Difference between revisions of "Features List Page"
(Created page with " == A Details Listing Of ProcessDB Features == Construct diagrams of your mechanistic cell biological theories using a beautiful and intuitive graphical editor Diagram color...") |
|||
| (19 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
| − | == A | + | == A Detailed Listing Of ProcessDB Features == |
| − | Construct diagrams of your mechanistic cell biological theories using a beautiful and intuitive graphical editor | + | Construct diagrams of your mechanistic biochemical, molecular cell biological, and physiological theories using a beautiful and intuitive graphical editor |
| − | + | '''Automatic translation of diagrams to quantitative models''' based on standard biophysical principles (This is the Run Initial Simulation tool.) | |
Concentrate on the biology while your diagram is kept visually appealing by ProcessDB's advanced layout tools | Concentrate on the biology while your diagram is kept visually appealing by ProcessDB's advanced layout tools | ||
| Line 13: | Line 13: | ||
Define Molecules, molecular Complexes and physiological Places using your lab's own terminology | Define Molecules, molecular Complexes and physiological Places using your lab's own terminology | ||
| + | |||
| + | Ground these molecules to the corresponding entries in international databases such as ChEBI and UniProt | ||
| + | |||
| + | Private free text notes can be attached to molecules, processes and models | ||
Add processes to your model (e.g. chemical reactions, transport, binding) with one simple but powerful tool | Add processes to your model (e.g. chemical reactions, transport, binding) with one simple but powerful tool | ||
| Line 18: | Line 22: | ||
Extract, examine, save and analyze subsystems of complex models | Extract, examine, save and analyze subsystems of complex models | ||
| − | Compare | + | '''Compare models with a single click'''; ProcessDB highlights those states and processes unique to each model. |
| + | |||
| + | '''Combine models with a single click'''; ProcessDB automatically resolves any overlap. | ||
Enter your experiments and the data you collect via a simple interface including Excel® import | Enter your experiments and the data you collect via a simple interface including Excel® import | ||
| − | Analyze all kinds of | + | Analyze all kinds of biological experiments including: |
| − | * agonist | + | * agonist addition |
| + | * inhibitor addition | ||
| + | * bolus injections (e.g. glucose tolerance test) | ||
* medium changes | * medium changes | ||
* infusions | * infusions | ||
* perfusions | * perfusions | ||
* radiotracers (bolus, infusion, primed infusion) | * radiotracers (bolus, infusion, primed infusion) | ||
| − | * stable isotope tracers | + | * stable isotope tracers |
* photobleaching (FRAP, iFRAP, FLIP) | * photobleaching (FRAP, iFRAP, FLIP) | ||
* photoactivation | * photoactivation | ||
| + | * using measured data as forcing functions to open loops and simplify analysis (can use forcing functions for tracer data or chemical system ("tracee") data or both) | ||
* any of these can be superimposed on both steady state and non-steady state systems | * any of these can be superimposed on both steady state and non-steady state systems | ||
| + | * experimentally initiated changes in conditions can be implemented at any time using a very general "events" tool | ||
Each experiment can have many measurements and multiple data sets | Each experiment can have many measurements and multiple data sets | ||
| − | + | Any experimental data set can be used as a '''forcing function''' to drive the model at its boundary or to decouple the model at points of high complexity | |
| − | + | Simulate any model with any number of relevant experiments | |
| − | Leverage a complete set of tools for solution, comparison of solutions and data, and parameter optimization | + | ProcessDB is one of the only tools available that was specifically designed to support the analysis of '''non-steady state tracer kinetic models'''. |
| + | |||
| + | Experimental protocols automatically imposed on models | ||
| + | |||
| + | Using standard biophysical principles, ProcessDB can automatically translate your models and their linked experiments to mathematics, ready to be simulated | ||
| + | |||
| + | To speed the transition from your model diagram to your first simulation, use the '''Run Initial Simulation tool'''. | ||
| + | |||
| + | Leverage a complete set of tools for [[Simulator|solution (CVODE)]], comparison of solutions and data, gradient parameter optimization (ODRPACK95), and global parameter optimization (Particle Swarm). | ||
| + | |||
| + | Optimize over many experiments, each with many data sets, simultaneously | ||
| + | |||
| + | Reports detailed '''parameter statistics''' including fractional standard deviations (FSDs) and 95% confidence intervals | ||
Many models can be open at once, each in a separate tab | Many models can be open at once, each in a separate tab | ||
| − | Automatically builds a personal | + | '''Flexible graphing''' for model output and comparison to data |
| + | *User-specified graph titles and axis labels | ||
| + | *Unlimited user-defined graphs of any model variable | ||
| + | *Expand any graph to full screen | ||
| + | *Automatic pairing of graphs for experimental data and associated model solutions | ||
| + | *Flexible control of Y-axis range for both linear and semi-log graphs | ||
| + | *Optional reference graphs for your current best parameter set | ||
| + | *User-control of solution and data point colors | ||
| + | *Display all graphs or a selected subset of graphs | ||
| + | *Import graph definitions from other models | ||
| + | *Visual parameter sensitivity tool | ||
| + | *Load saved parameter sets into reference solution for comparison | ||
| + | *Temporarily hide any plot in a graph by clicking its legend | ||
| + | *Copy any graph to the clipboard for pasting into reports | ||
| + | *Automatically plot precursors for any plotted state | ||
| + | *Apply user-defined tags to subsets of graphs so they can be displayed as a related group | ||
| + | |||
| + | |||
| + | Automatically builds a personal and searchable database of molecules, molecular complexes, processes and models as you work | ||
Everything in your database is instantly available for re-use | Everything in your database is instantly available for re-use | ||
| Line 50: | Line 90: | ||
Search your database by name or by unique ProcessDB IDs | Search your database by name or by unique ProcessDB IDs | ||
| − | Show all models in your database involving a | + | Show all models in your database involving a chosen molecule or molecular complex |
| + | |||
| + | Show all models in your database involving a chosen process | ||
| + | |||
| + | Show all models in your database involving a chosen physiological Place | ||
Keeps track of molecular components in a complex even if you rename it | Keeps track of molecular components in a complex even if you rename it | ||
Display all molecules with roles in a given model | Display all molecules with roles in a given model | ||
| + | |||
| + | Diagram colors can be easily changed | ||
Rename or delete a model | Rename or delete a model | ||
| − | |||
| − | |||
Specify an experiment based on a given model | Specify an experiment based on a given model | ||
Automatic detection of mismatched experiments and models | Automatic detection of mismatched experiments and models | ||
| + | |||
| + | From a model diagram, select a State and display a list of all models that include that molecule in that place | ||
Prompts user for rate laws when they cannot be determined from the diagram alone | Prompts user for rate laws when they cannot be determined from the diagram alone | ||
| Line 68: | Line 114: | ||
Models can be duplicated in two ways - one that keeps the two models linked so that changes to common processes are always synchronized, and another that separates the two models so they can evolve independently. | Models can be duplicated in two ways - one that keeps the two models linked so that changes to common processes are always synchronized, and another that separates the two models so they can evolve independently. | ||
| − | Online user guide and modeling textbook | + | Online user guide, reference manual, and modeling textbook |
| − | Experimental data can easily be imported from | + | More than 100 sample models in ProcessDB's Public Models database. Public models may be copied to your own database for study, practice or re-use. |
| + | |||
| + | Experimental data can easily be imported from Excel files (that have no formulas) or entered manually | ||
| + | |||
| + | Any data set can be used as a forcing function to implement open-loop analysis or to define boundary conditions. | ||
Professionally maintained and backed-up on our secure web server directly connected to the Internet backbone | Professionally maintained and backed-up on our secure web server directly connected to the Internet backbone | ||
All default rate laws can be displayed and modified if desired | All default rate laws can be displayed and modified if desired | ||
| + | |||
| + | Simulate models with the fast integrated [[Simulator]] based on CVODE and a custom interpreter that has proven [[Simulator#Performance|faster than other solvers/simulators]]. | ||
Latest revision as of 16:54, 29 June 2021
A Detailed Listing Of ProcessDB Features
Construct diagrams of your mechanistic biochemical, molecular cell biological, and physiological theories using a beautiful and intuitive graphical editor
Automatic translation of diagrams to quantitative models based on standard biophysical principles (This is the Run Initial Simulation tool.)
Concentrate on the biology while your diagram is kept visually appealing by ProcessDB's advanced layout tools
Keep track of even complex diagrams using ProcessDB's advanced diagram navigation tools
Share models or keep them private; allow them to be viewed and/or modified even by remote collaborators
Define Molecules, molecular Complexes and physiological Places using your lab's own terminology
Ground these molecules to the corresponding entries in international databases such as ChEBI and UniProt
Private free text notes can be attached to molecules, processes and models
Add processes to your model (e.g. chemical reactions, transport, binding) with one simple but powerful tool
Extract, examine, save and analyze subsystems of complex models
Compare models with a single click; ProcessDB highlights those states and processes unique to each model.
Combine models with a single click; ProcessDB automatically resolves any overlap.
Enter your experiments and the data you collect via a simple interface including Excel® import
Analyze all kinds of biological experiments including:
- agonist addition
- inhibitor addition
- bolus injections (e.g. glucose tolerance test)
- medium changes
- infusions
- perfusions
- radiotracers (bolus, infusion, primed infusion)
- stable isotope tracers
- photobleaching (FRAP, iFRAP, FLIP)
- photoactivation
- using measured data as forcing functions to open loops and simplify analysis (can use forcing functions for tracer data or chemical system ("tracee") data or both)
- any of these can be superimposed on both steady state and non-steady state systems
- experimentally initiated changes in conditions can be implemented at any time using a very general "events" tool
Each experiment can have many measurements and multiple data sets
Any experimental data set can be used as a forcing function to drive the model at its boundary or to decouple the model at points of high complexity
Simulate any model with any number of relevant experiments
ProcessDB is one of the only tools available that was specifically designed to support the analysis of non-steady state tracer kinetic models.
Experimental protocols automatically imposed on models
Using standard biophysical principles, ProcessDB can automatically translate your models and their linked experiments to mathematics, ready to be simulated
To speed the transition from your model diagram to your first simulation, use the Run Initial Simulation tool.
Leverage a complete set of tools for solution (CVODE), comparison of solutions and data, gradient parameter optimization (ODRPACK95), and global parameter optimization (Particle Swarm).
Optimize over many experiments, each with many data sets, simultaneously
Reports detailed parameter statistics including fractional standard deviations (FSDs) and 95% confidence intervals
Many models can be open at once, each in a separate tab
Flexible graphing for model output and comparison to data
- User-specified graph titles and axis labels
- Unlimited user-defined graphs of any model variable
- Expand any graph to full screen
- Automatic pairing of graphs for experimental data and associated model solutions
- Flexible control of Y-axis range for both linear and semi-log graphs
- Optional reference graphs for your current best parameter set
- User-control of solution and data point colors
- Display all graphs or a selected subset of graphs
- Import graph definitions from other models
- Visual parameter sensitivity tool
- Load saved parameter sets into reference solution for comparison
- Temporarily hide any plot in a graph by clicking its legend
- Copy any graph to the clipboard for pasting into reports
- Automatically plot precursors for any plotted state
- Apply user-defined tags to subsets of graphs so they can be displayed as a related group
Automatically builds a personal and searchable database of molecules, molecular complexes, processes and models as you work
Everything in your database is instantly available for re-use
Search your database by name or by unique ProcessDB IDs
Show all models in your database involving a chosen molecule or molecular complex
Show all models in your database involving a chosen process
Show all models in your database involving a chosen physiological Place
Keeps track of molecular components in a complex even if you rename it
Display all molecules with roles in a given model
Diagram colors can be easily changed
Rename or delete a model
Specify an experiment based on a given model
Automatic detection of mismatched experiments and models
From a model diagram, select a State and display a list of all models that include that molecule in that place
Prompts user for rate laws when they cannot be determined from the diagram alone
Models can be duplicated in two ways - one that keeps the two models linked so that changes to common processes are always synchronized, and another that separates the two models so they can evolve independently.
Online user guide, reference manual, and modeling textbook
More than 100 sample models in ProcessDB's Public Models database. Public models may be copied to your own database for study, practice or re-use.
Experimental data can easily be imported from Excel files (that have no formulas) or entered manually
Any data set can be used as a forcing function to implement open-loop analysis or to define boundary conditions.
Professionally maintained and backed-up on our secure web server directly connected to the Internet backbone
All default rate laws can be displayed and modified if desired
Simulate models with the fast integrated Simulator based on CVODE and a custom interpreter that has proven faster than other solvers/simulators.