Transform Research, LLC — Department of Health and Human Services SBIR Phase I: 100

Description

Project Summary Abstract We propose to develop and test the feasibility of a Recombinant Proteomic Data Resource RPDR a cloud based software system which provides a venue for researchers to i easily upload existing data for both productive and failed protein production outcomes ii find and compare experimental details and iii become more efficient by increasing research reproducibility The RPDR would provide the first working platform for future big data mining efforts to better understand the underlying drivers for successful protein production We will develop the RPDR software system consisting of a web hosted extensible protein production results database as well as UPLOADER EXPLORER and CONFIGURATOR companion web applications Aim We will test the server installed RPDR by uploading records from the publicly available TargetTrack DB Once deemed functional we will populate and test it by uploading protein production data records of non peer reviewed as well as negative expression results data from our seven collaborators Aim Our moderated upload process is designed to impose only minimal if any data format requirements namely unique target identification and a normalized score for experimental outcome In total we aim to enter and confirm the integrity of records from a minimum of four different sources We will test the performance of this new informatics system by making available to researchers the EXPLORER and CONFIGURATOR tools to find records in the RPDR and leverage these for the design of new protein production systems The search function of the EXPLORER module will be developed to include potentially helpful production results from related records by retrieving UniProt cross referenced homologous targets via an API and by sorting and grouping of records We will develop the CONFIGURATOR functionality to allow selection of data from preferred records and to aggregate these into a preliminary production plan Target Production Scratch Pad In order to attract users we will grant free of charge access to the EXPLORER and CONFIGURATOR modules by inviting a group of previously contacted interested researchers and promote the system at an industry event We will work with these researchers to use the RPDR and eventually upload new experimental results into the system We plan to carry out a validation study collecting feedback on the utility of the RPDR platform gather new feature requests and explore commercialization preferences Aim We plan to assess the systemandapos s utility for the creation of new recombinant protein production plans by benchmarking target production plans collecting user analytics and soliciting direct feedback from biomedical researchers Further development of the Recombinant Proteomic Data Resource will be pursued by a Phase SBIR proposal Narrative Exposing currently inaccessible protein production information to many researchers should have a major impact on the economics of establishing new recombinant protein production systems To achieve this goal we propose to develop a web based Recombinant Proteomic Data Resource allowing entry of a diverse set of recombinant protein production data and thereby facilitate configuration of new protein production systems