Software and Tools

The HMS LINCS project is creating and re-purposing various types of software to collect, manage and analyze data. Below is a summary table listing all tools as well as detailed descriptions of the key projects.

Summary table

Name / Link Description Source code
HMS LINCS DB Browse, search and download HMS LINCS datasets and information about experimental reagents hmslincs at GitHub
ImageRail Desktop software for image analysis of high-throughput microscopy imagery ImageRail at GitHub
OMERO Client-server software for visualization, management and analysis of biological microscope images openmicroscopy at GitHub
Kinase inhibitor pathway explorer Interactive map of key signal transduction pathways and relevant drug-target data hmslincs at GitHub
Interactive drug response data Explore responses of 50+ cell lines to 64 anticancer drugs hmslincs at GitHub
Breast cancer cell line signaling data Comprehensive analysis of ERK and Akt response to growth factor stimulation hmslincs at GitHub
Dynamics of perturbagen response in single living cells Live-cell data describing the responses of cells to 3 EGFR/Her2 inhibitors hmslincs at GitHub
TieDIE Connect genomic perturbations to gene expression changes characteristic of cancer subtypes TieDIE at GitHub

HMS LINCS Database

The HMS LINCS Database was developed in collaboration between the software development teams in the ICCB-Longwood Screening Facility and the Sorger Lab at Harvard Medical School. The Database is a public resource for browsing, searching and downloading LINCS data. The web standards-based API (application programming interface) can be used to query and access each of the data types managed by the database, including compound information, library descriptions and data sets. Please refer to the HMS LINCS Database URL scheme and programmatic access guide for more information.

For small molecule compounds stored in the LINCS Database, the system stores common names, chemical structure and properties, relevant publications, and links to other public resources, such as PubChem and ChEMBL, which contain additional information about each compound. As batches of compounds are received for screening at HMS, information about each batch is recorded, such as vendor/source information and quality control documents.

For experiments performed at HMS, the Database stores the layout and concentrations of compounds and other reagents across the wells of assay microplates, as well as information about experimental protocols, controls, and data analysis methods. Raw experimental data and subsequent analyzed results are all stored in the system, and may be browsed or downloaded for further review and analysis. LINCS experimental data are usually multi-dimensional, resulting from several different assays run in parallel that monitor the effects of different compounds, tested at multiple concentration on different cell lines and read out at multiple time points.

Compound profiling data provided by third-parties, such as KINOMEscan (DiscoveRx) or KiNativ, are imported and associated with the relevant compounds described in the Database. This allows profiling data to be viewed alongside the assay results of each screened compound and also downloaded by Database users.

ImageRail

ImageRail is desktop software which performs image analysis on high-throughput microscopy imagery.  It stores single-cell data using SDCubes (see below) and offers an adaptive experimental designer.  ImageRail is written in Java and is thus cross-platform, and native application installers are provided for Windows and Mac OS X. ImageRail is described in detail in Millard et al. 2011 (see below). ImageRail is used to collect and analyze data from many of the HMS LINCS fixed cell microscopy assays.

Semantically Typed Data Cubes

Semantically Typed Data Cube (SDCube) is a data model, software library, and file format built on top of HDF5 and XML for storing structured numerical data produced by multi-factorial biology experiments.  An SDCube consists of an HDF5 file with groups and datasets created according to the modular, hierarchical SDCube data model, as well as an accompanying XML file containing metadata such as Minimum Information annotations and a description of the experimental factors. A long term goal of our HMS LINCS project is to store most of our assay data in SDCube format.

OMERO

Because live and fixed-cell imaging constitute an important type of data for HMS-LINCS, we have deployed the OMERO server software from the Open Microscopy Environment project to manage this data. The server provides web-based viewing and downloads in a variety of formats including OME-TIFF as well as a programmatic interface (API) for integration with others systems such as the HMS LINCS Database.

For example, see dataset 20003 (Tang Mitosis/Apoptosis) in the HMS LINCS Database which integrates OMERO images with the assay results (see the “Image” column).