Tessa/Titus Agenda 2023-08-15 === ## Misc - Can Titus be backup for pyopensci issue Aug 16-22? https://github.com/pyOpenSci/software-submission/issues/129 - Find meeting time for Katrina Kalantar > During the week of August 22-25th I have quite a bit of flexibility Tu-Fri in the afternoons (PST) and during the week of August 28-Sept 1 I have a lot of flexibility in the mornings (PST). Are there any times that work particularly well for you? Also happy to look outside those ranges as needed! - Any immediate thoughts on OSCollective? I think I'm now +1. ## Project Updates - Read recruitment comparison workflow: - running; on github [here](https://github.com/bluegenes/2023-magsmash/blob/main/Snakefile) ## Upcoming grant applications ### Due Oct 11 https://grants.nih.gov/grants/guide/rfa-files/RFA-AI-23-038.html > Some examples of potential research software projects relevant to this NOFO include (but are not limited) to the following: - Data science approaches to mine, enhance, evaluate/identify linkages, integrate and (re)use data from electronic health records (EHR), clinical trial data, epidemiology, diagnostic, molecular or registry data. - Generalizable tools and workflows for the integration of heterogenous data; approaches for data/metadata acquisition and annotation, processing, provenance, wrangling, standards, and data exchange formats for domain-specific data; validating and benchmarking or performance analysis. - Community-based data models, automated metadata capture, and ontologies to facilitate data management, sharing and reuse. - Methods for secure federated learning, data visiting and tabularization. - Methods to improve the speed and accuracy of data analysis and re-analysis, - Methods to conduct data disambiguation for de-identified linkage of data across networks including use of cryptographic methods. - Advanced statistical and mathematical modeling methods, graph, and network theory approaches for predictive, interventional, and prognostic applications. - Artificial intelligence or machine learning approaches for the detection and diagnosis, treatment planning, and medical decision support, predictive and personalized medicine for data analytics of high-throughput and multi-dimensional data. - Intelligent text parsing/mining technologies (including Natural Language Processing) for biomedical data. - Systems modeling that can address data or link models across scales or support the integration of multi-modal data ### Rolling: Infrastructure Capacity https://www.nsf.gov/pubs/2023/nsf23580/nsf23580.htm ![](https://hackmd.io/_uploads/BkV5lHKn3.png) > Submit to Infrastructure Capacity for Biological Research solicitation (NSF 21-501) The Cyberinfrastructure Programmatic Area supports the i**mplementation of, scaling of, or major improvement to cyberinfrastructure for biology that advances or transforms contemporary biology and that is broadly applicable to a wide range of researchers**. Proposed projects may include **cyberinfrastructure related to any level of biological phenomena** (e.g., molecular, cellular organismal, ecosystem, biome), but there needs to be a clear articulation of how the proposed capacity will lead to scientific understanding in biology. PIs are encouraged, where possible, to leverage existing resources in lieu of acquiring or developing new ones. Examples using existing resources include: using shared computational or storage hardware such as xSede, Open Science Grid, or JetStream; incorporating existing software or middleware for basic services (e.g., cyber security or user identity management); and deploying new software through existing platforms such as CyVerse, Galaxy, or R. **The scope of the proposed infrastructure can include but is not limited to: design and construction of databases from new or existing data sources; software and methods for making use of new technologies for the acquisition, communication or visualization of biological data; software or ontologies related to data discovery, data mining, data integration or visualization; tools that facilitate biological research workflows, analytical pathways, or integration between the field and laboratory or between observations, experiments, and models; or scientific gateways (i.e., accessing shared computational and data resources).** It is expected that projects will **produce a finished product **that is publicly accessible and useable for the biological research community. Projects are expected to produce quality products, result in important science outcomes that will be achieved by the users of the resource, and have the potential to be used by a community of researchers beyond a single research team. ## Rolling: Joint with Germany NSF-DFG (Germany) joint proposal -- Molecular and Cellular Biology https://www.nsf.gov/pubs/2022/nsf22015/nsf22015.jsp --- NSF notes -- JGI, MGNify, etc -3 use cases spillover? JGI? etc == pillars mature use cases / letters farm outbreaks? agricultural?