GitHub
https://github.com/alleninstitute/patchseq_human_l1
supporting data and code for human L1 patchSeq manuscript
https://github.com/allfed/allfed-repository-template
Use this as a template for a new project: https://medium.com/programming-lite/repository-templates-in-github-why-how-75b1d1bd43f2
https://github.com/allfed/water-access
Global analysis of freshwater access by walking or cycling in the event of catastrophic infrastructure loss.
https://github.com/aloftdata/bird-migration-flow-visualization
Bird migration flow visualization
https://github.com/alondmnt/joplin-plugin-tag-navigator
A PKM system to organise, search, browse and convert inline tags, front matter and tasks in Joplin
https://github.com/amazon-science/job-posting-structure
Extract structured information from job postings.
https://github.com/amazon-science/wqa-multi-sentence-inference
This repository contains code used for our Multi Sentence Inference NAACL'22 paper.
https://github.com/amazon-science/recode
Releasing code for "ReCode: Robustness Evaluation of Code Generation Models"
https://github.com/amazon-science/latticealgorithms.jl
Algorithms to solve lattice problems in Julia
https://github.com/amber-md/cpptraj
Biomolecular simulation trajectory/data analysis.
https://github.com/amider-dev/exceltoxml
エクセルで入力されたツリー構造のデータをスキーマに従ってXMLファイルへ変換する。共通・非共通項目を持つ複数のXMLファイルを一括生成できる。Convert tree-structured datasets described in Excel table into multiple XML files following the schema.
https://github.com/amoneva/code_papers
A repository of R code used for analysis in scientific papers.
https://github.com/ampliconsuite/ec3d
Reconstruct the three-dimensional structure of extrachromosomal DNA
https://github.com/amrex-combustion/pelec
An AMR code for compressible reacting flow simulations
https://github.com/amrex-combustion/pelephysics
A collection of physics databases and implementation code for use with the Pele suite of of codes
https://github.com/anastassiavybornova/schelling-reloaded
Background material for the project "You Don't Have to Live Next to Me: A Critical Review of the Schelling Model and Its Reception"
https://github.com/andresgur/muse_project
Scripts to deal with some subtleties regarding MUSE data
https://github.com/anikfal/atmospheric_science
Codes and solutions for atmospheric data and modeling
https://github.com/anselmoo/useful-optimizer
A dedicated set of optimization algorithms for numeric problems.
https://github.com/anton-bushuiev/proteinttt
Training on test proteins improves fitness, structure, and function prediction
https://github.com/antsx/antsrnet
Medical image analysis framework merging ANTsR and deep learning
https://github.com/ap6yc/audeyart
Learning repo for Audrey and writing FuzzyART from scratch.
https://github.com/ap6yc/cfar
This repository is a workplace for the upcoming "Analysis of Catastrophic Forgetting and Adaptive Resonance Theory Algorithms" paper.
https://github.com/appfl/appfl-scifm
APPFL Demo for Federated Learning Tutorial at SciFM
https://github.com/aradfarahani/awesome-geophysics
Awesome Geophysics is a community-curated resource offering essential tools, datasets, and educational materials for geophysical exploration. It’s designed to empower students, researchers, and professionals to analyze data, model Earth processes, and stay connected with the latest industry trends.
https://github.com/aria-systems-group/sym_quant_reactive_synth
Symbolic Regret synthesis and graph search
https://github.com/arkadiusz-jedrzejewski/norm-formation-m
Matlab scripts used to analyze an agent-based model (ABM) used to study the impact of symmetric and nonsymmetric conformity functions on decision-making processes.
https://github.com/arkokupski-wat/hypothesis-of-cyclic-black-hole-eruptions-in-higher-dimensional-geometry
Unified Cyclic Black Hole Eruption Hypothesis: Proposes that extreme densities trigger matter-antimatter conversion, powering cosmic explosions via temporary event horizon loss. Emergent gravity arises from 5D spacetime tension between matter/antimatter branes. Predicts unique gamma-ray profiles and eruption cyclicity (T ∼ M/Ṁ).
https://github.com/arkokupski-wat/hypothesis-of-emergent-gravity-from-substrate-phase
The Emergent Gravity from Substrate Phase Hypothesis Core Idea: This hypothesis proposes that spacetime and matter are not fundamental but represent different phase states of a single, underlying entity—the Substrate.
https://github.com/arkokupski-wat/big-bang-as-a-detonation-explosive-material
The core mechanism is matter-antimatter annihilation, which acts as the engine of the cosmos. However, the model posits that annihilation does more than just release energy in the form of photons; it is the primary process responsible for generating spacetime itself and endowing it with an expansive property.
https://github.com/arkokupski-wat/asymmetric-spacetime-disk
A 5D geometric model unifying dark energy and matter-antimatter asymmetry. Predicts Hubble constant H 0 ≈ 67 H 0 ≈67 km/s/Mpc without dark energy
https://github.com/arkokupski-wat/g-2-force-spacetime-adhesion-revised-model-
Revised model of G-2 force.
https://github.com/arkokupski-wat/g-2-force-spacetime-adhesion-model-revised-
G-2-Force-Spacetime-Adhesion Model (Revised). The theory introduces: New "adhesion parameter" D quantifying spacetime coupling
https://github.com/arm61/sim_vs_trad
ESI for "Assessing molecular simulation for the analysis of lipid monolayer reflectometry"
https://github.com/arya-gaj/your-phone-can-spot-fashion-v1
A lightweight yet powerful system that analyzes short-form videos in real time to identify fashion products by combining computer vision and natural language processing, all processed locally.
https://github.com/aspuru-guzik-group/da_for_polymers
Augmenting Polymer Datasets via Iterative Rearrangement
https://github.com/aspuru-guzik-group/atlas
A brain for self-driving laboratories
https://github.com/aspuru-guzik-group/artificial-design-of-organic-emitters
Code and data for "Artificial Design of Organic Emitters via a Genetic Algorithm Enhanced by a Deep Neural Network".
https://github.com/aspuru-guzik-group/kreed
Code for Reflection-Equivariant Diffusion for 3D Structure Determination from Isotopologue Rotational Spectra in Natural Abundance
https://github.com/astrazeneca/multimodal-python-course
The purpose of the code is to facilitate a comprehensive understanding of multimodal data science applications within medical domain. The code serves to support the delivery of a cutting-edge workshop designed to introduce researchers to the rapidly evolving field of multimodal data science
https://github.com/astro-informatics/s2scat
Differentiable and GPU accelerated scattering covariance statistics on the sphere
https://github.com/astromusers/darkinferno
Library for computing the temperature profile within the core of rocky planets, including the Earth, due to heating from the annihilation of captured dark matter
https://github.com/atzberg/geo_neural_op
Geometric Neural Operators (GNPs) for machine learning tasks on point-cloud representations: curvature estimation, shape deformations, solvers for geometric PDEs. Also, includes weights of pretrained transferable GNP models.
https://github.com/ay-lab/signifrt
A Quantitative Framework for the Assessment of RT Changes upon CRISPR-mediated Dissection, from Turner and Hinojosa-Gonzalez et al. (2025))
https://github.com/b-cubed-eu/invasimapr
Workflow to visualise trait dispersion and assess invasibility
https://github.com/babots-project/cuda_agent_based_sim
A simple CUDA agent-based simulator
https://github.com/bammri/3d_dynamic_paper_2024
Code and data for the 3D Dynamic paper 2024
https://github.com/bamresearch/probeye
A general framework for setting up parameter estimation problems.
https://github.com/bandframework/rose
The Reduced-Order Scattering Emulator (rose) is a user-friendly software for building efficient surrogate models for nuclear scattering
https://github.com/barahona-research-group/multiscalemobilitypatterns
Code for the paper "Multiscale mobility patterns and the restriction of human movement" by Juni Schindler, Jonathan M Clarke and Mauricio Barahona: https://arxiv.org/abs/2201.06323
https://github.com/barathme/hen_multiscale_lowk
Explainable Multiscale Modeling of High-Entropy Nitride Superlattices for Low-Thermal-Conductivity Coatings
https://github.com/barricklab/ltee-ecoli
Genomics resources for the Long-Term Evolution Experiment with E. coli
https://github.com/bartongroup/sack1g-analysis
This is a GitHub Repository containing the data and code used for an structural analysis of FAM83G and FAM83G-CK1A 3D models
https://github.com/batmen-lab/diamond
Error-controlled interaction discovery in machine learning models
https://github.com/battmodels/diffthermo_ocv_paper
diffthermo, a python package for thermodynamically consistent OCV model construction
https://github.com/battmoteam/pybamm
Fast and flexible physics-based battery models in Python
https://github.com/bbglab/oncodrive3d
A computational approach for identifying cancer driver genes by detecting three-dimensional clusters of somatic missense mutations in protein structures.
https://github.com/bbopt/rungekutta
The RUNGE-KUTTA blackbox optimization problem
https://github.com/beatlab-mcmaster/schlichting_msc_thesis
Code and data to reproduce my master's thesis.
https://github.com/bede/deacon
FASTX search and [host] depletion using minimizers
https://github.com/beefathima-git/cloud-computing-for-real-time-surveillance-applications-
This project utilizes fog and cloud computing to enable low-latency, real-time surveillance by processing video and sensor data closer to the source. It improves responsiveness, reduces bandwidth usage, and enhances system scalability for smart surveillance applications.
https://github.com/beehive-lab/tornadovm
TornadoVM: A practical and efficient heterogeneous programming framework for managed languages
https://github.com/benjamindecker/quantum-cellular-automaton
A classical simulation of quantum cellular automata
https://github.com/benjaminhlina/nichetools
Complementary functions to extract and work with objects created by {nicheROVER} and {SIBER}
https://github.com/benjaminhlina/lake-ontario-ecoregions-ms
Data and code for paper centred on trophic differences among ecoregions in Lake Ontario
https://github.com/benweare/em_scripts
Electron microscopy scripts not associated with any specific publications.
https://github.com/berenslab/disentangling-retinal-images
This repository contains the code for the paper "Disentangling representations of retinal images with generative models".
https://github.com/bhklab/signaturesets
Compendium of published molecular signatures
https://github.com/bihealth/fracture-healing-and-aging-scseq
single-cell bone healing project
https://github.com/billbrod/spatial-frequency-model
Model from the spatial frequency preferences paper
https://github.com/billbrod/foveated-metamers
Create metamers using models of the ventral stream and run experiments to validate them
https://github.com/bin-cao/tcgpr
[NPJ Com Mat 2023 | Small 2024] Machine Learning Algorithm : outlier identifying, feature selection
https://github.com/biodt/general-soilgrids-soil-data
Building block for obtaining selected soil data at given location from SoilGrids and derived data sources (Soilgrids REST API, HiHydroSoil map).
https://github.com/biodt/uc-grassland-model
grassland simulation model source code
https://github.com/bioinfomachinelearning/gate
Graph transformer for estimating protein model accuracy
