NAMASTOX

A computational tool supporting the use of NGRA workflows

Software tool for supporting the implementation of New Assessment Methods (NAMs) within a New Generation Risk Assessment (NGRA) framework.

Install

A docker container (https://www.docker.com/), fully configured can be downloaded from DockerHub and installed using:
docker run -d -p 5000:5000 acabrera809/namastox:latest

Then, the NAMASTOX GUI will be accesible from a web browser at address http://localhost:5000

Please note that the port of this address is defined in the command line above and can be easily customized.

It is also possible to use an existing local folder for storing the RAs. Let’s assume you wish to use ‘c:\data’ as the local NAMASTOX repository. Start by creating a folder inside named ‘ras’. Then, run the following command:

docker run -d -p 5000:5000 -v c:\data:/data acabrera809/namastox:latest

Then, as in the previous example, you can acces the NAMASTOX GUI from a web broser at http://localhost:5000

NAMASTOX can be used in most Windows, Linux or macOS configurations, provided that a suitable execution environment is set up. We recommend, as a fist step, installing the Conda package and environment manager. Download a suitable Conda or Anaconda distribution for your operative system from here

Download the repository:

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

Go to the repository directory

cd NAMASTOX

and create the conda environment with all the dependencies and extra packages (numpy, RDKit…):

conda env create -f environment.yml

Once the environment is created type:

source activate namastox

to activate the environment.

Conda environments can be easily updated using a new version of the environment definition

conda env update -f new_environment.yml

NAMASTOX must be installed as a regular Python package. From the NAMASTOX directory type (note the dot at the end):

pip install .

or

python setup.py install

For development, use pip with the -e flag or setup with develop instead of install. This will made accesible the latest changes to other components

pip install -e .

or

python setup.py develop

Documentation (for the GUI)

We prepared a series of short (1 to 2 minutes) videos explaining how to carry out common tasks:

  • create a new RA here
  • executing a task here
  • making decisions here
  • review results and decisions here
  • generating reports here
  • project management here

Here is also the link to a quickstarting guide: here

Configuration

After installation is completed, you must run the configuration command to configure the directory where NAMASTOX will place the risk assessments. If NAMASTOX has not been configured previously the following command

namastox -c config

will suggest a default directory structure following the XDG specification in GNU/Linux, %APPDATA% in windows and ~/Library/Application Support/NAMASTOX_RA in Mac OS X.

To specify a custom path use the -d parameter to enter the root folder where the risk assessments will be placed:

namastox -c config -d /my/custom/path

will set up the risk assessments repository to /my/custom/path/ras

Once NAMASTOX has been configured, the current setting can be displayed using again the command

namastox -c config

As a fallback, NAMASTOX can also be configured using the following command

namastox -c config -a silent

This option sets up the risk assessments within the NAMASTOX installation directory (namastox\namastox\ras). Unlike other options, this command does not ask permision to the end-user to create the directories or set up the repositories and is used internally by automatic installers and for software development.

Acknowledgments

NAMASTOX has been developed for the project RISKHUNT3R (https://www.risk-hunt3r.eu/)

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This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 964537.