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. | + | '''Complex''' - A heteromultimer defined as two or more molecules bound together non-covalently. The ProcessDB icon for a complex is three spheres combined. |
| − | '''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. | + | '''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 defined by other ProcessDB users or you may create your own named molecules. | + | '''Molecule''' - A biological or pharmaceutical assembly of covalently bonded atoms identified by a name. You are free to use all the molecules defined 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. |
| − | '''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. | + | '''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 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. |
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| − | '''State''' - A state is a '''molecule''' or '''complex''' in a physiological '''place'''. | + | '''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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| + | '''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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| + | '''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. | ||
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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. | ||
Revision as of 15:57, 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.
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 defined 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.
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.
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.