A pharmaceutical company with extensive compound screening libraries wanted to further enhance their activity database with data from NIH's ever-expanding compound screening resource: PubChem. While user's can perform basic search queries of PubChem data on-line, the company wanted a way to perform more complex analyses against the data, to have the data updated on a regular schedule, and to notify users when new data was available for assays targeting specific genes of interest. Diatom Software an end-to-end system for automatic data acquisition, database design and implementation, and enhanced visualization tools to make the data more useful for internal scientists.

A director of scientific computing at a large pharmaceutical company wanted to help research staff navigate associations between genes, biological pathways, diseases, functional annotations, and compound screening assays to facilitate core research. Her goal was to support deeper queries from scientists who would otherwise spend hours each day trying to collate data from various on-line biological websites. The director also wanted the system to be flexible enough to support new data sources and connection types over time. Diatom's proprietary software, BioLink, was ideally suited for this type of initiative. It includes not only an interface and database to navigate these connections, but also provides an API to allow in-house personnel to write custom in-house applications.

A leader in next-generation sequencing technologies hired Diatom Software to work with their in-house informatics team to develop a multiplex PCR primer design pipeline critical to their technology's sample preparation protocol. Diatom leveraged Amazon EC2 cloud computing resources and our expertise in multi-objective optimization to help their informatics staff clarify some of the design tradeoffs involved.

Biological nomenclature is a constant source of difficulty for bio-medical scientists. There are millions of symbols, synonyms, aliases, and identifiers employed by NCBI, UniProt, HUGO, Ensembl, and others. A pharmaceutical company wanted a simple service that would manage these names and support translation of identifiers from one database to another. Diatom's proprietary Transom technology for biological nomenclature translation makes it possible to resolve thousands of identifiers at one time, and is flexible enough to support both public and proprietary identifiers.

A core mission of our nation's Centers for Disease Control and Prevention (CDC) is to intake data from state health departments to monitor cases of dozens of different diseases from Chicken Pox to Tuberculosis. The collection of this data helps CDC epidemiologists analyze trends, and better understand the state of health throughout the country. Over several months, Diatom Software was able to develop a high-performance integrated message processing system that would read and validate incoming thousands of messages per second and store event records in a database. Diatom Software is currently partnering with Epidemico and the CDC to bring a production version of the system into operation by the Fall of 2012.