Repository Index

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Ankh: Optimized Protein Language Model

OPEM (Open Source PEM Fuel Cell Simulation Tool)

• chemistry
• pem
• fuel-cell
• opem

Automated 3D cell detection in very large images

• microscopy
• cell-detection
• deep-learning
• image-analysis

High performance computational platform in Python for the spectral Galerkin method

• spectral-methods
• galerkin
• fenics
• turbulence

:spider_web: Simple mesh generator inspired by distmesh.

• mesh
• finite-elements
• mathematics
• mesh-generation

Converts medical images to more displayable formats, e.g. NIfTI to jpg.

A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.

PyTorch Connectomics: segmentation toolbox for EM connectomics

• computer-vision
• neuroscience
• connectomics
• pytorch

Medical LLM agent and MRI segmentation workspace built on PharmaLLM, with LangGraph, vLLM, and BEU-Net.

Code that makes the Iowa Environmental Mesonet run, or run into the ground.

• weather
• mesonet
• iowa

Associated Repository for "Translation between Molecules and Natural Language"

Wrapper for RDKit's RunReactants to improve stereochemistry handling

scPerturb: A resource and a python/R tool for single-cell perturbation data

• cite-seq
• database
• perturbation
• scatac-seq

:triangular_ruler: Orthogonal polynomials in all shapes and sizes.

• python
• mathematics
• engineering
• physics

A Python interface to access neuroanatomical atlases

• neuroscience
• python
• microscopy
• registration

A Python package for molecular docking with an extensive, highly-curated dataset and a set of realistic benchmark tasks for drug discovery.

MOGONET (Multi-Omics Graph cOnvolutional NETworks) is a novel multi-omics data integrative analysis framework for classification tasks in biomedical applications.

Molecule Validation and Standardization

• rdkit
• python
• chemistry
• cheminformatics

AI-based pathology predicts origins for cancers of unknown primary - Nature

• histology
• pathology
• wsi-images
• histopathology

Open source tumor evidence matching for sequencing labs and hospitals without molecular tumor boards. Research prototype; oncologist review required.

• bioinformatics
• cancer-research
• computational-biology
• drug-repurposing

Simple RDKit molecule editor GUI using PySide

The implementation code for "DAGAN: Deep De-Aliasing Generative Adversarial Networks for Fast Compressed Sensing MRI Reconstruction"

• generative-adversarial-network
• mri-reconstruction
• computer-vision
• deep-learning

ChemML is a machine learning and informatics program suite for the chemical and materials sciences.

• quantum-mechanics
• materials-informatics
• data-science
• machine-learning