Repositories list

• Cryo-EM-Heterogeneity-Challenge-1

  Public
  The Inaugural Flatiron Institute Cryo-EM Heterogeneity Community Challenge

  Jupyter Notebook

  •

  MIT License

  •1•8•34•6•Updated Jun 2, 2025Jun 2, 2025

• Disk-hospital

  Public
  This is an effort focused on automating disk problem resolution

  Python

  •0•0•0•0•Updated May 31, 2025May 31, 2025

• nemos

  Public
  NEural MOdelS, a statistical modeling framework for neuroscience.

  Python

  •

  MIT License

  •10•98•115•4•Updated May 30, 2025May 30, 2025

• CryoLike

  Public
  Python

  •

  MIT License

  •6•8•8•10•Updated May 30, 2025May 30, 2025

• CaImAn

  Public
  Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.

  2-photoncalcium-imagingmotion-correction+ 3source-extractiondeconvolutioncnmf

  Python

  •

  GNU General Public License v2.0

  •382•663•82•11•Updated May 30, 2025May 30, 2025

• sciware

  Public
  Learning materials for scientific software development

  learningscienceeducation+ 1software-development

  HTML

  •38•84•2•0•Updated May 29, 2025May 29, 2025

• nifty-ls

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

  time-serieslomb-scargle-periodogramspectral-analysis

  Python

  •

  Apache License 2.0

  •3•41•4•0•Updated May 28, 2025May 28, 2025

• nixpack

  Public
  nix+spack = nixpack (spanix?)

  Nix

  •

  MIT License

  •4•47•1•4•Updated May 28, 2025May 28, 2025

• cppdlr

  Public
  Discrete Lehmann representation of imaginary time Green's functions

  C++

  •

  Apache License 2.0

  •6•11•2•0•Updated May 27, 2025May 27, 2025

• finufft

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

  C++

  •

  Other

  •87•351•44•8•Updated May 27, 2025May 27, 2025

• spack

  Public
  A flexible package manager that supports multiple versions, configurations, platforms, and compilers.

  Python

  •

  Other

  •2.4k•2•0•12•Updated May 27, 2025May 27, 2025

• clair

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

  C++

  •

  Apache License 2.0

  •2•16•1•0•Updated May 23, 2025May 23, 2025

• neurosift

  Public
  Browser-based NWB visualization and DANDI exploration

  TypeScript

  •

  Apache License 2.0

  •10•57•26•0•Updated May 21, 2025May 21, 2025

• neuroRSE

  Public
  Website for CCN's neuroRSE group

  CSS

  •

  MIT License

  •0•1•0•0•Updated May 20, 2025May 20, 2025

• hp1_mundy

  Public
  Interphase chromatin project using MuNDy

  C++

  •

  GNU General Public License v3.0

  •2•0•0•0•Updated May 20, 2025May 20, 2025

• sciware-intern-mentors

  Public
  Guidance from sciware for summer intern mentors at Flatiron

  Apache License 2.0

  •0•2•2•0•Updated May 19, 2025May 19, 2025

• cryoSBI

  Public
  Python

  •1•11•15•2•Updated May 15, 2025May 15, 2025

• sparse_dot

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

  pythonsparsesparse-matrix+ 4numpymatrix-multiplicationscipymkl

  Python

  •

  MIT License

  •11•84•3•0•Updated May 13, 2025May 13, 2025

• jax-finufft

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

  Python

  •

  Apache License 2.0

  •3•95•7•0•Updated May 13, 2025May 13, 2025

• c2py

  Public
  Clair/c2py low level library

  C++

  •

  Apache License 2.0

  •1•1•0•0•Updated May 13, 2025May 13, 2025

• slurm

  Public
  Slurm: A Highly Scalable Workload Manager

  C

  •

  Other

  •703•1•0•0•Updated May 9, 2025May 9, 2025

• slurm-prometheus-exporter

  Public
  Prometheus exporter for slurm job/node data

  Haskell

  •9•38•5•1•Updated May 5, 2025May 5, 2025

• disBatch

  Public
  Dynamic dispatch of a list of command-line tasks, locally or on a cluster. Supports retrying failed tasks, and adding/removing compute resources on-the-fly.

  distributed-computingbatch-processing

  Python

  •

  Apache License 2.0

  •9•45•7•0•Updated May 5, 2025May 5, 2025

• lineage_viewer

  Public
  Graphical interface for editing a lineage and viewing related microscopy images

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •1•1•7•0•Updated May 1, 2025May 1, 2025

• stan-playground

  Public
  Run Stan models in the browser

  TypeScript

  •

  Apache License 2.0

  •1•43•11•1•Updated May 1, 2025May 1, 2025

• PyBenchFramework

  Public
  BenchmarkToolkit is a Python library designed to simplify and streamline benchmarking tasks. This library provides a high-level abstraction over various benchmarking functions, allowing developers to easily perform performance testing and analysis with minimal setup.

  Python

  •1•0•0•0•Updated Apr 30, 2025Apr 30, 2025

• nbfiddle

  Public
  TypeScript

  •

  Apache License 2.0

  •1•1•0•0•Updated Apr 22, 2025Apr 22, 2025

• blastoSPIM_web

  Public
  Generate a web site supporting the Blastospim mouse embryo research project.

  JavaScript

  •

  BSD 2-Clause "Simplified" License

  •0•0•12•0•Updated Apr 18, 2025Apr 18, 2025

• AnaVox

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •1•4•0•0•Updated Apr 17, 2025Apr 17, 2025

• cephdu

  Public
  A ncdu-like TUI for the Ceph File System, using xattrs instead of crawling

  cephdisk-usagencdu

  Rust

  •

  MIT License

  •0•2•9•0•Updated Apr 9, 2025Apr 9, 2025