The HMS LINCS project is creating and re-purposing various types of software to collect, manage and analyze data.
HMS LINCS Database
The HMS LINCS Database is a relational database that stores summary information about small molecule perturbagens, experimental protocols, and some assay data produced as part of the HMS LINCS project. Visitors may browse and search this database through its web front end.
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 (PMID 21516115). 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.
Because live and fixed-cell imaging constitute an important type of data for HMS-LINCS, we have deployed an OMERO server that conforms to Open Microscopy Environment standards. This server manages web viewing and downloads in a variety of formats including OME-TIFF; previously existing OMERO code was modified to simplify handling of images in 96-well and 384-well formats. The LINCS OMERO interface is accessible via the HMS LINCS Database.