CellMLToolkit.jl

CellMLToolkit.jl is a Julia library that connects CellML models to the Scientific Julia ecosystem. CellMLToolkit.jl acts as a bridge between CellML and ModelingToolkit.jl. It imports a CellML model (in XML) and emits a ModelingToolkit.jl intermediate representation (IR), which can then enter the SciML ecosystem.

CellML

CellML is an XML-based open-standard for the exchange of mathematical models. CellML originally started in 1998 by the Auckland Bioengineering Institute at the University of Auckland and affiliated research groups. Since then, its repository has grown to more than a thousand models. While CellML is not domain-specific, its focus has been on biomedical models. Currently, the active categories in the repository are Calcium Dynamics, Cardiovascular Circulation, Cell Cycle, Cell Migration, Circadian Rhythms, Electrophysiology, Endocrine, Excitation-Contraction Coupling, Gene Regulation, Hepatology, Immunology, Ion Transport, Mechanical Constitutive Laws, Metabolism, Myofilament Mechanics, Neurobiology, pH Regulation, PKPD, Protein Modules, Signal Transduction, and Synthetic Biology. There are many software tools to import, process and run CellML models; however, these tools are not Julia-specific.

SciML

SciML is a collection of Julia libraries for open source scientific computing and machine learning. The centerpiece of SciML is DifferentialEquations.jl, which provides a rich set of ordinary differential equations (ODE) solvers. One major peripheral component of SciML is ModelingToolkit.jl. It is a modeling framework for high-performance symbolic-numeric computation in scientific computing and scientific machine learning. The core of ModelingToolkit.jl is an IR language to code the scientific problems of interest in a high level. Automatic code generation and differentiation allow for the generation of a usable model for the other components of SciML, such as DifferentialEquations.jl.

Installation

To install CellMLToolkit.jl, use the Julia package manager:

using Pkg
Pkg.add("CellMLToolkit")

Contributing

Please refer to the SciML ColPrac: Contributor's Guide on Collaborative Practices for Community Packages for guidance on PRs, issues, and other matters relating to contributing to SciML.
See the SciML Style Guide for common coding practices and other style decisions.
There are a few community forums:
- The #diffeq-bridged and #sciml-bridged channels in the Julia Slack
- The #diffeq-bridged and #sciml-bridged channels in the Julia Zulip
- On the Julia Discourse forums
- See also SciML Community page

Example

  using CellMLToolkit, DifferentialEquations, Plots

  ml = CellModel("models/lorenz.cellml.xml")

  tspan = (0, 100.0)
  prob = ODEProblem(ml, tspan)
  sol = solve(prob, TRBDF2(), dtmax=0.01)
  X = map(x -> x[1], sol.u)
  Z = map(x -> x[3], sol.u)
  plot(X, Z)

Reproducibility

The documentation of this SciML package was built using these direct dependencies,

      Status `~/work/CellMLToolkit.jl/CellMLToolkit.jl/docs/Project.toml`
  [03cb29e0] CellMLToolkit v2.11.0 `~/work/CellMLToolkit.jl/CellMLToolkit.jl`
  [e30172f5] Documenter v0.27.24

and using this machine and Julia version.

Julia Version 1.6.7
Commit 3b76b25b64 (2022-07-19 15:11 UTC)
Platform Info:
  OS: Linux (x86_64-pc-linux-gnu)
  CPU: Intel(R) Xeon(R) Platinum 8171M CPU @ 2.60GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-11.0.1 (ORCJIT, skylake-avx512)

A more complete overview of all dependencies and their versions is also provided.

      Status `~/work/CellMLToolkit.jl/CellMLToolkit.jl/docs/Manifest.toml`
  [a4c015fc] ANSIColoredPrinters v0.0.1
  [c3fe647b] AbstractAlgebra v0.29.2
  [1520ce14] AbstractTrees v0.4.4
  [79e6a3ab] Adapt v3.6.1
  [ec485272] ArnoldiMethod v0.2.0
  [4fba245c] ArrayInterface v7.4.3
  [e2ed5e7c] Bijections v0.1.4
  [62783981] BitTwiddlingConvenienceFunctions v0.1.5
  [2a0fbf3d] CPUSummary v0.2.2
  [00ebfdb7] CSTParser v3.3.6
  [49dc2e85] Calculus v0.5.1
  [03cb29e0] CellMLToolkit v2.11.0 `~/work/CellMLToolkit.jl/CellMLToolkit.jl`
  [d360d2e6] ChainRulesCore v1.15.7
  [9e997f8a] ChangesOfVariables v0.1.6
  [fb6a15b2] CloseOpenIntervals v0.1.12
  [861a8166] Combinatorics v1.0.2
  [a80b9123] CommonMark v0.8.10
  [38540f10] CommonSolve v0.2.3
  [bbf7d656] CommonSubexpressions v0.3.0
  [34da2185] Compat v4.6.1
  [b152e2b5] CompositeTypes v0.1.3
  [187b0558] ConstructionBase v1.5.1
  [adafc99b] CpuId v0.3.0
  [a8cc5b0e] Crayons v4.1.1
  [9a962f9c] DataAPI v1.14.0
  [864edb3b] DataStructures v0.18.13
  [e2d170a0] DataValueInterfaces v1.0.0
  [b429d917] DensityInterface v0.4.0
  [2b5f629d] DiffEqBase v6.122.2
  [459566f4] DiffEqCallbacks v2.26.1
  [163ba53b] DiffResults v1.1.0
  [b552c78f] DiffRules v1.13.0
  [b4f34e82] Distances v0.10.8
  [31c24e10] Distributions v0.25.87
  [ffbed154] DocStringExtensions v0.9.3
  [e30172f5] Documenter v0.27.24
  [5b8099bc] DomainSets v0.6.6
  [fa6b7ba4] DualNumbers v0.6.8
  [7c1d4256] DynamicPolynomials v0.4.6
  [4e289a0a] EnumX v1.0.4
  [e2ba6199] ExprTools v0.1.9
  [8f5d6c58] EzXML v1.1.0
  [7034ab61] FastBroadcast v0.2.5
  [1a297f60] FillArrays v1.0.0
  [6a86dc24] FiniteDiff v2.19.0
  [59287772] Formatting v0.4.2
  [f6369f11] ForwardDiff v0.10.35
  [069b7b12] FunctionWrappers v1.1.3
  [77dc65aa] FunctionWrappersWrappers v0.1.3
  [46192b85] GPUArraysCore v0.1.4
  [c27321d9] Glob v1.3.1
  [86223c79] Graphs v1.8.0
  [0b43b601] Groebner v0.3.2
  [d5909c97] GroupsCore v0.4.0
  [34004b35] HypergeometricFunctions v0.3.14
  [b5f81e59] IOCapture v0.2.2
  [615f187c] IfElse v0.1.1
  [d25df0c9] Inflate v0.1.3
  [18e54dd8] IntegerMathUtils v0.1.0
  [8197267c] IntervalSets v0.7.4
  [3587e190] InverseFunctions v0.1.8
  [92d709cd] IrrationalConstants v0.2.2
  [82899510] IteratorInterfaceExtensions v1.0.0
  [692b3bcd] JLLWrappers v1.4.1
  [682c06a0] JSON v0.21.3
  [98e50ef6] JuliaFormatter v1.0.25
  [ccbc3e58] JumpProcesses v9.6.1
  [b964fa9f] LaTeXStrings v1.3.0
  [2ee39098] LabelledArrays v1.14.0
  [984bce1d] LambertW v0.4.6
  [23fbe1c1] Latexify v0.15.18
  [10f19ff3] LayoutPointers v0.1.14
  [50d2b5c4] Lazy v0.15.1
  [d3d80556] LineSearches v7.2.0
  [2ab3a3ac] LogExpFunctions v0.3.23
  [1914dd2f] MacroTools v0.5.10
  [d125e4d3] ManualMemory v0.1.8
  [abcecc63] MathML v0.1.14
  [c03570c3] Memoize v0.4.4
  [e1d29d7a] Missings v1.1.0
  [961ee093] ModelingToolkit v8.51.0
  [46d2c3a1] MuladdMacro v0.2.4
  [102ac46a] MultivariatePolynomials v0.4.7
  [d8a4904e] MutableArithmetics v1.2.3
  [d41bc354] NLSolversBase v7.8.3
  [2774e3e8] NLsolve v4.5.1
  [77ba4419] NaNMath v1.0.2
  [bac558e1] OrderedCollections v1.6.0
  [90014a1f] PDMats v0.11.17
  [d96e819e] Parameters v0.12.3
  [69de0a69] Parsers v2.5.8
  [e409e4f3] PoissonRandom v0.4.4
  [f517fe37] Polyester v0.7.3
  [1d0040c9] PolyesterWeave v0.2.1
  [d236fae5] PreallocationTools v0.4.12
  [21216c6a] Preferences v1.3.0
  [27ebfcd6] Primes v0.5.3
  [1fd47b50] QuadGK v2.8.2
  [fb686558] RandomExtensions v0.4.3
  [e6cf234a] RandomNumbers v1.5.3
  [3cdcf5f2] RecipesBase v1.3.3
  [731186ca] RecursiveArrayTools v2.38.3
  [189a3867] Reexport v1.2.2
  [ae029012] Requires v1.3.0
  [79098fc4] Rmath v0.7.1
  [7e49a35a] RuntimeGeneratedFunctions v0.5.6
  [94e857df] SIMDTypes v0.1.0
  [0bca4576] SciMLBase v1.91.6
  [c0aeaf25] SciMLOperators v0.2.0
  [efcf1570] Setfield v1.1.1
  [727e6d20] SimpleNonlinearSolve v0.1.14
  [699a6c99] SimpleTraits v0.9.4
  [66db9d55] SnoopPrecompile v1.0.3
  [a2af1166] SortingAlgorithms v1.1.0
  [276daf66] SpecialFunctions v2.2.0
  [aedffcd0] Static v0.8.6
  [0d7ed370] StaticArrayInterface v1.3.0
  [90137ffa] StaticArrays v1.5.19
  [1e83bf80] StaticArraysCore v1.4.0
  [82ae8749] StatsAPI v1.6.0
  [2913bbd2] StatsBase v0.33.21
  [4c63d2b9] StatsFuns v1.3.0
  [7792a7ef] StrideArraysCore v0.4.9
  [2efcf032] SymbolicIndexingInterface v0.2.2
  [d1185830] SymbolicUtils v1.0.4
  [0c5d862f] Symbolics v5.2.0
  [3783bdb8] TableTraits v1.0.1
  [bd369af6] Tables v1.10.1
  [8290d209] ThreadingUtilities v0.5.1
  [a759f4b9] TimerOutputs v0.5.22
  [0796e94c] Tokenize v0.5.25
  [a2a6695c] TreeViews v0.3.0
  [410a4b4d] Tricks v0.1.7
  [781d530d] TruncatedStacktraces v1.3.0
  [5c2747f8] URIs v1.4.2
  [3a884ed6] UnPack v1.0.2
  [1986cc42] Unitful v1.12.4
  [a7c27f48] Unityper v0.1.2
  [700de1a5] ZygoteRules v0.2.3
  [94ce4f54] Libiconv_jll v1.16.1+2
  [efe28fd5] OpenSpecFun_jll v0.5.5+0
  [f50d1b31] Rmath_jll v0.4.0+0
  [02c8fc9c] XML2_jll v2.10.3+0
  [0dad84c5] ArgTools
  [56f22d72] Artifacts
  [2a0f44e3] Base64
  [ade2ca70] Dates
  [8ba89e20] Distributed
  [f43a241f] Downloads
  [9fa8497b] Future
  [b77e0a4c] InteractiveUtils
  [b27032c2] LibCURL
  [76f85450] LibGit2
  [8f399da3] Libdl
  [37e2e46d] LinearAlgebra
  [56ddb016] Logging
  [d6f4376e] Markdown
  [a63ad114] Mmap
  [ca575930] NetworkOptions
  [44cfe95a] Pkg
  [de0858da] Printf
  [3fa0cd96] REPL
  [9a3f8284] Random
  [ea8e919c] SHA
  [9e88b42a] Serialization
  [1a1011a3] SharedArrays
  [6462fe0b] Sockets
  [2f01184e] SparseArrays
  [10745b16] Statistics
  [4607b0f0] SuiteSparse
  [fa267f1f] TOML
  [a4e569a6] Tar
  [8dfed614] Test
  [cf7118a7] UUIDs
  [4ec0a83e] Unicode
  [e66e0078] CompilerSupportLibraries_jll
  [deac9b47] LibCURL_jll
  [29816b5a] LibSSH2_jll
  [c8ffd9c3] MbedTLS_jll
  [14a3606d] MozillaCACerts_jll
  [05823500] OpenLibm_jll
  [83775a58] Zlib_jll
  [8e850ede] nghttp2_jll
  [3f19e933] p7zip_jll

You can also download the manifest file and the project file.