uaanchorage/GSoC

Alaska Project Ideas, mentored by the researchers and collaborators of University of Alaska and supported by open-source entities and enthusiasts in Alaska.

Size: 992 KB - Last synced at: about 9 hours ago - Pushed at: about 10 hours ago - Stars: 51 - Forks: 13

BaranziniLab/KG_RAG

Empower Large Language Models (LLM) using Knowledge Graph based Retrieval-Augmented Generation (KG-RAG) for knowledge intensive tasks

Language: Jupyter Notebook - Size: 10.3 MB - Last synced at: about 9 hours ago - Pushed at: 6 months ago - Stars: 832 - Forks: 101

marekkoc/project-archive

A comprehensive collection of my programming projects, research work, and technical experiments. This repository showcases my experience in data science, image processing, 2D/3D visualization, and GUI application development. Projects are organized by domain and technology stack for easy navigation.

Size: 7.81 KB - Last synced at: about 24 hours ago - Pushed at: 1 day ago - Stars: 0 - Forks: 0

CNAG-Biomedical-Informatics/convert-pheno

A software toolkit for the interconversion of standard data models for phenotypic data

Language: Perl - Size: 121 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 13 - Forks: 1

cancervariants/disease-normalization

Services and guidelines for normalizing disease terms

Language: Python - Size: 4.4 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 6 - Forks: 0

MaayanLab/GeneSetCart

GeneSetCart is an interactive web-based platform that enables investigators to gather gene sets from various sources; augment these sets with gene-gene co-expression correlations and protein-protein interactions; perform set operations on these sets such as union, consensus, and intersection; and visualize and analyze these gene sets.

Language: TypeScript - Size: 17.7 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 0 - Forks: 0

AnthonyMRios/pymetamap

Python wraper for MetaMap

Language: Python - Size: 45.9 KB - Last synced at: 4 days ago - Pushed at: almost 5 years ago - Stars: 172 - Forks: 63

deweylab/MetaSRA-pipeline

MetaSRA: normalized sample-specific metadata for the Sequence Read Archive

Language: Python - Size: 27.5 MB - Last synced at: 6 days ago - Pushed at: 7 days ago - Stars: 43 - Forks: 14

mne-tools/mne-cpp

MNE-CPP: A Framework for Electrophysiology

Language: C++ - Size: 349 MB - Last synced at: 2 days ago - Pushed at: about 1 year ago - Stars: 164 - Forks: 144

Sage-Bionetworks/schematic

Package for biomedical data model and metadata ingress management

Language: Python - Size: 11.8 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 25 - Forks: 26

maxkayser/ectmetrics

A Python Library for Calculating Seizure Quality Indices in Electroconvulsive Therapy

Language: Python - Size: 2.05 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 0 - Forks: 1

monarch-initiative/omim

Data ingest pipeline for OMIM.

Language: Jupyter Notebook - Size: 88.4 MB - Last synced at: about 6 hours ago - Pushed at: about 8 hours ago - Stars: 7 - Forks: 3

cancervariants/gene-normalization

Services and guidelines for normalizing genes

Language: Python - Size: 2.32 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 2 - Forks: 4

CNAG-Biomedical-Informatics/pheno-ranker

Pheno-Ranker is a tool for comparing phenotypic data structured in JSON/YAML format, such as Beacon v2 Models or Phenopackets v2.

Language: Perl - Size: 39 MB - Last synced at: 21 days ago - Pushed at: 21 days ago - Stars: 6 - Forks: 1

metadatacenter/cedar-project

Build project for all CEDAR Java repositories

Size: 148 KB - Last synced at: 25 days ago - Pushed at: 25 days ago - Stars: 14 - Forks: 1

chardyb/Prob-and-Stats-BMI6106

A repository for Spring 2025 BMI 6106: Statistics and Probability. This repository contains coursework, code examples, and projects exploring statistical methods and probabilistic models in biomedical informatics.

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nlpie/biomedicus

BioMedICUS: A biomedical and clinical NLP engine.

Language: Java - Size: 6.75 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 18 - Forks: 7

pscedu/singularity

Just a list of Singularity definition files maintained by the Biomed Applications Group

Language: Python - Size: 182 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

raghavagps/NTxPred2

NTxPred2: An improved method for predicting neurotoxicity of peptides and proteins

Language: Python - Size: 3.7 MB - Last synced at: 17 days ago - Pushed at: about 2 months ago - Stars: 2 - Forks: 0

dipendrapant/Health_Biomedical_Informatics_Conference_Journals

List with overview of significant conferences and journals related to Biomedical & Health Informatics

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SohelRana-aiub-Pro/Biomedical-Engineering-Research-Projects

Artificial intelligence (AI) is gradually changing medical practice. With recent progress in digitized data acquisition, machine learning and computing infrastructure, AI applications are expanding into areas that were previously thought to be only the province of human experts.

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ram-compbio/CANDO

Computational Analysis of Novel Drug Opportunities

Language: Python - Size: 12.1 MB - Last synced at: 16 days ago - Pushed at: 3 months ago - Stars: 36 - Forks: 11

JuliaHealth/juliahealth.github.io

Website for the JuliaHealth organization (powered by Franklin.jl).

Language: Julia - Size: 2.17 MB - Last synced at: 29 days ago - Pushed at: 3 months ago - Stars: 16 - Forks: 10

datneuro/Immunoproteasome_PD

PSMB8 Immunoproteasome in Parkinson's disease

Language: Jupyter Notebook - Size: 20.5 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

bcbi/julia_tutorials

Materials used for introductory classes using Julia for statistics, biomedical queries and plotting

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AnthonyMRios/multi-label-zero-shot

Few- and Zero-shot Multi-Label Learning for Structured Label Spaces

Language: Python - Size: 598 KB - Last synced at: about 1 month ago - Pushed at: about 5 years ago - Stars: 48 - Forks: 12

karthiksoman/biomixQA

Repository for BiomixQA benchmark dataset

Language: Jupyter Notebook - Size: 13.7 KB - Last synced at: about 1 month ago - Pushed at: 8 months ago - Stars: 3 - Forks: 0

hms-dbmi/EHRtemporalVariability

R package for delineating temporal dataset shifts in Eletronic Health Records

Language: HTML - Size: 11.7 MB - Last synced at: about 1 month ago - Pushed at: about 1 year ago - Stars: 17 - Forks: 8

tisimpson/pbi

Programming for Biomedical Informatics, School of Informatics, The University of Edinburgh

Language: Jupyter Notebook - Size: 369 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 15 - Forks: 4

monarch-initiative/icd10who

ICD10WHO ingest.

Language: Python - Size: 511 KB - Last synced at: about 1 month ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

carnival-data/carnival-demo-biomedical

Demonstration Carnival Micronaut application.

Language: Groovy - Size: 10.2 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 2 - Forks: 0

EBISPOT/DUO

Ontology for consent codes and data use requirements

Language: Makefile - Size: 6.43 MB - Last synced at: 5 months ago - Pushed at: over 2 years ago - Stars: 64 - Forks: 15

amarrammadhu/Biomedical-Engineering-

My assignments and projects concerned with Biomedical Engineering

Language: TeX - Size: 5.26 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 2 - Forks: 0

pwatrick/ddiwas

Language: R - Size: 4.64 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 1

pwatrick/DrugRepurposingToolKit

Language: R - Size: 5.51 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 3 - Forks: 6

deepzx987/deepzx987.github.io

Website

Language: CSS - Size: 3.1 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

Michu-dev/ai-university-labs

AI labs - solutions

Language: Jupyter Notebook - Size: 151 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

IVN-RIN/bio-med-BIT

Data and source code for Localising In-Domain Adaptation of Transformer-Based Biomedical Language Models

Language: Jupyter Notebook - Size: 13.2 MB - Last synced at: 12 months ago - Pushed at: about 2 years ago - Stars: 4 - Forks: 0

lmichan/PFR

Proyecto de manejo de información digital sobre pruebas de función respiratoria mediante anotación semántica con Hypothes.is

Size: 33.2 KB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 1 - Forks: 0

MUSC-TBIC/lexicon-tools

Language: Python - Size: 77.1 KB - Last synced at: about 1 year ago - Pushed at: almost 2 years ago - Stars: 3 - Forks: 0

MUSC-TBIC/etude-engine

ETUDE (Evaluation Tool for Unstructured Data and Extractions) is a Python-based tool that provides consistent evaluation options across a range of annotation schemata and corpus formats

Language: Jupyter Notebook - Size: 2.28 MB - Last synced at: about 1 year ago - Pushed at: almost 3 years ago - Stars: 12 - Forks: 0

DavidAI2024/DrugGeneExplorer

This Python script is designed to provide detailed information on interactions between drugs and genes using the Sydney module for natural language processing and the Drug Gene Interaction Database (DGIdb) API. Users can input the names of three drugs separated by commas and receive information on the interactions with the corresponding genes.

Language: Python - Size: 129 KB - Last synced at: 25 days ago - Pushed at: about 1 year ago - Stars: 5 - Forks: 2

tanmaybasu/Extract-Anxiety-Outcome-Measures-From-Literature

A sentence classification framework for extraction of anxiety outcome measures from relevant literature

Language: Python - Size: 18.6 MB - Last synced at: about 1 year ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 0

tanmaybasu/Qualitative-Text-Analysis-of-Healthcare-Data-Using-NLP

A text summarization framework to identify major opinions from healthcare text

Language: Python - Size: 46.9 KB - Last synced at: about 1 year ago - Pushed at: about 4 years ago - Stars: 5 - Forks: 0

ICBI/Open-Science-Projects

Open Science Projects at Georgetown-ICBI

Size: 1.36 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 4 - Forks: 0

biolab-unige/xtens-app

A digital repository for biomedical data based on a flexible JSON data model ( The project has been moved to a new address https://github.com/xtens-suite/xtens-app.git )

Language: JavaScript - Size: 3 MB - Last synced at: about 1 year ago - Pushed at: over 7 years ago - Stars: 6 - Forks: 1

pscedu/apptainer

Just a list of Apptainer definition files maintained by the Biomed Applications Group

Language: Python - Size: 3.91 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

suamin/MedDistant19

MedDistant19: Towards an Accurate Benchmark for Broad-Coverage Biomedical Relation Extraction (COLING 2022)

Language: Python - Size: 213 KB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 15 - Forks: 2

mida-project/meta Fork of MIMBCD-UI/meta

:paperclip: About MIDA Project

Size: 143 MB - Last synced at: about 1 year ago - Pushed at: over 4 years ago - Stars: 12 - Forks: 1

timsbiomed/tims-website

The overall and public TIMS repository.

Language: HTML - Size: 33.2 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

krishnakumarsekar/Ant-Colony-Optimization-in-TensorFlow

Ant colony optimazation is a famous algorithm in image segmentation and biomedical , This project is to effectively apply ACO in tensorflow and for production purpose

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tranSMART-Foundation/transmart-core

Core components and documentation of the tranSMART platform.

Language: JavaScript - Size: 329 MB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 6 - Forks: 2

Jeanvit/AndroidDynamometer

An Android app developed in my Master's (2014) for a biomedical electronic dynamometer with bluetooth interface.

Language: Java - Size: 14.5 MB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 1 - Forks: 1

rcolinp/clinical_informatics_umls

An exploratory, tutorial and analytical view of the Unified Medical Language System (UMLS) & the software/technologies provided via being a free UMLS license holder. This repo will subset 2021AB UMLS native release, introduce/build upon UMLS provided tools to load a configured subset into first a relational database --> MySQL, SQLite, PostgreSQL and MariaDB all covered within this repo. Next the UMLS subset which is stored in a relational DB will be queried, modeled and lastly loaded into a defined Neo4j label property graph. Lastly, Neo4j database containing UMLS 2021AB subset in schema promoting intuitive analysis and rich visualization will become the central datastore for analysis. The datastore contains ~5 million distinct nodes & >40 million distinct relationships (edges). Currently, Neo4j is running via Docker but deployment options are NOT limited to Docker. If choosing to deploy via Neo4j Aura, server, Neo4j Desktop, VM etc... Please note and be aware of the specific volumes and environment variables specified within this repository (docker run). The ability for the loaded Neo4j Graph to interact with RDF data (i.e. import/export RDF data to and from Neo4j) may not be possible via all Neo4j deployment avenues (i.e. Neo4j Aura currently does not support RDF integration that is demonstrated in this repository).

Language: Python - Size: 6.96 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 22 - Forks: 1

bhklab/CREAM

CREAM (Clustering of Functional Regions Analysis Method) is a new method for identification of clusters of functional regions (COREs) within chromosomes.

Language: R - Size: 2.47 MB - Last synced at: 27 days ago - Pushed at: about 4 years ago - Stars: 12 - Forks: 3

pleiadian53/tpheno

Prototypes for EHR-sequencing and temporal phenotyping. Key methods: sequence models, LSTM, attention mechanism, cluster analysis, word & document embeddings, and other NLP methods.

Language: Python - Size: 51 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

mikaeldusenne/haskupcake

haskell library to send requests to the PIC-SURE api

Language: Haskell - Size: 167 KB - Last synced at: over 1 year ago - Pushed at: almost 7 years ago - Stars: 1 - Forks: 0

giffordlabcvr/HCV-NABS

Extension to HCV-GLUE project, to analyse binding sites for HCV neutralising antibodies.

Language: JavaScript - Size: 697 KB - Last synced at: almost 2 years ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0

uw-bionlp/ards

A PyTorch Wrapper of Hierarchical Attention Network with Sentence Objectives Framework for ARDS Identification

Language: Python - Size: 678 KB - Last synced at: almost 2 years ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 0

SubhamoyBiswas/Simulation-of-Arrhythmia-in-a-computer-model-of-the-heart

Language: Python - Size: 951 KB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 0

tanmaybasu/Data-Elements-Extrcation-from-Literature-Using-NLP-and-Machine-Learning

A novel sentence classification framework for information extraction from relevant literature

Language: Python - Size: 1.14 MB - Last synced at: about 1 year ago - Pushed at: almost 4 years ago - Stars: 2 - Forks: 1

ICBI/.github

Welcome to Georgetown University Innovation Center for Biomedical Informatics !

Size: 3.76 MB - Last synced at: about 1 year ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

ReggieScript/ECG_arrythmia_detection

Arrythmia detection machine learning model using logistic regression ❤️

Language: Jupyter Notebook - Size: 6.63 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

tanmaybasu/Early-Prediction-of-Anorexia-and-Depression-Over-Social-Media

A text classification framework to identify anorexia and depression over social media text

Language: Python - Size: 44.9 KB - Last synced at: about 1 year ago - Pushed at: almost 4 years ago - Stars: 2 - Forks: 1

sejas/muia-assessment-applewatch-atrial-fibrillation-ontology

Basic ontology to represent the article: "Large-Scale Assessment of a Smartwatch to Identify Atrial Fibrillation"

Size: 2.45 MB - Last synced at: 6 days ago - Pushed at: over 5 years ago - Stars: 2 - Forks: 0

CompBtBs/FalseDiscoveriesAnalysis

Adjusting for false discoveries in constraint- and sampling-based differential metabolic flux analysis

Language: Jupyter Notebook - Size: 24.1 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0

visanuwan/Nek2_singlecell

Nek2 single cell analysis

Language: R - Size: 5.86 KB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

visanuwan/CD24_CART_singlecell

CD24 CART single cell analysis

Language: R - Size: 8.79 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

carsaesi/covid19sdtool

R code for the discovery of COVID-19 subgroups by symptoms and comorbidities.

Language: HTML - Size: 3.59 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 5 - Forks: 0

a-r-j/DrugTranslatoR

R package for translating between drug identifiers using the Chemical Translation Service (CTS)

Language: R - Size: 6.84 KB - Last synced at: 26 days ago - Pushed at: over 2 years ago - Stars: 3 - Forks: 2

zbmed-semtec/BioMedSem-IR-KD

A course on Biomedical Semantics, Information Retrieval and Knowledge Discovery

Language: HTML - Size: 197 MB - Last synced at: about 1 month ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 0

EunBinChoi/biomedical-syntactic-analysis-master

The keywords of biomedical materials are extracted with biomedical and clinical syntactic analysis and named entity recognition models offered in Stanza.

Language: HTML - Size: 172 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

mgpopinjay/nlp-qa-outdomain

Out-domain Question Answering (QA) on SQuAD with bi-directional LSTM

Language: Python - Size: 97.5 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 0

FedericaPaoli1/Respiration-rate-and-heart-rate-detection

Respiration-rate-and-heart-rate-detection is a project developed for the Biomedical Signal Processing exam at the University of Milan (academic year 2020-2021). It implements an algorithm to analyze accelerometric signals collected with a smartphone positioned on the thorax while supine.

Language: MATLAB - Size: 3.69 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 2

aimanmuhamad/StanzaDemo

These packages offer accurate syntactic analysis and named entity recognition capabilities for biomedical and clinical text.

Language: Jupyter Notebook - Size: 320 KB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 1

bionlproc/multi-label-zero-shot Fork of AnthonyMRios/multi-label-zero-shot

Few- and Zero-shot Multi-Label Learning for Structured Label Spaces

Language: Python - Size: 12.7 KB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 21 - Forks: 1

carsaesi/EHRsourceVariability

Measuring and visualizing biomedical data variability/heterogeneity across data sources

Language: R - Size: 183 KB - Last synced at: about 2 years ago - Pushed at: almost 6 years ago - Stars: 3 - Forks: 0

hms-dbmi/connections.careers

Website for a video project that documents the training experiences of predoctoral and postdoctoral trainees from 16 National Library of Medicine-funded biomedical informatics and data science training programs.

Language: JavaScript - Size: 20.6 MB - Last synced at: about 1 year ago - Pushed at: almost 4 years ago - Stars: 1 - Forks: 0

sharmalab/Emory-BMI-GSoC

Emory BMI GSoC 2020 Project Ideas

Size: 268 KB - Last synced at: about 1 year ago - Pushed at: about 4 years ago - Stars: 8 - Forks: 2

snikol03/Markov-Chain-Project

Perl implementation of Markov Chain for the course BIO331

Language: Perl - Size: 12.5 MB - Last synced at: over 1 year ago - Pushed at: about 8 years ago - Stars: 2 - Forks: 1

cdcai/enriched-LSTMs Fork of scotthlee/enriched-LSTMs

Classifying multimodal health data with LSTMs

Language: Python - Size: 53.7 KB - Last synced at: about 2 years ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 1

bionlproc/med-match-cnn Fork of AnthonyMRios/med-match-cnn

Implementation of our matching network CNN

Language: Python - Size: 19.5 KB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 2 - Forks: 2

AnthonyMRios/med-match-cnn

Implementation of our matching network CNN

Language: Python - Size: 22.5 KB - Last synced at: about 1 month ago - Pushed at: about 7 years ago - Stars: 2 - Forks: 2

xcollantes/biomed-machine-learning-CUI

Application interacts with NIH API

Language: Java - Size: 3.94 MB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

Glewando/Neuroinflammation-Memory

Impact of neuroinflammation of contextual memory and neuronal circuit activity

Language: R - Size: 1.48 MB - Last synced at: about 2 years ago - Pushed at: about 8 years ago - Stars: 0 - Forks: 1