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Data Science Tools for Infectious and Immune-mediated Disease Research


Fast Track proposals will be accepted. Direct to Phase II proposals will not be accepted. Number of anticipated awards: 1-3 Page 116 Budget (total costs): Phase I: $300,000 for up to 1 year; Phase II: $1,000,000 for up to 3 years. Background Data intense infectious and immune-mediated research projects are generating unprecedented amounts of complex and diverse basic research and clinical data sets. Increasing the use and re-use of these data by basic and clinical scientists studying infectious, immune and allergic diseases will drive discovery and accelerate the development of diagnostic, preventative and therapeutic interventions. Yet, managing, preserving, sharing, finding, accessing, integrating, visualizing, and analyzing these data sets from multiple sources and platforms remains challenging. Innovation in optimal search and discovery of biomedical data is still lacking. Moreover, non-interoperable data impedes the ability to answer sophisticated biological questions across diverse data types without significant harmonization. Although there is considerable effort in developing standards and data curation programs to address these challenges, they are mostly manual, expensive, and not scalable. Visualization tools that integrate new and emerging 3D technologies to visualize and communicate research data are also needed. This broad topic includes investments in data resources and repositories, development of computational tools, their use, and tools to enhance timely data sharing and adherence to FAIR Data Principles (Findable, Accessible, Interoperable, and Reusable). Tools that can enhance privacy in an environment that maximizes sharing are also sought. This includes novel approaches to share de-identified individual patient level data while maintaining the complexity of the original data. If developed, they have the potential to confirm reproducibility, promote transparency of clinical studies, increase confidence in therapeutic interventions, and inform and accelerate new clinical research and trials. Project Goal The goal is to support the new development of innovative, robust informatics/data science tools, or enhancement or adaptation of existing tools for use in infectious, immune, and allergic diseases. These tools should be appropriate for, but not limited to, data from natural history studies, biomarkers, in vitro assays, correlates of vaccine protection, animal models and non-human primates. The tools can aim to improve data management, or the FAIR-ness of data, or can focus on data visualization, integration, or analysis. Potential projects relevant but not limited to this topic include the development, enhancement, modification, or adaptation of existing informatics and data science tools for • Increase the findability of data by utilizing information that includes, but is not limited to data, metadata, associated literature, and text; • Improve indexing by popular search engines and recommend or discover relevant data sets beyond the original search; • Visualize and integrate analysis of “big”, multi-scale, complex data from multiple sources and their dissemination; • Perform automated curation and quality control; • increase data interoperability and query-ability across multiple resources by application and adoption of community standards and ontologies that may include software pipelines or platforms to automate annotation, markup, or curate datasets not compatible with community standards, formats, or controlled vocabularies; • Harmonize clinical data via customized data harmonization pipelines which among other features could combine data sets or un-merge combined data sets; • Standardize the de-identification, and other privacy-preserving approaches, of individual patient level data and allow the timely sharing of human clinical research data including tools that can assess and minimize the risk of re-identification. Phase I Activities: • Establish a project team composed of experts in software development and as appropriate to the project include but not limited to expertise in statistics, infectious and immune mediated diseases, or clinical research. • Provide an overall development plan with milestones and deliverables for the proposed tool. • Provide justification and unique value proposition for the development, adaptation or enhancement of this specific tool in light of the currently available tools. • Describe the potential user communities and provide relevant use cases. Page 117 • Develop an (early) prototype for the tool, perform alpha testing, and address issues from testing and solicit feedback from the appropriate user community. Phase II Activities: • Enhance and optimize the prototype developed in phase I. • Improve robustness, scalability, and usability of the tool. • Conduct beta tests for the software tool with the appropriate user communities and use cases, demonstrate the usability of the tool by the infectious, immune or allergic community. • Gather feedback from the beta testing by the research community. • Add functionalities and capabilities based on feedback and deploy a production version. • Develop documentation, user guides, SOPs and training materials. The SBIR will not support: • Projects proposing significant data generation and analysis for validation and testing of the tool. • Projects developing wet-laboratory, experimental methods, research or technologies. • Projects that are not focused on developing tools directly applicable to infectious, immune or allergic basic and clinical research.
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