Modules for reusable and collaborative modeling of biological mathematical systems


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Presentation delivered at the 3rd IEEE Track on
Collaborative Modeling & Simulation - CoMetS'12.

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Modules for reusable and collaborative modeling of biological mathematical systems

  1. 1. 3rd IEEE Track on Collaborative Modelling and Simulation – CoMetS 12 Modules for Reusable and Collaborative Modelling ofMathematical Biological Systems Mandeep Gill, Steve McKeever, David Gavaghan
  2. 2. Overview● Biological and Cardiac Modelling● Ode DSL● Collaborative Model Reuse● Modules● Model Module Repositories● Partial Results● Summary
  3. 3. Biological Modelling● Overall goal to model entire human body, from genomic level upto organ and body level in an integrative manner – DNA, Protein, Cellular Compartments, Cells, Tissue, Organs, Entire Body● Several major aims, including, – Increased understanding of biological processes – Personalised medicine and treatment – In-silico experiments into disease and drug function
  4. 4. Biological Modelling● Individual models are painstakingly derived from multiple sets of experimental data, from multiple disciplines, even across multiple species in a collaborative process● Requires a knowledge and research in a variety of disciplines from multiple users utilising a range of modelling approaches – Physiologists – Biologists / Biochemists – Mathematicians – Software Engineers / Computer Scientists
  5. 5. Biological Modelling● Typically model from a continuous, deterministic perspective, using ODEs and PDEs – i.e. Cell cycles, signalling pathways, cardiac electrophysiology● Our research is focused on cardiac modelling as it is highly developed with a range of specific models backed by experimental data● Cardiac diseases and disorders comprise one of the largest sets of health risks in the Western world
  6. 6. Cardiac Modelling● Computational modelling of the electrical and mechanical activity of the heart is recognised as a powerful technique in the detailed investigation of cardiac behaviour – Particularly in respect to modelling disease and the effects of drugs on cardiac function● Cardiac cell models typically investigate electrical changes during an action potential – These are governed by the function of ion channels within the cell – Flow of charged ions within capacitative membrane causes changes in cellular potential
  7. 7. Cardiac Modelling● We traditionally model cardiac function at multiple levels – Cellular level, treated as spatially homogeneous entity and modelled using ODEs – Tissue level and organ level, using PDEs● Simulation complex, solvers specific to each model● Simulation extremely computationally intensive – Modern cell models can require 20min – Whole organ models can require 9min to simulate 100ms of rabbit ventricular activity ● Utilising a 2048-core computer cluster
  8. 8. Cardiac Cell Model Example −I stim + ∑ I ionδV = Cm
  9. 9. Multi-Scale Cardiac Models
  10. 10. Ode DSL● DSL for developing mathematical (cardiac) biological cell models● Features – Numbers, Booleans, Functions, structures and mathematical operators – Direct support for ODEs (potentially DAEs) – Syntax similar to Python and MATLAB – Based on sound, computational foundation – Support for model validation and model reuse
  11. 11. Ode DSL Aims and Goals● Enable rapid model construction and prototyping● Executable model specification● Facilitate model reuse and collaborative development● Ease of use for non-programmers● Specific support for biological modelling● High simulation performance● Investigation into multi-scale APIs/integration
  12. 12. Model Validation - Type System● Ode is type checked statically during compilation to enforce correctness of model equations – i.e. checks nonsensical statements, – 5 + True // error● This ensures that a valid model may always be simulated successfully – although makes no guarantees regarding the correctness of the results● Type information is used to guide optimisations during implementation
  13. 13. Model Validation - Units System● Many models of physical systems are expressed in terms of units-of-measure – type-system extended to support static checking of units – speed : m/s = 100m / 10s● Units can be created within the model and assigned to values – used to check that all equations are dimensionally consistent● Algorithm can infer the correct units in many cases,● Where proven safe, the system can automatically convert between units of the same dimension
  14. 14. Collaborative Model Reuse● Models are continuously developed and improved from, – newer experimental research and data – previous models and simulations● More complex, integrative models derived from the composition of existing, smaller models, e.g. – Cardiac models derived from multiple ion channel models – 2D and 3D tissue and whole organ models derived from finite element method and single cell models● Require a mechanism to reuse models within DSL
  15. 15. Collaborative Model Reuse● Cardiac models have gone from 2 channels with 4 ODEs to over 11 channels with 60 ODEs to describe the same cell type within a species● We can consider the single cell model as composed from multiple independent channels
  16. 16. Collaborative Model Reuse● From modelling perspective, can consider each individual component as implementing an interface● This interface is then utilised by the structure/cell to comprise the final model● Providing these components exhibit the same interface, they may be, – developed by multiple users – replaced by different implementations – altered to investigate differing model properties ● Effect of drugs on well-known models
  17. 17. Modules● The idea of reusable, composed components shown in the cell model is encapsulated with a flexible module system – enables sharing/reuse within and between models – leads to repository of reusable model components● Module system allows grouping logically related model components into an connected, independent structure● Type system used to generate a signature for the module that forms its interface – ensures module may be correctly used and composed
  18. 18. Modules Potassium Sodium Calcium Channel Channel Channel Interface calc_I :: (milliV, milliV) -> microA/cm^2 Cardiac Modelmodule CardiacModel { import HH.CaChannel import HH.KChannel import HH.NaChannel // model code goes here }
  19. 19. Parameterised Modules● Allows a module to take user-defined modules as parameters● Increases module flexibility and enables specialisation by module users● Type system ensures safe module composition, checks all implementations exhibit same interface module CardiacModel(KChannel) { Potassium Parameterised // as before... Channel #1 Cardiac } model Potassium Interface calc_I :: (milliV, milliV) Channel #2 -> microA/cm^2
  20. 20. Module Repositories● Modules may be contained within repositories● Multiple repository hierarchies may be enabled by the modeller and utilised within the simulation environment● Modules are referenced by a unique name derived from location within the repository directory structure Repo1/Cardiac/HH58.ode module SodiumChannel {...} ... Name import Repo1.Cardiac.HH58.SodiumChannel
  21. 21. Module Repositories● When backed by version control software a repository can form a collaborative environment – Multiple users can create, modify and share modules● Simulation-time type and units system ensures integrity of modules and their valid composition – Invalid modules easily detected● Intend to have multiple repositories for differing biological modelling domains – Including a canonical model repository
  22. 22. Model Repositories – Future areas● Semantic Metadata – quality, correctness, origins, ontologies● Web interface to repository● Best Practices – i.e. Module naming and name-spacing – Recommended interfaces for known entities● Dependencies – Intra- and Inter-repository – Automatic retrieval of dependencies● Some of these handled by CellML – XML language for biological model curation
  23. 23. (Partial) Results● We are using DSL to create several human cardiac cell models that share a common lineage● Use module features to parametrise modules through ion channels into reusable components with common interface● Intend to simulate ad-hoc model variants derived from module composition in order to investigate parameter differences and relate to initial experimental data● Intend to simulate models utilising custom high- performance GPU-based simulation engine
  24. 24. Summary● DSL created to enable rapid prototyping of models (and high-performance simulation)● Modularisation enables development by multiple parties within an interdisciplinary field● Modules may be reused, composed and customised within more complex models – Usage validated by strong type and units-checking present at the module interfaces● Module repositories combined with a version control system enable both collaborative and centralised development
  25. 25. Acknowledgements● Supervisors – Dr. Steve McKeever, University of Oxford, UK – Prof. David Gavaghan, University of Oxford, UK● Thank you for listening● Questions?