Recombinant Proteomic Data Resource

Period of Performance: 08/15/2016 - 02/14/2017

$225K

Phase 1 SBIR

Recipient Firm

Transform Research, LLC
BAINBRIDGE ISLAND, WA 98110
Principal Investigator

Abstract

Project Summary / AbstractWe propose to develop and test the feasibility of a Recombinant Proteomic Data Resource (RPDR), a cloudbased software system which provides a venue for researchers to (i) easily upload existing data for bothproductive and failed protein production outcomes, (ii) find and compare experimental details, and (iii) becomemore efficient by increasing research reproducibility. The RPDR would provide the first working platform for futurebig data mining efforts to better understand the underlying drivers for successful protein production. We willdevelop the RPDR software system, consisting of a web-hosted extensible protein production results databaseas well as UPLOADER, EXPLORER and CONFIGURATOR companion web applications (Aim 1). We will testthe server-installed RPDR by uploading 10,000 records from the publicly available TargetTrack DB. Oncedeemed functional we will populate and test it by uploading ~40,000 protein production data records of non-peer-reviewed as well as negative expression results data from our seven collaborators (Aim 2). Our moderatedupload process is designed to impose only minimal ? if any ? data format requirements, namely unique targetidentification and a normalized score for experimental outcome. In total we aim to enter and confirm the integrityof 30,000 records from a minimum of four different sources. We will test the performance of this new informaticssystem by making available to researchers the EXPLORER and CONFIGURATOR tools to find records in theRPDR and leverage these for the design of new protein production systems. The search function of theEXPLORER module will be developed to include potentially helpful production results from related records byretrieving UniProt cross-referenced homologous targets via an API and by sorting and grouping of records. Wewill develop the CONFIGURATOR functionality to allow selection of data from preferred records and to aggregatethese into a preliminary production plan (Target Production Scratch Pad). In order to attract users, we will grantfree-of-charge access to the EXPLORER and CONFIGURATOR modules by inviting a group of previouslycontacted interested researchers, and promote the system at an industry event. We will work with theseresearchers to use the RPDR and eventually upload new experimental results into the system. We plan to carryout a validation study, collecting feedback on the utility of the RPDR platform, gather new feature requests andexplore commercialization preferences (Aim 3). We plan to assess the system's utility for the creation of newrecombinant protein production plans by benchmarking target production plans, collecting user analytics andsoliciting direct feedback from biomedical researchers. Further development of the Recombinant Proteomic DataResource will be pursued by a Phase 2 SBIR proposal.