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🖥️ Open-Source Projects

A Platform for Drug Repurposing & Biomarker Screening

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

Title Language Description
BioMedGPS Rust, TypeScript, Python A knowledge graph system with graph neural network for drug repurposing, disease mechanism and biomarker screening.
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.

Knowledge Curation and Databases

Title Description
Prophet Studio A data labeling and annotation tool for biomedical publications.
GuideScoper Find the Best sgRNAs and Design top-scoring guide RNAs for gene knockout
GlioMarker An integrated Database for Knowledge Exploration of Diagnostic Biomarkers in Gliomas

Collections

Title Description
Antibody DL A Collection of Platform, Tools, and Resources for Antibody Engineering
BioMedical Knowledgebases A collection of biomedical knowledgebases, ontologies, and datasets.

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