TOXTRUST

TOXTRUST is a flexible package allowing for a probablistic evaluation of toxicological evidence as well as for the combination of individual evidence pieces using rigorous rules based on the Dempster-Shafer theory (DST).

Architecture

TOXTRUST can be used in two different ways, either directly through a Python interpreter (e.g., Jupyter notebook) or a graphical user interface (GUI). TOXTRUST backend and the GUI make use of Anaconda (Anaconda Software Distribution 2020) to define the essential libraries, facilitate their automatic installation in a private environment, and keep track of package versions to avoid incompatibilities.

The backend is interconnected with the API (https://github.com/phi-grib/TOXTRUST_api) using Flask web framework, which provides the tools and libraries needed to set up a server, define routes (URLs), and handle HTTP requests. In this setup, Flask runs on the backend as a server that receives incoming requests from the frontend, processes them, and returns appropriate responses.

The GUI (https://github.com/phi-grib/TOXTRUST_web) built using Angular which interacts with Flask by sending HTTP requests to interact with data through RESTful API endpoints. Flask processes these requests, performs the necessary backend operations, and returns JSON responses. Angular uses this data to dynamically update the GUI in real-time. The GUI was designed to run locally as a desktop application, requiring the web server and the backend to operate on the same computer.

Installation

TOXTRUST can be used in most Windows, Linux or macOS configurations, provided that a suitable execution environment is set up. It is recommended to begin with an installation of the Conda package and the environment manager. A suitable Conda or Anaconda distribution for your operative system can be downloaded from here.

Download the repository:

git clone https://github.com/phi-grib/TOXTRUST.git

Go to the repository directory

cd TOXTRUST

and create the "toxtrust" conda environment with all the dependencies and extra packages:

conda env create -f environment.yml

Once the environment is created type:

source activate toxtrust

to activate the environment.

TOXTRUST must ve installed as a regular Python package. From the "TOXTRUST" directory (note the dot at the end) execute:

pip install . 

If you wish to modify the code for development purposes, use pip with the -e flag, execute:

pip install -e .

In order to work with the TOXTRUST in Jupyter Notebook, the installation is required. You can install the notebook either in the "base" conda environment or in the "toxtrust" conda environment. Select the appropriate environment, activate it and run

pip install notebook

Then, although not required, it is also recommended to install the ipykernel within the toxtrust environment in order to correctly set the jupyter notebook kernel. Make sure your "toxtrust" conda environment is activated in the terminal and run:

pip install ipykernel

Lastly, to set the kernel run:

python -m ipykernel install --user --name toxtrust --display-name "Python (toxtrust)"

To open jupyter notebook, switch back to the environment in which jupyter is installed and type:

jupyter notebook

Description

All funtional and technical aspects of TOXTRUST were extensively described in the manuscript: (TBD, manuscript in submission).

Licensing

TOXTRUST was produced at the PharmacoInformatics lab (http://phi.upf.edu), in the framework of the eTRANSAFE project (http://etransafe.eu). eTRANSAFE has received support from IMI2 Joint Undertaking under Grant Agreement No. 777365. This Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation programme and the European Federation of Pharmaceutical Industries and Associations (EFPIA). Moreover, the project received funding from the European Union’s Horizon 2020 Research and Innovation programme under Grant Agreement No. 964537 (RISK-HUNT3R), which is part of the ASPIS cluster .

Copyright 2024 Karolina Kopańska & Manuel Pastor (karolinaweronika.kopanska@upf.edu / manuel.pastor@upf.edu)

TOXTRUST is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation version 3.

TOXTRUST is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.