Dataset Card for seqedge-data

Dataset Description

This repository serves as the official public data backend for GalibierHub, an interactive web platform for genomic cohort analytics. The dataset hosts reference bundles, release archives, and sample-level files designed for academic research and downstream bioinformatics pipelines. It currently contains approximately 1.3 GB of open-access data published under the MIT license.

Dataset Structure

The repository is organized into distinct directories to support both traditional bioinformatics workflows and machine learning applications.

Core Academic Data (GalibierHub Records)

• Records/Reference_Genomes/: Contains the global reference files, including reference.fasta and annotation.gff3.
• Records/Variant_Calling_VCF/: Contains 12 sample-specific .vcf.gz files tailored for variant and population genetics analysis.
• Records/ML_Ready_FASTA/: Contains 12 full .fasta files optimized for machine learning sequence extraction and promoter prediction.

Additional Resources

• SARS-CoV-2 Reference Files: Root-level files including scov2.fa, scov2.gb, scov2.genes.bed, and scov2.genes.gff3.
• Learning-Resources/: A collection of educational materials and bioinformatics reference PDFs.
• Graduate-student-textbooks/: Supplemental textbooks for graduate-level study.

Source Data Details

The 12 primary demo samples located in the Records/ directory (e.g., CNhs13076, CNhs13080, CNhs13195, CNhs13216) are derived from public test files.

• Source: FANTOM5 human primary-cell CAGE data (hg19)
• Cohort: FANTOM5 human.primary_cell.hCAGE
• Platform: HeliScope CAGE
• Project URL: https://fantom.gsc.riken.jp/5/
• Reference Publication: https://www.nature.com/articles/sdata2017112

How to Use This Data

Files can be downloaded directly from this repository using the Hugging Face CLI, wget, or curl. However, for the optimal experience, we recommend using the GalibierHub Downloads Interface, which provides:

• Automated generation of Python, SLURM, and .bat batch download scripts for recursive folder downloads.
• MD5 and SHA-256 integrity verification commands to ensure data is uncorrupted after transfer.
• Seamless routing from the embedded JBrowse 2 genome visualization directly to the corresponding file downloads.

About GalibierHub

GalibierHub is a comprehensive scientific data portal built for modern researchers. Key end-user capabilities include:

• Search & Discovery: Advanced filtering of promoter records by locus, gene, score, tissue, cohort, and BMI class.
• Data Visualization: An embedded genome browser with a distraction-free fullscreen zen mode and floating promoter detail panels.
• Community & Moderation: A rich discussion board featuring Markdown support, image lightboxes, real-time WebSocket notifications, and a gamified badge system to reward community contributions.
• User Profiles: Persistent profiles synced via Supabase with activity feeds, online status, and secure authentication (GitHub OAuth or Turnstile-protected email).