# \#catalyst

**URL:** https://discourse.julialang.org/tag/catalyst/754.md

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## [Arrow types in Catalyst JumpProblem](https://discourse.julialang.org/t/arrow-types-in-catalyst-jumpproblem/136709)

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**Author:** [@hhindley](https://discourse.julialang.org/u/hhindley)\
**Replies:** 6\
**Last updated:** [April 14, 2026, 4:04pm UTC](https://discourse.julialang.org/t/arrow-types-in-catalyst-jumpproblem/136709 "2026-04-14T16:04:11Z")

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I have a question about the arrow types in Catalyst models when simulating jump processes. I build the model as a reaction network in Catalyst and simulate it as a JumpProblem. It’s a large model and so I’m trying to opt…

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## [Precompilation error with Catalyst (Circular dependency)](https://discourse.julialang.org/t/precompilation-error-with-catalyst-circular-dependency/136013)

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**Author:** [@Luca\_Maria\_Moccia](https://discourse.julialang.org/u/Luca_Maria_Moccia)\
**Replies:** 3\
**Last updated:** [March 4, 2026, 4:23pm UTC](https://discourse.julialang.org/t/precompilation-error-with-catalyst-circular-dependency/136013 "2026-03-04T16:23:37Z")

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Hello everyone, I am currently working on a biology modeling project for my Master’s internship, using an environment provided by my lab. When trying to load our local package (which depends heavily on the SciML ecosys…

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## [Catalyst.jl and ModelingToolkit (question after reading about ModelingToolkit license changes)](https://discourse.julialang.org/t/catalyst-jl-and-modelingtoolkit-question-after-reading-about-modelingtoolkit-license-changes/135303)

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**Author:** [@twcawm](https://discourse.julialang.org/u/twcawm)\
**Replies:** 1\
**Last updated:** [January 28, 2026, 4:06am UTC](https://discourse.julialang.org/t/catalyst-jl-and-modelingtoolkit-question-after-reading-about-modelingtoolkit-license-changes/135303 "2026-01-28T04:06:51Z")

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Hi, I have been investigating and trying out the Catalyst.jl package (it’s really awesome, by the way!). I saw recently the discussions on ModelingToolkit license changes. Is the plan to keep maintaining Catalyst.jl a…

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## [Can a callback be triggered at the initial time point (at t=0)](https://discourse.julialang.org/t/can-a-callback-be-triggered-at-the-initial-time-point-at-t-0/114376)

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**Author:** [@valerdam](https://discourse.julialang.org/u/valerdam)\
**Replies:** 3\
**Last updated:** [December 16, 2025, 10:54am UTC](https://discourse.julialang.org/t/can-a-callback-be-triggered-at-the-initial-time-point-at-t-0/114376 "2025-12-16T10:54:09Z")

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I am using the code from advanced\_simulations - (the one using CallbackSets) and just modified the time to include t=0.0. ps\_cb\_1 = PresetTimeCallback(\[3.0, 7.0\], integ -\> integ\[:X1\] += 5.0) and added a time zero ps\_c…

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## [Constructing a chemical reaction network from an ode system](https://discourse.julialang.org/t/constructing-a-chemical-reaction-network-from-an-ode-system/132682)

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**Author:** [@adhalanay](https://discourse.julialang.org/u/adhalanay)\
**Replies:** 1\
**Last updated:** [September 26, 2025, 8:02pm UTC](https://discourse.julialang.org/t/constructing-a-chemical-reaction-network-from-an-ode-system/132682 "2025-09-26T20:02:36Z")

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The so called Hungarian Lemma states that a system of ODEs with polynomial RHS x'\_j =f\_j(x),j=\\overline{1,n} comes from a mass-action chemical reaction network if and only if all the negative monomials of f\_f have x\_j …

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## [Latexify/Catalyst introduces extra exponent - issue with mm and hill?](https://discourse.julialang.org/t/latexify-catalyst-introduces-extra-exponent-issue-with-mm-and-hill/131819)

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**Author:** [@orkun\_soyer](https://discourse.julialang.org/u/orkun_soyer)\
**Replies:** 6\
**Last updated:** [August 26, 2025, 2:54pm UTC](https://discourse.julialang.org/t/latexify-catalyst-introduces-extra-exponent-issue-with-mm-and-hill/131819 "2025-08-26T14:54:08Z")

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‘‘‘ ppGppSys1 = @reaction\_network begin kin, ∅ --\> G6P hill(G6P,v01,k01,1), G6P → F6P end odesys = convert(ODESystem, ppGppSys1; combinatoric\_ratelaws=false, remove\_conserved = true) latexif…

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## [Calling complete() adds differential constraints to algebraic extension of ReactionSystem](https://discourse.julialang.org/t/calling-complete-adds-differential-constraints-to-algebraic-extension-of-reactionsystem/131115)

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**Author:** [@spackman](https://discourse.julialang.org/u/spackman)\
**Replies:** 2\
**Last updated:** [July 28, 2025, 2:07pm UTC](https://discourse.julialang.org/t/calling-complete-adds-differential-constraints-to-algebraic-extension-of-reactionsystem/131115 "2025-07-28T14:07:17Z")

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Hey guys, I’m doing some experimentation with Catalyst.jl and algebraic equations to define systems where the system volume is not constant. This can occur when the major solvent is a reactant in appreciable quantities…

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## [Catalyst.jl - updating kinetic parameters to be time-dependent after loading a reaction network](https://discourse.julialang.org/t/catalyst-jl-updating-kinetic-parameters-to-be-time-dependent-after-loading-a-reaction-network/130989)

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**Author:** [@spackman](https://discourse.julialang.org/u/spackman)\
**Replies:** 12\
**Last updated:** [July 27, 2025, 8:23pm UTC](https://discourse.julialang.org/t/catalyst-jl-updating-kinetic-parameters-to-be-time-dependent-after-loading-a-reaction-network/130989 "2025-07-27T20:23:59Z")

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Hi there, I am trying to build a ReactionSystem with time-varying parameters using ReactionNetworkImporters.jl function loadrxnetwork(). I want to initialize the network with placeholder time-varying kinetic parameters …

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## [Catalyst.jl - what is the appropriate way to model equilibrium (i.e. pKa?)](https://discourse.julialang.org/t/catalyst-jl-what-is-the-appropriate-way-to-model-equilibrium-i-e-pka/130149)

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**Author:** [@spackman](https://discourse.julialang.org/u/spackman)\
**Replies:** 8\
**Last updated:** [July 24, 2025, 11:28am UTC](https://discourse.julialang.org/t/catalyst-jl-what-is-the-appropriate-way-to-model-equilibrium-i-e-pka/130149 "2025-07-24T11:28:16Z")

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Hello again, I’m working to add some additional equilibrium conditions to a reaction network, particularly pKa. I’m inclined to think that algebraic constraint equations are the appropriate choice here assuming that th…

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## [Issue with scoping rules of parameter (and variable) declaration in components (Catalyst vs ModelingToolkit)](https://discourse.julialang.org/t/issue-with-scoping-rules-of-parameter-and-variable-declaration-in-components-catalyst-vs-modelingtoolkit/130232)

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**Author:** [@Cedric\_Lhoussaine](https://discourse.julialang.org/u/Cedric_Lhoussaine)\
**Replies:** 8\
**Last updated:** [July 2, 2025, 3:19pm UTC](https://discourse.julialang.org/t/issue-with-scoping-rules-of-parameter-and-variable-declaration-in-components-catalyst-vs-modelingtoolkit/130232 "2025-07-02T15:19:18Z")

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Working with Catalyst v15.0.8 and ModelingToolkit v9.80.5, I found a strange and misleading behavior w.r.t. parameter declarations in reaction components: suppose I declare a parameter (k) in two different components (n…

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## [Catalyst.jl - what is the appropriate way to model energy?](https://discourse.julialang.org/t/catalyst-jl-what-is-the-appropriate-way-to-model-energy/130088)

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**Author:** [@spackman](https://discourse.julialang.org/u/spackman)\
**Replies:** 6\
**Last updated:** [June 23, 2025, 1:33am UTC](https://discourse.julialang.org/t/catalyst-jl-what-is-the-appropriate-way-to-model-energy/130088 "2025-06-23T01:33:40Z")

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Hi there! I’m interested in tracking the thermodynamics of a chemical system along with the kinetics, but I don’t see any example documentation that would indicate the best/native way to do this. I think in an older ve…

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## [Building Catalyst.jl reaction network from a .csv file - error in construction?](https://discourse.julialang.org/t/building-catalyst-jl-reaction-network-from-a-csv-file-error-in-construction/130043)

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**Author:** [@spackman](https://discourse.julialang.org/u/spackman)\
**Replies:** 6\
**Last updated:** [June 20, 2025, 8:51pm UTC](https://discourse.julialang.org/t/building-catalyst-jl-reaction-network-from-a-csv-file-error-in-construction/130043 "2025-06-20T20:51:51Z")

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Hey Julia crew! I am trying to import a reaction network from a .csv file to use with Catalyst.jl via Reaction NetworkImporters.jl. I have been able to successfully construct a ReactionSystem object which can print its…

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## [Time-plotting the derivative of a species (reaction velocity) in catalyst](https://discourse.julialang.org/t/time-plotting-the-derivative-of-a-species-reaction-velocity-in-catalyst/129927)

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**Author:** [@Andre\_Renard](https://discourse.julialang.org/u/Andre_Renard)\
**Replies:** 1\
**Last updated:** [June 16, 2025, 9:37pm UTC](https://discourse.julialang.org/t/time-plotting-the-derivative-of-a-species-reaction-velocity-in-catalyst/129927 "2025-06-16T21:37:32Z")

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Hello, I can’t find an easy way to time-plot a derivative of a species, although I’m sure data are stored somewhere. Thanks for help. Andre

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## [Using Catalyst and Symbolics/ModelingToolkit together](https://discourse.julialang.org/t/using-catalyst-and-symbolics-modelingtoolkit-together/127601)

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**Author:** [@Menno](https://discourse.julialang.org/u/Menno)\
**Replies:** 7\
**Last updated:** [April 8, 2025, 1:00pm UTC](https://discourse.julialang.org/t/using-catalyst-and-symbolics-modelingtoolkit-together/127601 "2025-04-08T13:00:21Z")

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Hi there! I have been very impressed by Catalyst and using it to solve (stochastic) differential equations, but have been having trouble using the generated equations for other tasks. More specifically, I have been tryin…

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## [Modelling caffeïne effect on alertness in humans with Catalyst](https://discourse.julialang.org/t/modelling-caffeine-effect-on-alertness-in-humans-with-catalyst/127736)

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**Author:** [@modeler32](https://discourse.julialang.org/u/modeler32)\
**Replies:** 4\
**Last updated:** [April 7, 2025, 5:08pm UTC](https://discourse.julialang.org/t/modelling-caffeine-effect-on-alertness-in-humans-with-catalyst/127736 "2025-04-07T17:08:03Z")

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Hi everyone, I am trying to make a reaction network object in Pluto notebook, in which I have to model the effect of caffeine intake on alertness in humans. I’m trying to keep it simple, and this is what I have for now: …

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## [Adding jump to JumpProblem defined from Catalyst model](https://discourse.julialang.org/t/adding-jump-to-jumpproblem-defined-from-catalyst-model/127790)

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**Author:** [@hhindley](https://discourse.julialang.org/u/hhindley)\
**Replies:** 2\
**Last updated:** [April 7, 2025, 4:35pm UTC](https://discourse.julialang.org/t/adding-jump-to-jumpproblem-defined-from-catalyst-model/127790 "2025-04-07T16:35:09Z")

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Hi, Does anyone know if it’s possible to add a newly defined jump to a JumpProblem which is directly defined from a Catalyst.jl model? This is easily done when building a model straight from Jumps, just add another one …

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## [Is there a way to dynamically add/remove of reactions from ReactionSystem in catalyst](https://discourse.julialang.org/t/is-there-a-way-to-dynamically-add-remove-of-reactions-from-reactionsystem-in-catalyst/127411)

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**Author:** [@atiyabzafar](https://discourse.julialang.org/u/atiyabzafar)\
**Replies:** 3\
**Last updated:** [April 7, 2025, 7:22am UTC](https://discourse.julialang.org/t/is-there-a-way-to-dynamically-add-remove-of-reactions-from-reactionsystem-in-catalyst/127411 "2025-04-07T07:22:05Z")

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Hi I am trying to figure out a way to dynamically add/remove reactions once I have defined a ReactionSystem programmatically. Suppose I define the system using this function. function generate\_creation(n,MAT) # Cre…

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## [Cannot recreate JumpProcess example in Catalyst](https://discourse.julialang.org/t/cannot-recreate-jumpprocess-example-in-catalyst/127248)

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**Author:** [@contejuz](https://discourse.julialang.org/u/contejuz)\
**Replies:** 0\
**Last updated:** [March 22, 2025, 1:47am UTC](https://discourse.julialang.org/t/cannot-recreate-jumpprocess-example-in-catalyst/127248 "2025-03-22T01:47:02Z")

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I’ve been using Catalyst successfully for the past few weeks. It’s pretty great! However, I recently tried to update PlutoUI from 0.7.14 to 0.7.51 (not sure why such an old version was installed). I then updated all my p…

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## [Time dependent inputs to reaction network in Catalyst](https://discourse.julialang.org/t/time-dependent-inputs-to-reaction-network-in-catalyst/121078)

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**Author:** [@contejuz](https://discourse.julialang.org/u/contejuz)\
**Replies:** 5\
**Last updated:** [February 11, 2025, 3:20pm UTC](https://discourse.julialang.org/t/time-dependent-inputs-to-reaction-network-in-catalyst/121078 "2025-02-11T15:20:25Z")

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I’m trying to create a simple reaction network that takes external input. Here is one example (adapted from the docs): # Create model. model = @reaction\_network begin kB\*I(t), S + E --\> SE kD, SE --\> S + E k…

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## [Error: MethodError: no method matching validate](https://discourse.julialang.org/t/error-methoderror-no-method-matching-validate/123354)

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**Author:** [@Jax\_Xu](https://discourse.julialang.org/u/Jax_Xu)\
**Replies:** 9\
**Last updated:** [December 2, 2024, 4:14pm UTC](https://discourse.julialang.org/t/error-methoderror-no-method-matching-validate/123354 "2024-12-02T16:14:02Z")

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Hi! I’m new to Julia and Catalyst.jl. I am trying to follow the tutorial of Introduction to learn how to use catalyst. I install packages, including Blockquote Status C:\\Users\\23954749\\.julia\\environments\\v1.10\\Projec…

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## [Possibility of factorization for ODEs produced by a mass action chemical reaction network](https://discourse.julialang.org/t/possibility-of-factorization-for-odes-produced-by-a-mass-action-chemical-reaction-network/122950)

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**Author:** [@adhalanay](https://discourse.julialang.org/u/adhalanay)\
**Replies:** 1\
**Last updated:** [November 22, 2024, 11:29am UTC](https://discourse.julialang.org/t/possibility-of-factorization-for-odes-produced-by-a-mass-action-chemical-reaction-network/122950 "2024-11-22T11:29:12Z")

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In the algebraic approach to mass action chemical reaction networks there is a very useful factorization of the RHS of the ODE system \\frac{dx}{dt}=Y\\cdot A\_k \\cdot \\Phi(x), where Y is the complex stoichiometric matr…

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## [Getting Catalyst and Oscar to work together](https://discourse.julialang.org/t/getting-catalyst-and-oscar-to-work-together/121299)

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**Author:** [@adhalanay](https://discourse.julialang.org/u/adhalanay)\
**Replies:** 10\
**Last updated:** [November 20, 2024, 9:34pm UTC](https://discourse.julialang.org/t/getting-catalyst-and-oscar-to-work-together/121299 "2024-11-20T21:34:06Z")

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This more of an extension of the previous topic https://discourse.julialang.org/t/finding-steady-states-symbolicaly/119545/18. First some background: commutative algebra is of great use for studying mass-action chemical…

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## [Finding steady-states symbolicaly](https://discourse.julialang.org/t/finding-steady-states-symbolicaly/119545)

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**Author:** [@adhalanay](https://discourse.julialang.org/u/adhalanay)\
**Replies:** 17\
**Last updated:** [October 14, 2024, 3:06pm UTC](https://discourse.julialang.org/t/finding-steady-states-symbolicaly/119545 "2024-10-14T15:06:05Z")

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Maybe the question is trivial, but I cannot find an answer. Using Catalyst.jl I introduced a reaction network rn and constructed the corresponding system of ODEs with convert(ODESystem,rn). The system has a number of pa…

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## [Parameters modified by events are not captured in ODE the solution](https://discourse.julialang.org/t/parameters-modified-by-events-are-not-captured-in-ode-the-solution/114592)

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**Author:** [@valerdam](https://discourse.julialang.org/u/valerdam)\
**Replies:** 1\
**Last updated:** [May 23, 2024, 9:23pm UTC](https://discourse.julialang.org/t/parameters-modified-by-events-are-not-captured-in-ode-the-solution/114592 "2024-05-23T21:23:23Z")

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It seems that parameters modified by callback events are not captured as time dependent in the ODE solution. Using a slight modification of the example in here, parameter k changes from 1.0 to 5.0 at time t=5. However t…

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## [Callback function modifying model parameter](https://discourse.julialang.org/t/callback-function-modifying-model-parameter/114478)

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**Author:** [@valerdam](https://discourse.julialang.org/u/valerdam)\
**Replies:** 15\
**Last updated:** [May 22, 2024, 12:17pm UTC](https://discourse.julialang.org/t/callback-function-modifying-model-parameter/114478 "2024-05-22T12:17:19Z")

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I need to modify a parameter in an ODE problem in a callback. I found an example that does exactly what I want in here. (on the page search for PresetTimeCallback and it is the code including the first occurrence). Copie…

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## [Implement Matlab/Simbiology concepts (e.g. compartments, repeated assignments) in Julia/Catalyst](https://discourse.julialang.org/t/implement-matlab-simbiology-concepts-e-g-compartments-repeated-assignments-in-julia-catalyst/114266)

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**Author:** [@valerdam](https://discourse.julialang.org/u/valerdam)\
**Replies:** 9\
**Last updated:** [May 15, 2024, 2:13pm UTC](https://discourse.julialang.org/t/implement-matlab-simbiology-concepts-e-g-compartments-repeated-assignments-in-julia-catalyst/114266 "2024-05-15T14:13:21Z")

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I am testing ways to code Matlab/Simbiology concepts (e.g. compartments, repeated assignments) in Julia/Catalyst and I would appreciate both general pointers on where to find more information as well as figuring out one…

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## [Gradient-based parameter estimation for Catalyst.jl models](https://discourse.julialang.org/t/gradient-based-parameter-estimation-for-catalyst-jl-models/112542)

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**Author:** [@dhowsmon](https://discourse.julialang.org/u/dhowsmon)\
**Replies:** 1\
**Last updated:** [April 5, 2024, 3:03am UTC](https://discourse.julialang.org/t/gradient-based-parameter-estimation-for-catalyst-jl-models/112542 "2024-04-05T03:03:48Z")

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Hi, I am trying to estimate parameters/initial conditions in an ODE system built with Catalyst.jl. I first find the steady-state using a callback, and then in a separate simulation I add some input to get my actual desir…

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## [Zero Order Extinction Reaction](https://discourse.julialang.org/t/zero-order-extinction-reaction/108749)

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**Author:** [@kkakosim](https://discourse.julialang.org/u/kkakosim)\
**Replies:** 21\
**Last updated:** [March 27, 2024, 3:25pm UTC](https://discourse.julialang.org/t/zero-order-extinction-reaction/108749 "2024-03-27T15:25:57Z")

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Is there any way to achieve the positive\_domain effect with the Catalyst.jl syntax? In my example (decomposition of CaC2 yielding Calcium gas and solid Carbon): CaC2 → Ca(g) + 2C(s) I am looking for a way to “remove” …

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## [@unpack from Catalyst reaction system and unused variables](https://discourse.julialang.org/t/unpack-from-catalyst-reaction-system-and-unused-variables/110766)

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**Author:** [@johannesnauta](https://discourse.julialang.org/u/johannesnauta)\
**Replies:** 9\
**Last updated:** [February 26, 2024, 3:26pm UTC](https://discourse.julialang.org/t/unpack-from-catalyst-reaction-system-and-unused-variables/110766 "2024-02-26T15:26:27Z")

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Hi all. I have happily been using Catalyst.jl (and of course related packages, such as ModelingToolkit.jl and DifferentialEquations.jl), but when remaking problems while using EnsembleProblem I encountered some odd behav…

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## [SBMLToolkit and Catalyst Warnings](https://discourse.julialang.org/t/sbmltoolkit-and-catalyst-warnings/107533)

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**Author:** [@Nick1](https://discourse.julialang.org/u/Nick1)\
**Replies:** 3\
**Last updated:** [January 29, 2024, 10:14pm UTC](https://discourse.julialang.org/t/sbmltoolkit-and-catalyst-warnings/107533 "2024-01-29T22:14:12Z")

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I am importing an SBML file without a problem but I got the following warnings: Warning: Stoichiometries of SpeciesReferences are not defined. Setting to 1. WARNING: both Symbolics and ModelingToolkit export “suprem…

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