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Platform & Resources

Introduction to Our Platform

🖥️ Open-Source Projects from Our Lab

Knowledge Curation and Databases

Title Description Open Source Repo Feedback
BioMedGPS Data How to build biomedical knowledge graph & graph neural network models for drug repurposing. GitHub Repo Post an Issue
Prophet Studio A data labeling and annotation tool for biomedical publications. GitHub Repo Post an Issue
GuideScoper Find the Best sgRNAs and Design top-scoring guide RNAs for gene knockout GitHub Repo
GlioMarker An integrated Database for Knowledge Exploration of Diagnostic Biomarkers in Gliomas GitHub Repo

A Platform for Drug Repurposing, Disease Mechanism, and Biomarker Screening

Such as Knowledge Graph, Omics Data Analyzer, QC Tools, Data Repo for BioMedical Models, DL Models etc.

Title Language Description Feedback
BioMedGPS Rust, TypeScript, Python A knowledge graph system with graph neural network for drug repurposing, disease mechanism and biomarker screening. Post an Issue
Chat Publications Python Ask questions and get answers from publications.

Online Quality Assessment Platform for Multi-omics Data

Title Description
Quartet Data Portal The Quartet Project provides publicly accessible multi-omics reference materials and practical tools to enhance the reproducibility and reliability of multi-omics results. Well-characterized multiomics reference materials and quality control metrics pertinent to precision medicine study purposes can be used to measure and mitigate technical variation, enabling more accurate cross-batch and cross-omics data integration in increasingly large-scale and longitudinal studies such as the International Human Phenome Project. GitHub Repo

Multi-omics Data Management and Analysis Platform

Title Language Description
Choppy Pipe Python Choppy is a command-line & web tool for executing WDL workflows on Cromwell servers. (Based on widdler, but more.)
BioMiner Clojure, Vue Online analysis platform for multi-omics data.
BioMiner Indexd Rust Index engine for biomedical data files. We epect it will be a indexing engine for indexing high quality data, such as clinical data (EHR), multi-omics data, whole slide image, etc.
PreQC Pack Rust A quality assessment tool for high throughput sequence data.

📁 Collections

Title Description
Omics Datasets A collection of omics datasets for cancer and auto-immune diseases. [Only for Group Members]
Antibody DL A Collection of Platform, Tools, and Resources for Antibody Engineering
BioMedical Knowledgebases A collection of biomedical knowledgebases, ontologies, and datasets.
Toxicant Datasets A collection of toxicant dataset.
Raman Spectra Datasets A collection of raman spectra dataset.

🗄️ Data Repositories

For Quality Control of Multi-omics Data

Title Description
Quartet Data Portal A data portal for quality control of multi-omics data. It contains a lot of high quality multi-omics data based on the quartet reference materials. If you want to ensure your data quality, you can use it as a reference.

Last update: 2025-04-23
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