Discover flatironinstitute/nemos Open Source project

Deep functional residue identification

620

DeepFRI

Non-uniform fast Fourier transform library of types 1,2,3 in dimensions 1,2,3

300

finufft

Complete Matlab pipeline for large scale calcium imaging data analysis

293

CaImAn-MATLAB

Matlab routines for online non-rigid motion correction of calcium imaging data

248

NoRMCorre

Neural Networks for Protein Sequence Alignment

142

deepblast

Flatiron Institute Fast Multipole Libraries --- This codebase is a set of libraries to compute N-body interactions governed by the Laplace and Helmholtz equations, to a specified precision, in three dimensions, on a multi-core shared-memory machine.

110

FMM3D

Nonuniform fast Fourier transforms of types 1 and 2, in 1D, 2D, and 3D, on the GPU

cufinufft

Cuda

jax-finufft

JAX bindings to the Flatiron Institute Non-uniform Fast Fourier Transform (FINUFFT) library

Python wrapper for Intel Math Kernel Library (MKL) matrix multiplication

sparse_dot

Learning materials for scientific software development

sciware

HTML

mountainsort

Spike sorting software

Task-based gene regulatory network inference using single-cell or bulk gene expression data conditioned on a prior network.

inferelator

MountainLab is data processing, sharing and visualization software for scientists. It is built around MountainSort, spike sorting software, but is designed to be more generally applicable.

mountainlab-js

Bayesian inference and posterior analysis for Python

bayes-kit

Browser-based NWB visualization and DANDI exploration

neurosift

A collection of computationally efficient algorithms for online subspace learning and principal component analysis

online_psp

SpikeForest -- spike sorting analysis for website -- version 2

spikeforest2

Monitor MCMC runs in the browser

mcmc-monitor

nix+spack = nixpack (spanix?)

nixpack

A fast Lomb-Scargle periodogram. It's nifty, and uses a NUFFT!

nifty-ls

Shareable, interactive scientific figures in the cloud

figurl

Tool to distribute a list of computational tasks over a pool of compute resources. The pool can grow or shrink.

disBatch

MountainSort spike sorting algorithm, version 5

mountainsort5

Spike sorting software being developed at Flatiron Institute, based on JRCLUST (Janelia Rocket Cluster)

ironclust

A Python implementation of the model described in our publication "A convolutional neural network for common-coordinate registration of high-resolution histology images" developed principally for applications to registration of spatial transcriptomics image data.

st_gridnet

Examples of using MountainSort spike sorting software.

mountainsort_examples

Hydrodynamic Cytoskeleton Simulator

SkellySim

This codebase is a set of libraries to compute N-body interactions governed by the Laplace and Helmholtz equations, to a specified precision, in two dimensions, on a multi-core shared-memory machine.

fmm2d

Categorical Variational Autoencoders

catvae

Benchmark of online PCA algorithms

online_psp_matlab

Spike sorting benchmarking system

spikeforest

Prometheus exporter for slurm job/node data

slurm-prometheus-exporter

Haskell

kachery-cloud

Analyze neuroscience data in the cloud

dendro

Computational Tools for PDEs with Complicated Geometries and Interfaces workshop materials, June 10-14, 2024.

comptools24

a Living ENsemble Simulator -- a lens to help you watch biophysics

aLENS

SpikeForest -- spike sorting analysis for website

spikeforest_old

An adaptive fast function approximator based on tree search

baobzi

ISO-SPLIT clustering (stand-alone version)

isosplit5

Code for reproducing the experiment from the paper "A biologically plausible neural network for Slow Feature Analysis"

bio-sfa

Pytorch wrappers for the FINUFFT library

pytorch-finufft

Special function benchmarks

sf_benchmarks

Manifold-tiling Localized Receptive Fields are Optimal in Similarity-preserving Neural Networks

mantis

A simple elasticsearch frontend for serving astrophysical simulation catalog data

flathub

Haskell

ccq-software-build

CCQ software build scripts

Shell

Ensemble-reweighting-using-Cryo-EM-particles

Point Cloud regression with new algebraic representation on ModelNet dataset (ICCV 2023)

PointCloud_Regression

Basic templates for individual user pages in the public/_www directory

public_www

SCSS

inferelator-prior

Gene regulatory network inference using DNA-binding motifs and chromatin accessibility data.

This repository contains box codes for evaluating volume potentials for Laplace, Helmholtz, Maxwell, and Stokes

boxcodes3d

Code for reproducing the experiments in the paper "Bio-NICA: A biologically inspired single-layer network for Nonnegative Independent Component Analysis"

bio-nica

Discrete Lehmann representation of imaginary time Green's functions

cppdlr

nixpkgs-based module builds of cluster packages

nix-modules

Nix

bio-cca

Code accompanying the paper "A biologically plausible neural network for multi-channel Canonical Correlation Analysis"

React components paired with Python classes for backend computation

reactopya

Clair (Clang Introspection and Reflection) tools. A set of clang tools developed for Flatiron/CCQ

clair

Adaptive Pole Fitting for Quantum Many-Body Physics

adapol

DLR_DMFT_scripts

System for sharing data for scientific research

kbucket

Template repository for CCN software projects

ccn-template

neuron segmentation and synapse detection using PyTorch

neutorch

slurm monitoring tools and interface

SlurmUtil

A qiime2 plugin for case-control differential abundance analysis

q2-matchmaker

Scientific data analysis, sharing, and visualization

mountainlab

Least absolute error regression implemented using Linear Programming, primarily to illustrate repository structure conventions.

least_absolute_regression

Example neuropixels datasets for purposes of developing spike sorting algorithms

neuropixels-data-sep-2020

Neurophysiology visualization components deployable to the notebook, web, or desktop

ephys-viz

This repository contains codes for solving inverse obstacle scattering problems to recover the shape of the obstacle for sound soft, sound hard, and penetrable objects

inverse-obstacle-scattering2d

cryoSBI

Peer-to-peer content-addressable file sharing using kachery

kachery-p2p

Benchmark and compare large-scale Gaussian process regression methods in 1D, 2D, and 3D, from MATLAB

gp-shootout

Materials for CCN software workshop at FENS 2024

ccn-software-fens-2024

Test of displaying 3d genomic data using webgl in a "Looking glass" holographic display

looking_glass_3d_test

caiman_central

Central hub for resources related to Caiman calcium imaging analysis package.

labbox-ephys

Canine breast cancer analysis pipeline

FREYA

Notes on metrics and datasets for community spike sorting comparison and validation

spikesortercomparison

TeX

hither

Run batches of Python functions in containers and on remote servers

Gene regulatory networks for intestinal innate lymphoid cells

ILCnetworks

Interactive visualization of Fermi surfaces representing electron energies and velocities in crystal structures.

Fermi_surface_visualization

Meet your colleagues across the Institute

flatiron-coffee

Front end tool for benchmarking spike sorting algorithms.

spike-front

Reactopya widgets of relevance to the Center for Computational Mathematics, Flatiron Institute

ccm_widgets

The Inaugural Flatiron Institute Cryo-EM Heterogeneity Community Challenge

Cryo-EM-Heterogeneity-Challenge-1

Key value storage server. Light weight (single python module with no non-standard module dependencies). Simple protocol minimizes effort needed to write a client (example for C and FORTRAN provided).

kvsstcp

Code accompanying the paper "A linear discriminant analysis model of imbalanced associative learning in the mushroom body compartment"

bio-lda

Wrapper library for Baobzi interpolator library

Baobzi.jl

Julia

ftk

Factorization of the translation kernel for fast rigid image alignment

sciware-testing-cpp

Visualizations and other code for exploring binary classification metrics.

binary_classification_metrics

This repository contains beta MATLAB codes for data generation of forward medium problems using a hybrid HPS-HBS solver, and an inverse medium solver

inverse-volume-scattering2d

Run Stan models in the browser

stan-playground

Visualization of spike sorting experiments to be used as a plugin package to mountainlab-js

qt-mountainview

This repository contains codes for evaluating sums and integrals of gaussians in two dimensions

fgt2d

Ephys recordings for the SpikeForest project

spikeforest_recordings

Playing with quantum computing algorithms for protein and peptide design and structure prediction, with interfaces for the Rosetta software suite. (Repository created by Vikram K. Mulligan, [email protected]).

quantum_rosetta_private

mcmc-monitor-old

Monitor MCMC runs

Represent hdf5 files via json, separating out large binary content into individual files

h5_to_json

Examples for getting started with MountainSort spike sorting software

100

mountainsort_examples-old