Dependencies

installtion with pip -> computation descriptor RDKIT developed in parrallel

$pip install -i https://test.pypi.org/simple/ CompDesc $pip install rdkit $pip install fontawesome $pip install django $pip install scipy $pip install psycopg2

lib and sofwares

Development in python3.12 with

• Django
• RDKit (> 3.1): http://rdkit.org/docs/index.html
• molVS (> 1): https://molvs.readthedocs.io/en/latest/index.html
• Open Babel > 3.0.0 (March 2020): (http://openbabel.org/wiki/Main_Page) (sudo apt install openbabel) or https://open-babel.readthedocs.io/en/latest/Installation/install.html#compiling-open-babel (additional some function will not work in case of no install)
• OPERA2.3_CL (https://github.com/kmansouri/OPERA/releases), fix the minor error in the install folder add a "/" at the path beginning
• OPERA will install PADEL in the same folder

install OPERA --> install command line

$sudo ./OPERA2.6_XXX_mcr.install -mode silent -agreeToLicense yes

run the server

$python manage makemigrations $python migrate $python manage.py runserver

Upade the DSSTOX

Download chemicals from the pubchem Current download => 866794 chemicals => limited to 500,000 structures

• https://www.ncbi.nlm.nih.gov/pcsubstance?term=%22EPA%20DSSTox%22%5BSourceName%5D%20AND%20hasnohold%5Bfilt%5D
• with the mapping from the pubmed ID

Keys updates

• 7-8-19: init ncsu git
• 7-8-19: add gitignore to no include png in chemmaps
• 9-8-19: Error interferences, revert on sandbox version
• 18-8-19: Fix ChemMaps for VM and create git tree
• 22-8-19: Add bodyMap project
• 23-8-19: develop bodyMap
• 17-9-19: Add version 17-9-19 of molecular descriptors computation
• 19-9-19: connect chemmaps on DB
• 20-9-19: Fix case where chemicals uploaded are a mix between in DB and new
• 08-10-19: Update footer and header for interference and chemmaps + connect pfas and tox21 to DB
• 11-10-19: Add Connection to server and optimize the DSSTOX map
• 18-10-19: Update body map and change statics
• 21-10-19: Fix Tox21 map error, add distance in the neighbor download and fix search bar error
• 23-10-19: Fix extraction for DrugMap, optimize the loading in case of pre existing chemical, add DB interactions
• 5-11-19: Update barplot for AC50 and added chemical informatio
• 20-11-19: Update bodymap results pages
• 01-12-19: Update bodymap
• 16-12-19: connected bodymap to DB
• 18-12-19: Fix error in chemmaps with user DB
• 19-12-19: Fix error meighbor dl + fix NaN in the info panel
• 19-12-19: add help and index pages for bodymap
• 20-12-19: Fix color link bodymap + error upload chemmaps
• 20-12-19: Fix error replicate in chemmaps user DB
• 25-01-20: last update from the NTP
• 26-03-20: fix error bodymap and chemmaps as well as added option in bodymap for interactive network
• 21-04-20: Fix error in case of O division in gene expression
• 21-04-20: Fix spealing errors and add ratio assays tested
• 09-20: add ILS ICE data
• 12-20: update bodymap with the assays results from ICE and QC
• 18-05-21: fix map navigation bug on color and selection
• 4-13-22: Fix help page
• March 2023 release of chemmaps V2
• July 2024 update python and django