1. Welcome to the NSR Physiome Project!
  2. Physiome about
  3. Technical Projects

Technical Projects

Technical projects support the efforts of the Scientific projects. It likely the scope of Technical projects will expand as technology changes and progresses.

  • Database Design
    • Since the variety of Physiome projects is so diverse, including images and image sequences, it is recognized that standard relational databases will not suffice. More likely, object relational databases will be most useful. New search engines may allow for deep searching of many different types of databases, but commonalities of style and form will be most useful.
    • This group's aim should be to plan for these various contingencies and to design and implement the optimal database settings.
  • Markup Language Development
    • XML is spawning many variants for specific purposes. It would be useful to have a minimal number of variant markup languages to convey mathematical models and data sets form platform to platform.
    • This group should work to find the best communal path of effective and complete markup languages to serve this communicty. Since no current developments is highly advanced, or in general use, variants such as CellML, AnatML, and FieldML (all three from the University of Auckland), and SBML (The SBML Team; North America, Europe, Asia) need to be sorted out and developed. Ideally, SBML (Systems Biology Markup Language) might be developed to subsume CellML. Since both CellML and SBML handle ODEs but not PDEs, the latter will be in FieldML.
  • Simulation and Analysis Platforms
    • The underlying principle for the design of simulation and analysis platforms for the Physiome project is to accommodate the iterative processes from hypothesis, models, experimental design, validation or invalidation of the model hypothesis against real data, and revise the hypothesis. Data analysis, optimization, goodness of fit, and parameter confidence ranges are via such platform.
    • This group should focus on the overall process, pulling together information and techniques from other groups on authoring tools, schematics, visualization, analysis software, model verification, and computational methods.
  • Simulation Software Sites
  • Web Site Design
    • It is presumed that this web site will be one of many Physiome project sites. This site is to serve as a source site, providing templates to other Physiome web sites.
    • This group's focus should be on the parent web site and the relationship of parent to affiliate sites, as well as on the generic design of particular components of Physiome project web site design and development.
  • Tools for Schematics
    • Models usually begin from a schematic diagram of relationships among components. The schematics for genomic relationship are an example of useful approaches to the structuring of systems. Subsequent stages require quantifications of the relationships. designing model structures.
  • Authoring Tools
    • Icon-based modeling, using elements defined through a Biological Component Language, will speed the process of model development by providing pre-formed model components and allowing them to be linked. This will foster "run-time modeling" similiar to what is allowed at the equation level in languages like Basic and JSim, but would allow the linking of large subsystems within composite models. Apart from semantic issues it is vital to provide a user with the exact specifications for an icon.
  • Visualization
    • Data display and model solution display via 2-D and 3-D colored graphics with contouring can also be used for displays of sensitivity functions, behavioral analysis with parameter variation, and clustering of parameter estimates in data analysis. Although there are many examples of such visualization programs, a generally accessible toolkit is not available.
    • The goal of this group should be the creations of an accessible visualization toolkit.
  • Model Verification Methods
    • Methods for testing or determining the accuracy of different numerical solutions for models need to be worked out and should be the focus of this group.
  • Computational Methods
    • This Working Group would serve as a resource for guiding the modeling community to the available computational tools, including the linking between supercomputers and desktops or laptops. Methods include numerical and computational.
  • Analysis Software
    • This Working Group should consider optimization methods for fitting models to data, the assessment of goodness of fit, as well as population kinetic analysis for ascertaining parameter estimates from multiple experiments, to name a few.
  • Intellectual Property Management
    • The complex arrangements between Universities, investigators, inventors, and commercial developers are such that a Working Group encompassing such arrangements is needed. Figuring out how to keep the models and data in the public domain while preserving intellectual investment, would save an immense amount of time, if procedures can be developed to serve all the Physiome projects.

Model development and archiving support at https://www.imagwiki.nibib.nih.gov/physiome provided by the following grants: NIH U01HL122199 Analyzing the Cardiac Power Grid, 09/15/2015 - 05/31/2020, NIH/NIBIB BE08407 Software Integration, JSim and SBW 6/1/09-5/31/13; NIH/NHLBI T15 HL88516-01 Modeling for Heart, Lung and Blood: From Cell to Organ, 4/1/07-3/31/11; NSF BES-0506477 Adaptive Multi-Scale Model Simulation, 8/15/05-7/31/08; NIH/NHLBI R01 HL073598 Core 3: 3D Imaging and Computer Modeling of the Respiratory Tract, 9/1/04-8/31/09; as well as prior support from NIH/NCRR P41 RR01243 Simulation Resource in Circulatory Mass Transport and Exchange, 12/1/1980-11/30/01 and NIH/NIBIB R01 EB001973 JSim: A Simulation Analysis Platform, 3/1/02-2/28/07.