MENELMACAR

To be pronounced mene'lmakar.

Making Execution of (Nearly) Every Life-science Model ACcessible to All Researchers.

OdinViewer is a tool designed to visualise models published on EBI's Biomodels website where researchers can upload their models and associated papers. You can visualise these models through time or see an automatically generated graph for each model.

Running this tool locally

You can run this website locally with the following commands:

npm install & npm run dev
npm install & npm run build & npm run preview

Once you've done this just copy the url you shell returns (it should look like this: http://localhost:5173/) and paste it in your browser.

Adding models to the website

All models are imported manually on the website to be displayed.

To add a new model on the website, you need several files:

• A JavaScript file to describe the ODEs of the model
• A JSON file to get a graph of the model

Exporting an Odin model into JavaScript

To get the JavaScript file of the model, you should use SBMLtoOdin and export the resulting odin model into a JavaScript file using the following commands:

# install.packages("odin")
library(odin)
# install.packages("devtools")
library(devtools)
library(stringr)

load_all() # loads functions from SBMLtoOdin package

id <- "BIOMD0000000002" # change with the id of the model you want

output_file <- paste("../",id, ".R", sep = "")
importSBMLfromBioModels(id,output_file)

js_code <- odin::odin_js_bundle(output_file)
code <- js_code$model$code
code[1] <- paste("export",code[1])
splited_code <- str_split_1(code[1]," ")
splited_code[3] <- "model"
code[1] <- paste(splited_code, collapse = " ")
output_file <- paste("../",id, ".js", sep = "")
writeLines(code, con = output_file)

The JavaScript file should deposited into the public/models folder. You should also add the name of the model you just added to file_names.txt in the same folder.

Turning SBML files to JSON for the graph construction

For this part to work, all models should appear in the file_names.txt file. You can do the conversion by reading the README file in the TurningSBMLfilesToJSON folder.