VERA Entities

This version of VERA allows to performe a read-across analysis in two different ways:

  1. VERA Alerts, as described in the papers 1,2. VERA Alerts assess similarity between chemicals using structural alerts specific to the property, pre-defined molecular groups and structural similarity.
  2. VERA Entities. Starting with an unsupervised analysis, VERA Entities analysed several chemical, biotic and abiotic properties independently from the endpoint and used these entities to provide the assessment.

Preliminary check

Note: VERA works only on Windows environments.

Verify your Java version Open the Command Prompt (on Windows write "cmd" on the search bar and click on the application Terminal or Command Prompt) and type:
>java -version

If you have a Java version greater than 11 and a Java Development Kit (JDK) version greater than 11, you’re good to go ✅

Otherwise, you need to install the latest JDK by following the instructions here. Selecting the correct installer for your operating system and download it (x64 Installer).

The JDK installation is sufficient to run VERA. If you already have an older Java version installed, please uninstall it before using VERA.

After downloading and installing the JDK, please open a new Command Prompt and verify that the installation was successful:

>java -version

You should see a message similar to this one:

Java(TM) SE Runtime Environment 18.9 (build 11.0.6+8-LTS)
Java HotSpot(TM) 64-Bit Server VM 18.9 (build 11.0.6+8-LTS, mixed mode)

Antivirus Notice

If you are using AVG Antivirus, please note that it may block the application the first time you run it. Simply allow the permission warning — after that, the application will run normally.

For all antivirus systems, when you unzip and open the .exe file, make sure to grant any necessary permissions (if prompted) to allow the application to run correctly.

How the VERA Entities and Alerts GUI work

You can download the new version of VERA here. The VERA GUI is a stand-alone application; it is not necessary to install the software.

  1. Extract the .zip folder

  2. Double-click the .exe file to open it. A CMD window will appear, allowing you to monitor the VERA process in detail. Do not close this window, as it is required for the software to operate properly. Note: The first time you run VERA, you may need to wait a few seconds for the graphical interface to open. If it hasn’t appeared after a minute, close the CMD window and double-click the .exe file again; the interface should open within a few seconds.

  3. In a few seconds, the VERA GUI will open. Click on the Load File button in the top left corner of the application to upload an .xlsx file containing the SMILES of the molecule you want to assess with VERA. The SMILES list should be placed in the first column of the .xlsx file, and the column header should be "SMILES". If you have other identifiers, you can use the Chemical Resolver application to search for SMILES.

  4. Then, you can select the endpoint to be evaluated and the type of output: an Excel file containing all predictions and/or an HTML report for each molecule with detailed information on how VERA performs the assessment. Please do not remove the HTML file from the folder, as this will cause parts of the output to be missing.
  1. By clicking on START CALCULATION, the GUI will prompt you to choose a folder to save the output files. It will automatically create a results folder within the selected directory to store all reports. If an output folder already exists, VERA will automatically date the output folders.
  2. Then, the read-across process will start. In the Log window, you can check the current step of the algorithm, and the progress bar will indicate the percentage of molecules processed. At the end of the calculation, a window will confirm that VERA has completed the assessment of all provided substances and that the results are available in the selected folder.
  3. Before processing other chemicals, click on Clean Work.

Contacts

Edoardo Luca Viganò - Laboratory of Environmental Chemistry and Toxicology - Department of Environmental Health Sciences - Istituto di Ricerche Farmacologiche Mario Negri IRCCS - Via Mario Negri 2, 20156 Milano, Italy - e-mail: edoardo.vigano@marionegri.it

Erika Colombo - Laboratory of Environmental Chemistry and Toxicology - Department of Environmental Health Sciences - Istituto di Ricerche Farmacologiche Mario Negri IRCCS - Via Mario Negri 2, 20156 Milano, Italy -e-mail: erika.colombo@marionegri.it