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Archival Research

Archival Research

Some researchers gain access to large amounts of data without interacting with a single research participant. Instead, they use existing records to answer various research questions. This type of research approach is known as archival research. Archival research relies on looking at past records or data sets to look for interesting patterns or relationships. For example, a researcher might access the academic records of all individuals who enrolled in college within the past ten years and...

$X-ray Diffraction of Biological Samples$ 01:10

X-ray Diffraction of Biological Samples

X-ray diffraction or XRD is an analytical tool that utilizes X-rays to study ordered structures such as crystalline organic and inorganic samples, polycrystalline materials, proteins, carbohydrates, and drugs.
According to Bragg's law, when X-rays strike the sample positioned on a stage, the rays are scattered by the electron clouds around the sample atoms. The X-ray diffraction or scattering is caused by constructive interference of the X-ray waves that reflect off the internal...

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Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

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Large-File Raw Data Synchronization for openBIS Research Repositories.

Aleksei Dudchenko¹, Friedemann Ringwald¹, Felix Czernilofsky²

¹Institute of Medical Informatics, Heidelberg University Hospital, Germany.

Studies in Health Technology and Informatics

|May 25, 2022

Summary

Systems medicine research uses openBIS for data storage, enhanced by Nextcloud for efficient large file uploads. This integration ensures automatic raw mass spectrometry data import and comprehensive data provenance.

Keywords:

mass spectrometry research platform systems medicine

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Area of Science:

Systems Medicine
Bioinformatics
Data Management

Background:

Research data repositories are crucial for managing complex biological datasets.
Efficient handling of large experimental files, such as mass spectrometry data, presents a significant challenge in research.
Integrating diverse data sources is key for comprehensive analysis in systems medicine.

Purpose of the Study:

To describe the implementation of openBIS and Nextcloud for a systems medicine research consortium.
To demonstrate an automated workflow for importing large raw mass spectrometry data files.
To ensure comprehensive data provenance within the research data repository.

Main Methods:

Utilizing openBIS as the central research data repository.
Implementing Nextcloud as a complementary data cloud system for large file management.
Employing a Nextcloud client for automated, background import of raw mass spectrometry data into openBIS.

Main Results:

Successful integration of openBIS and Nextcloud systems.
Automated and efficient background import of large mass spectrometry data files.
Establishment of comprehensive data provenance for all imported data.

Conclusions:

The combined use of openBIS and Nextcloud provides an efficient solution for managing large research datasets.
Automated data import workflows enhance data accessibility and provenance in systems medicine.
This approach supports robust data management practices essential for collaborative research.