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Ruebel, Oliver

Publications and source records attributed to Ruebel, Oliver.

Bioenergy Research Centers Data Sharing Portal

The bioenergy.org website is the end product of the Data Sharing Shared Research objective for the Bioenergy Centers. The objective is to Enhance BRC data legacy through the development and use of shared software tools to make previously published datasets more findable and accessible through the Inter-BRC Data Products Portal, and to explore the use of generative AI to assist in the exploration of published datasets. The software repository is released per the license information below.

Thrower, Nicholas↗

AqNWB v0.1

This is a C ++ acquisition API for neurophysiological data in the NeurodataWithoutBorders (NWB) data standard.

Prince, Stephanie↗

Metabolite, annotation, and gene integration system and method

Disclosed herein are systems and methods for associating metabolites with genes. In some embodiments, after potential metabolites are identified based on spectroscopy data of the content of an organism, possible reactions capable of producing the potential metabolites are determined. The possible reactions are compared to gene sequences in a database, and an association score for the likelihood that a gene sequence is related to the potential metabolites is calculated.

Erbilgin, Onur↗

Simple Scattering: Lipid nanoparticle structural data repository

Lipid nanoparticles (LNPs) are being intensively researched and developed to leverage their ability to safely and effectively deliver therapeutics. To achieve optimal therapeutic delivery, a comprehensive understanding of the relationship between formulation, structure, and efficacy is critical. However, the vast chemical space involved in the production of LNPs and the resulting structural complexity make the structure to function relationship challenging to assess and predict. New components and formulation procedures, which provide new opportunities for the use of LNPs, would be best identified and optimized using high-throughput characterization methods. Recently, a high-throughput workflow, consisting of automated mixing, small-angle X-ray scattering (SAXS), and cellular assays, demonstrated a link between formulation, internal structure, and efficacy for a library of LNPs. As SAXS data can be rapidly collected, the stage is set for the collection of thousands of SAXS profiles from a myriad of LNP formulations. In addition, correlated LNP small-angle neutron scattering (SANS) datasets, where components are systematically deuterated for additional contrast inside, provide complementary structural information. The centralization of SAXS and SANS datasets from LNPs, with appropriate, standardized metadata describing formulation parameters, into a data repository will provide valuable guidance for the formulation of LNPs with desired properties. To this end, we introduce Simple Scattering, an easy-to-use, open data repository for storing and sharing groups of correlated scattering profiles obtained from LNP screening experiments. Here, we discuss the current state of the repository, including limitations and upcoming changes, and our vision towards future usage in developing our collective knowledge base of LNPs.

59 BASIC BIOLOGICAL SCIENCES↗

VTK-m v. 2.0

VTK-m is a toolkit of scientific visualization algorithms for emerging processor architectures. VTK-m supports the fine-grained concurrency for data analysis and visualization algorithms required to drive extreme scale computing by providing abstract models for data and execution that can be applied to a variety of algorithms across many different processor architectures.

Moreland, Kenneth [Oak Ridge National Lab. (ORNL),↗

System and method of managing large data files

Disclosed are systems and software that provide a high-performance, extensible file format and web API for remote data access and a visual interface for data viewing, query, and analysis. The described system can support storage of raw spectroscopic data such as neural recording data, MSI data, metadata, and derived analyses in a single, self-describing format that may be compatible by a large range of analysis software.

Bowen, Benjamin P.↗

Neurodata Extensions Catalog (NDX Catalog) v1.0.0

The Neurodata Extensions Catalog (NDX Catalog) is a novel web archive and associated software tools that enable users to easily create, search for, test, review, and install extensions to the Neurodata Without Borders (NWB) data standard for neurophysiology. The Catalog consists of several software repositories that can be found at https://github.com/nwb-extensions.

Tritt, Andrew↗

OpenMSI Arrayed Analysis Tools (OMAAT) v2.0

Mass spectrometry (MS) is an analytical technique that enables all chemical species within a complex mixture to be resolved and identified based on their mass:charge ratio. MS is an increasingly important tool in life science research and development because it can resolve or separate small molecules, peptides, lipids, proteins, biopolymers and fragments of all of these structures. Unfortunately, the use of MS has been limited for lack of software tools to visualize, manipulate, store and transfer MS data. Ben Bowen, Oliver Ruebel and colleagues made a huge advance on the resolution of these limitations with the invention of "OpenMSI" (#2013-004), a computational method that makes the handling of these very large files (up to 50 Tb) much easier, especially for scientists with limited background in bioinformatics or sophisticated software applications of the type needed to handle such data files. With the OpenMSI Arrayed Analysis Tool (OMAAT, #2016-188) invention, the authors take MS data analysis one step further by providing tolls for automatic sample position optimization and ion selection. Even though sample deposition technologies have improved greatly, there is always the chance of encountering outliers in a predefined roster, especially in very large sample sets. Manual curation of the data would be extremely time consuming, so the inventors have included an algorithm that automatically finds the outliers. OMAAT is written in Python with accompanying Jupyter (formerly iPython) notebook and is fully integrated with OpenMSI.

Bowen, Benjamin↗