### Author:  [@spackman](https://discourse.julialang.org/u/spackman)
#### Post date: [June 19, 2025, 10:13pm UTC](https://discourse.julialang.org/t/building-catalyst-jl-reaction-network-from-a-csv-file-error-in-construction/130043/1 "2025-06-19T22:13:22Z")
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 itself using latexify, but additional commands fail with **MethodErrors**.
Here is a minimal example:
```julia
using Pkg
Pkg.activate(".")
using Catalyst, OrdinaryDiffEq, Plots, Latexify, CSV, DataFrames, ReactionNetworkImporters, GraphMakie, CairoMakie, NetworkLayout
function read_CRN(csvfile::String)
"""
read_CRN(csvfile::String)
Reads a CSV file containing the net reaction stoichiometry (products - reactants) and returns
two DataFrames containing substrate and product stoichiometry matrices, as well as a
numeric vector of rate constants from the first column.
### Arguments
- `csvfile::String`: The path to the input CSV file. The file should have a non-numeric
first column (rate constants) and numeric data in subsequent columns, where each row represents a reaction.
### Returns
- `product_matrix::Matrix{Int64}`: A transposed matrix with the stoichiometric coefficients of the products in each reaction.
- `substrate_matrix::Matrix{Float64}`: A transposed matrix with the stoichiometric coefficients of the substrates in each reaction.
- `rate_constants::Vector{Float64}`: A numeric vector containing the rate constants from the first column of the CSV.
- `species::Vector{String}`: A vector of species names corresponding to the columns in the stoichiometry matrix.
- `m_reactions::Int`: The number of reactions.
- `n_species::Int`: The number of species.
### Example
product_matrix, substrate_matrix, rate_constants, species, m_reactions, n_species = read_CRN("path/to/file.csv")
"""
# Read the CSV file into a DataFrame
data = CSV.read(csvfile, DataFrame)
species = names(data)[2:end]
rate_constants = Vector{Float64}(data[!, 1])
data_matrix = Matrix{Float64}(data[:, 2:end])
product_matrix = max.(data_matrix, 0)
substrate_matrix = -min.(data_matrix, 0)
# Transpose the product and substrate matrices for compatibility with catalyst.jl
product_matrix = Matrix(transpose(product_matrix))
substrate_matrix = Matrix(transpose(substrate_matrix))
# Get the number of reactions (rows) and species (columns)
m_reactions = size(data_matrix, 1) # Number of reactions (rows)
n_species = size(data_matrix, 2) # Number of species (columns)
# Convert the product matrix to integers
product_matrix = convert(Matrix{Int}, product_matrix)
# Return the transposed matrices, rate constants, species names, number of reactions, and number of species
return product_matrix, substrate_matrix, rate_constants, species, m_reactions, n_species
end
(prod, sub, k, species, m_reactions, n_species) = read_CRN("test_CRN.csv")
@species S(t)[1:n_species]
@parameters k[1:m_reactions]
@variables t
# Collect to a Vector{Num} type
pars = collect(k)
species = collect(S)
# Create the MatrixNetwork with correct types
mn = MatrixNetwork(pars, sub, prod; species=species, params=pars)
prn = loadrxnetwork(mn)
rn = prn.rn
latexify(rn)
```
When run on a `.csv` file with this contents:
| rate | S1 | S2 | S3 |
| --- | --- | --- | --- |
| 1 | -2 | 1 | 0 |
| 2 | 2 | -1 | 0 |
| 3 | -1 | -1 | 1 |
| 4 | 1 | 1 | -1 |
| 5 | 3 | 0 | -3 |
The expected latex is printed (edited here to render properly):
\begin{align\*} 2.0 \mathrm{\mathtt{S\_1}} &\leftrightarrow \mathrm{\mathtt{S\_2}} \quad (k\_1, k\_2) \\ \mathrm{\mathtt{S\_1}} + \mathrm{\mathtt{S\_2}} &\leftrightarrow \mathrm{\mathtt{S\_3}} \quad (k\_3, k\_4) \\ 3.0 \mathrm{\mathtt{S\_3}} &\rightarrow 3.0 \mathrm{\mathtt{S\_1}} \quad (k\_5) \end{align\*}
However, the network has not been properly constructed. Using
```julia
plot_network(rn)
```
returns this system:
Further, any additional calls to other functions appear to fail. Here is an example:
```julia
deficiency(rn)
```
```error
MethodError: no method matching exactdiv(::Float64, ::Float64)
The function `exactdiv` exists, but no method is defined for this combination of argument types.
Closest candidates are:
exactdiv(!Matched::Integer, ::Any)
@ ModelingToolkit C:\.julia\packages\ModelingToolkit\Z9mEq\src\systems\alias_elimination.jl:376
```
All similar functions throw the same error (i.e. \ exists but no method for this combination of argument types), which suggests that the `ReactionSystem` object was not actually constructed properly.
* * *
**Does anyone have any advice for this issue?**
I am using Catalyst 15.0.8. and ReactionNetworkImporters 0.16.1
---
### Author:  [@ChrisRackauckas](https://discourse.julialang.org/u/ChrisRackauckas)
#### Post date: [June 19, 2025, 10:55pm UTC](https://discourse.julialang.org/t/building-catalyst-jl-reaction-network-from-a-csv-file-error-in-construction/130043/2 "2025-06-19T22:55:22Z")
Is your stoichiometry represented using floats instead of integers? You may need to convert that.
---
### Author:  [@spackman](https://discourse.julialang.org/u/spackman)
#### Post date: [June 19, 2025, 11:17pm UTC](https://discourse.julialang.org/t/building-catalyst-jl-reaction-network-from-a-csv-file-error-in-construction/130043/3 "2025-06-19T23:17:57Z")
In a previous version I had issues with the dataframe automatically reading in as a `Matrix{Float}` instead of a `Matrix{Int}`, which causes `MatrixNetwork()` to fail. Either way I don’t think this is the root cause of the error…
---
### Author:  [@ChrisRackauckas](https://discourse.julialang.org/u/ChrisRackauckas)
#### Post date: [June 19, 2025, 11:35pm UTC](https://discourse.julialang.org/t/building-catalyst-jl-reaction-network-from-a-csv-file-error-in-construction/130043/4 "2025-06-19T23:35:19Z")
It is missing a dispatch that is expecting an integer. So it does need to convert at some point.
---
### Author:  [@isaacsas](https://discourse.julialang.org/u/isaacsas)
#### Post date: [June 20, 2025, 1:44am UTC](https://discourse.julialang.org/t/building-catalyst-jl-reaction-network-from-a-csv-file-error-in-construction/130043/5 "2025-06-20T01:44:43Z")
Network analysis functions generally require integer stoichiometry, so they will fail if you aren’t creating a network with integer stochioimetric coefficients as Chris said.
The graph looks ok to me modulo that the species nodes are incorrectly labeled. That seems like a Catalyst bug with labeling graphs when using array species. I’ve opened an issue so we can hopefully get that fixed.
---
### Author:  [@spackman](https://discourse.julialang.org/u/spackman)
#### Post date: [June 20, 2025, 5:55pm UTC](https://discourse.julialang.org/t/building-catalyst-jl-reaction-network-from-a-csv-file-error-in-construction/130043/6 "2025-06-20T17:55:06Z")
Awesome! Thanks!
In the future is it better to raise an issue directly or start with a discussion here? I figured that this did not relate to underlying functionality/structure of the code and was instead a user error which is why I posted here instead.
---
### Author:  [@isaacsas](https://discourse.julialang.org/u/isaacsas)
#### Post date: [June 20, 2025, 8:51pm UTC](https://discourse.julialang.org/t/building-catalyst-jl-reaction-network-from-a-csv-file-error-in-construction/130043/7 "2025-06-20T20:51:51Z")
Issues are better for feature requests and/or bugs. Discourse is good for general usage questions.