namastox

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 mpastorphi/namastox

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 flame repository. Start by creating a folder inside named 'ras'. Then, run the following command:

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

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 .

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 .

python setup.py develop

Configuration

After installation is completed, you must run the configuration command to configure the directory where flame 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/flame_models 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.

NAMASTOX commands

Command interface synthax

Command	Description
-c/ --command	Action to be performed. Acceptable values are new, kill, list, update, report
-r/ --raname	Name of the risk assessment
-a/ --action	Use 'silent' to configure the program using default RA repositories
-d/ --directory	Use this parameter in action configure to define the RA repositories
-i/ --infile	Name of the input file used by the command.
-o/ --outfile	Name of the output file used by the command.
-p/ --pdf	Name of the report in PDF format
-w/ --word	Name of the report in Word format
-h/ --help	Shows a help message on the screen

Command examples and description

Command	Example	Description
new	namastox -c new -r myproject -o template.yaml	Creates a new entry in the risk assessments repository named myproject and generates a yaml file that is used as a template for updating the risk assessement
kill	namastox -c kill -r myproject	Removes myproject from the risk assessment repository. Use with extreme care, since the program will not ask confirmation and the removal will be permanent and irreversible
list	namastox -c list	Lists the risk assessments present in the repository
update	namastox -c update -r myproject -i result.yaml -o template.yaml	Update the risk assessment with the new information present in the result.yaml file. The new data is processed internally, progressing to the new workflow node and the new data is stored in a local repository. The output is a template for entering new information
report	namastox -c report -r myproject -w report.docx

Quickstart

Configure using

namastox -config -a silent

Create a new risk assessment

namastox -c new -r myproject -o template.yaml

This creates a yaml file which can be used as a template for add information about the substances to study or the endpoints which should be studied

Update a risk assessment, using a delta.yaml file containing new data. The file generates a new version of the yaml file

namastox -c update -r myproject -i result.yaml -o template.yaml

Generate a report with the current status of the risk assessment (in Word format):

namastox -c report -r myproject -w report.docx

Remove completely a risk assessment

namastox -c kill -r myproject

List all the risk assessments present in the current repository

namastox -c list

Acknowledgments

Part of the project RISKHUNT3R (https://www.risk-hunt3r.eu/)

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