Parameter identifiability analysis is an analysis that describes whether the parameters of a dynamical system can be identified from data or whether they are redundant. There are two forms of identifiability analysis: structural and practical. Structural identifiability analysis relates changes in the solution of the ODE directly to other parameters, showcasing that it is impossible to distinguish between parameter A being higher and parameter B being lower, or the vice versa situation, given only data about the solution because of how the two interact. This could be done directly on the symbolic form of the equation as part of ModelingToolkit.jl. Meanwhile, practical identifiability analysis looks as to whether the parameters are non-identifiable in a practical sense, for example if two parameters are numerically indistinguishable (given possibly noisy data). In this case, numerical techniques being built in DiffEqSensitivity.jl, such as a nonlinear likelihood profiler or an information sensitivity measure can be used to showcase whether a parameter has a unique enough effect to be determined.
Recommended Skills: A basic background in differential equations and the ability to use numerical ODE solver libraries. Background in the numerical analysis of differential equation solvers is not required.
Expected Results: Efficient and high-quality implementations of parameter identifiability methods.
Mentors: Chris Rackauckas
Expected Project Size: 350 hour.
Difficulty: Hard.
Model order reduction is a technique for automatically finding a small model which approximates the large model but is computationally much cheaper. We plan to use the infrastructure built by ModelingToolkit.jl to implement a litany of methods and find out the best way to accelerate differential equation solves.
Recommended Skills: A basic background in differential equations and the ability to use numerical ODE solver libraries. Background in the numerical analysis of differential equation solvers is not required.
Expected Results: Efficient and high-quality implementations of model order reduction methods.
Mentors: Chris Rackauckas
Expected Project Size: 350 hour.
Difficulty: Medium to Hard depending on the chosen subtasks.
Numerically solving a differential equation can be difficult, and thus it can be helpful for users to simplify their model before handing it to the solver. Alas this takes time... so let's automate it! ModelingToolkit.jl is a project for automating the model transformation process. Various parts of the library are still open, such as:
Support for DAEs, DDEs, and SDEs
Pantelides algorithm for DAE index reduction
Lamperti transforms
Automatic construction of adjoint solutions
Tearing in nonlinear solvers
Solving distributed delay equations
Recommended Skills: A basic background in differential equations and the ability to use numerical ODE solver libraries. Background in the numerical analysis of differential equation solvers is not required.
Expected Results: Efficient and high-quality implementations of model transformation methods.
Mentors: Chris Rackauckas and Yingbo Ma
Expected Project Size: 175 hour or 350 hour depending on the chosen subtasks.
Difficulty: Medium to Hard depending on the chosen subtasks.
Catalyst is a great tool to model chemical reactions, but often reaction rate coefficients are usually suspect. There are well established methods to calculate what these coefficients should be given the activation energy of a reaction. We want to automate part of this modeling, allowing the user to provide atom-bond graphs and have coefficients determined for free.
Data structures to represent chemical species, compounds, ions, and isotopes
Arrhenius equation calculation of reaction rate coefficients k(T)
Automatically balancing reactions using above data structures
Verifying conservation of energy for each Reaction in a ReactionSystem
Recommended Skills: Strong understanding of chemistry and Julia open-source programming, particularly Symbolics.jl and ModelingToolkit.jl.
Expected Results: Define an interface for providing a Symbolics.jl object that contains relevant metadata for calculating activation energy and reaction rate coefficients using the Arrhenius equation.
Mentors: Chris Rackauckas, Anand Jain and Samuel Isaacson
Expected Project Size: 175 hour or 350 hour depending on the chosen subtasks.
Difficulty: Easy to Medium depending on the chosen subtasks.
Catalyst.jl provides the ability to create symbolic models of chemical reaction networks, generate symbolic differential equation and stochastic process models from them, and offers some limited ability to analyze the symbolic chemical reaction networks. There are a variety of ways Catalyst.jl's core capabilities could be expanded, including adding
tooling for detecting and classifying steady-states and their equilibria for mass-action systems (i.e. polynomial ODE systems).
tooling to infer from reaction network graph representations possible dynamic and equilibrium behaviors using chemical reaction network theory.
methods to reduce the size of reaction networks via the elimination of conserved species.
support for elimination of aliased species between different Catalyst model components to enable more modular composition of Catalyst-based models.
new ModelingToolkit-based systems to represent τ-leaping and/or abstract master equation representations, along with translation layers to generate such systems from Catalyst reaction network models.
new ModelingToolkit-based representations for hybrid systems mixing reactions across modeling scales (ODEs, SDEs, jump processes), along with translation layers to generate such systems from Catalyst reaction network models.
the ability for Catalyst reactions to allow random variables or general parameters to encode reaction stoichiometry, with updates to ModelingToolkit and Symbolics to support the generation of corresponding ODE, SDE and jump process models.
Recommended Skills: Strong understanding of ODE models for chemical systems and Julia open-source programming, particularly Symbolics.jl and ModelingToolkit.jl.
Expected Results: Extend Catalyst with one or more of the preceding features, with corresponding ModelingToolkit updates, enabling users to build, analyze, and simulate Catalyst-derived models incorporating the new components.
Mentors: Samuel Isaacson and Chris Rackauckas.
Expected Project Size: 175 hour or 350 hour depending on the chosen subtasks.
Difficulty: Easy to Hard depending on the chosen subtasks.