Abstract
MotivationDrug synergies are sought to identify combinations of drugs particularly beneficial. User-friendly software solutions that can assist analysis of large-scale datasets are required.ResultsCImbinator is a web-service that can aid in batch-wise and in-depth analyzes of data from small-scale and large-scale drug combination screens. CImbinator offers to quantify drug combination effects, using both the commonly employed median effect equation, as well as advanced experimental mathematical models describing dose response relationships.Availability and ImplementationCImbinator is written in Ruby and R. It uses the R package drc for advanced drug response modeling. CImbinator is available at http://cimbinator.bioinfo.cnio.es, the source-code is open and available at https://github.com/Rbbt-Workflows/combination_index. A Docker image is also available at https://hub.docker.com/r/mikisvaz/rbbt-ci_mbinator/.Supplementary information Supplementary data are available at Bioinformatics online.
Highlights
The discovery of growth inhibiting drug synergies is important because they allow for a lower dosage of each drug while preserving effects
CImbinator is a web-service that can aid in batch-wise and in-depth analyzes of data from small-scale and large-scale drug combination screens
While currently available software have typically been devised for small scale experiments, the increase in sizes of drug panels demand software solutions designed to batch-wise analyze large-scale combination screen data
Summary
The discovery of growth inhibiting drug synergies is important because they allow for a lower dosage of each drug while preserving effects. Drug synergies can be exploited to increase drug treatment responses to levels that are normally limited by the toxicity and side effects of each drug. These properties warrant large drug combination screens to discover new synergies (Axelrod et al, 2013; Crystal et al, 2014; Mathews Griner et al, 2014). We here present CImbinator, a software tool that offers substantial advance in assisting assessment of drug response effects and synergies from small and large-scale experiments. CImbinator enables the user to quickly orient in a large experimental search space through its display in a single web window of color-coded synergy assessments for all drug combinations describing each dose tested. The source code is freely available and allows to deploy the web page locally or use the functionalities from the command-line or from Ruby scripts (Fig. 1)
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