A state is a '''molecule''' or '''complex''' in a physiological '''place'''. The ProcessDB icon for a state is a red spherical molecule superimposed on the dented pillow place icon. | '''State''' - A state is a '''molecule''' or '''complex''' in a physiological '''place'''. The ProcessDB icon for a state is a red spherical molecule superimposed on the dented pillow place icon. | ||
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+ | '''Traced Process''' | ||
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+ | '''Traced State''' | ||
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+ | '''Tracer Molecule''' |
Revision as of 16:06, 27 February 2014
Complex - A heteromultimer defined as two or more molecules bound together non-covalently. The ProcessDB icon for a complex is three spheres combined.
Database pane
Experiment - An experiment is a time line of perturbations or investigator-initiated changes carried out in a laboratory or clinic using isolated biological molecules, living cells, tissues, organs or organisms. ProcessDB applies these perturbations to a model so that the modeler can compare model solutions directly with experimental data. The ProcessDB icon for an experiment is a small blue notebook with the word "Lab" on the front.
Molecule - A biological or pharmaceutical assembly of covalently bonded atoms identified by a name. You are free to use all the molecules named by other ProcessDB users or you may create your own named molecules. The ProcessDB icon for a molecule is three spherical atoms connected by straight lines. It looks like a ball-and-stick model of a water molecule. If everyone in your workgroup uses the same molecule names, you will be able to compare and combine different models with a single click.
Model - A model or model diagram defines the structure of your biological working hypothesis or theory. It consists of three kinds of processes: 1) biochemical reactions, 2) binding, and 3) transport. The ProcessDB icon for a model is a white cube of connected states.
Model Realization (MR) - A model realization is a quantitative model. The MR has differential equations and process rate laws in addition to the diagram or structure of its underlying model. The ProcessDB icon for a model realization is a blue cube of connected states.
Model Of Experiments (MOE) - A model of experiments is an MR combined with one or more experiments. The ProcessDB icon for a model of experiments is a green cube of connected states.
Model Tree Structure Pane
MR Pane
Parameter Set
Place - A place is a defined physiological location where one or more molecules or complexes can reside. See State. The ProcessDB icon for a place looks like a dented pillow or and orange red blood cell.
Process - A process is a chemical reaction, a binding reaction, or a transport reaction. A model can be seen as a collection of processes. The ProcessDB icon for a process is an "S-shaped" curve with a black triangular arrowhead.
State - A state is a molecule or complex in a physiological place. The ProcessDB icon for a state is a red spherical molecule superimposed on the dented pillow place icon.
Traced Process
Traced State
Tracer Molecule