Small Molecule Suite Website

This repository contains the R Shiny code powering https://smallmoleculesuite.org.

HMS-LINCS Small Molecule Suite Applications

This website consists of three related applications that were developed as part of the NIH LINCS Consortium in a collaboration between Harvard Medical School's Sorger Lab and Laboratory of Systems Pharmacology (LSP) and the University of Cincinnati's Laboratory for Statistical Genomics and Systems Biology. The former (HMS) is one of the LINCS Data and Signature Generation Centers (DSGCs) and the latter (Cincinnati) is part of the BD2K-LINCS Data Coordination and Integration Center (DCIC). All of the web applications are implemented in R, using the Shiny framework for interactive applications.

Publication

Nienke Moret, Nicholas A. Clark, Marc Hafner, Yuan Wang, Eugen Lounkine, Mario Medvedovic, Jinhua Wang, Nathanael Gray, Jeremy Jenkins, Peter K. Sorger. Cheminformatics Tools for Analyzing and Designing Optimized Small-Molecule Collections and Libraries. Cell Chem Biol (2019). doi:10.1016/j.chembiol.2019.02.018

Development and links

Design/idea by Nienke Moret and Marc Hafner (HMS - LINCS data and signature generation center)

R code by Nienke Moret (HMS - LINCS data and signature generation center) and Clemens Hug (HMS - Laboratory of Systems Pharmacology)

Shiny/R web application development by ZevRoss Spatial Analysis and Clemens Hug (HMS - Laboratory of Systems Pharmacology) patterned after an earlier application created by Nicholas Clark (U of Cincinnati - LINCS data coordination and integration center)

The package morgancpp, developed by Artem Sokolov, Jeremy Muhlich and Clemens Hug, is used for the computation of tanimoto distances between compound fingerprints.

RDKit was used for the computation of molecular fingerprints.

Data on commercial availability was sourced from ZINC.

Supervision by Peter Sorger (HMS - LINCS data and signature generation center)

Icon design and development by Vasileios Stathias (U of Miami - LINCS data coordination and integration center)

This work was supported by NIH grants U54-HL127365, U24-DK116204 and U54-HL127624.

Deployment

This app is meant to be deployed to Posit Connect or Shiny server.

Dependencies are managed using renv. The current versions used are listed in renv.lock.

1. Clone repository using git clone https://github.com/labsyspharm/smallmoleculesuite.git
2. Install R version 4.2 or higher
3. Install the R packages renv andrsconnect
4. For downloading Small Molecule Suite data, a free Synapse account and the non-CRAN R packages synapser and synExtra are required
5. Download Small Molecule Suite data from Synapse using Rscript utils/dev/import_data.R and Rscript utils/dev/import_download_data.R. This unfortunately can take a while
6. In R, run renv::restore() to download and install all dependencies
7. renv adds source("renv/activate.R") to the local .Rprofile file, which conflicts with deployment to Connect servers. Remove this line from .Rprofile and restart R
8. Run source("renv/activate.R") in a fresh R terminal
9. In order to avoid problems with large uploads run options(rsconnect.http = "curl")
10. Deploy app using rsconnect::deployApp() with the appropriate server credentials, for example rsconnect::deployApp(account = "clemens", appName = "smallmoleculesuite")

Related web-tools

LINCS data portal - A unified resource for accessing all LINCS dataset packages and entities.
http://lincsportal.ccs.miami.edu/dcic-portal/

iLINCS - A data analysis platform aimed at developing statistical methods and computational tools for integrative analysis of the data produced by the LINCS program.
http://www.ilincs.org/

BD2K-LINCS Project

HMS-LINCS Small Molecule Library
http://lincs.hms.harvard.edu/db/sm/

NIH LINCS Consortium
http://www.lincsproject.org/

HMS LINCS Center
http://lincs.hms.harvard.edu/

LINCS Data and Signature Generation Centers (DSGCs)
http://www.lincsproject.org/LINCS/centers/data-and-signature-generating-centers

BD2K-LINCS Data Coordination and Integration Center (DCIC)
http://lincs-dcic.org/

Harvard Medical School

Laboratory of Systems Pharmacology (LSP)
http://hits.harvard.edu/the-program/laboratory-of-systems-pharmacology/

Sorger Lab
http://sorger.med.harvard.edu/

University of Cincinnati

Laboratory for Statistical Genomics and Systems Biology
http://eh3.uc.edu/