Science - John Pellman's Curated GitHub Stars

eman2: A scientific image processing software suite with a focus on CryoEM and CryoET
continuous_analysis: Computational reproducibility using Continuous Integration to produce verifiable end-to-end runs of scientific analysis.
fpzip: Lossless compressor of multidimensional floating-point arrays
edam-bioimaging: Ontology of bioimage informatics operations, topics, types of data, and data formats. EDAM-Bioimaging is an extension of the EDAM ontology (edamontology.org) dedicated to bioimaging data analysis, and developed in an open collaboration including partners from NEUBIAS (neubias.org), COMULIS (comulis.eu), and ELIXIR (elixir-europe.org)..
pybossa: PYBOSSA is the ultimate crowdsourcing framework (aka microtasking) to analyze or enrich data that can't be processed by machines alone.
whole-tale: The Whole Tale - Merging Science and Cyberinfrastructure Pathway
fqzcomp: Fastq compression tool
pyqtgraph: Fast data visualization and GUI tools for scientific / engineering applications
jhub_cas_authenticator: CAS authenticator for Jupyterhub
NixTemplates: Several basic templates that are meant to be used as the basis for other Singularity Spec files using nixpkgs
scipy-lecture-notes: Tutorial material on the scientific Python ecosystem
StarCluster: StarCluster is an open source cluster-computing toolkit for Amazon's Elastic Compute Cloud (EC2).
ResearchKit: ResearchKit is an open source software framework that makes it easy to create apps for medical research or for other research projects.
alapy_arc: ALAPY COMPRESSOR: FASTQ lossless compressor
ResearchStack: An SDK for building research study apps on Android.
ReScience: The ReScience journal. Reproducible Science is Good. Replicated Science is better.
pyslurm: Python Interface to Slurm
cornell-ssw.github.io: Home page of the Scientific Software Club at Cornell
datalad: Keep code, data, containers under control with git and git-annex
neuropower-core: This repository contains the core functions from neuropower in a python package.
fastr: A high-performance implementation of the R programming language, built on GraalVM.
gini: Calculate the Gini coefficient of a numpy array.
julia: The Julia Programming Language
Science-on-GitHub: Resources to accompany Nature Toolbox article on Science on GitHub
eyestalker: Robust video-based eye tracking using recursive estimation of pupil characteristics
cbrain: CBRAIN is a flexible Ruby on Rails framework for accessing and processing of large data on high-performance computing infrastructures.
Psychtoolbox-3: Psychophysics Toolbox Version 3 (PTB-3) is a free set of Matlab and GNU Octave functions for vision and neuroscience research.
microdraw: Collaborative vectorial annotation tool for ultra high resolution data
stanfordtownhall: Slides for a talk at the Stanford Reproducibility Town Hall, April 12, 2017
popper: Container-native task automation engine.
arborCollections: managing collections of functions and workflows in arbor
python-mrcz: Python module for compressed MRCZ-file format
the-turing-way: Host repository for The Turing Way: a how to guide for reproducible data science
IntroductionToResearchComputing: None
BigJob: SAGA-based Pilot-Job Implementation for Compute and Data
numpy: The fundamental package for scientific computing with Python.
sortingQuality: Functions to assess quality of spike sorting results
eyetrackingR: This package is designed to make dealing with eye-tracking data easier. It addresses tasks along the pipeline from raw data to analysis and visualization.
dvn: Dataverse Network (DVN) 3.x, distinct from the newer code base at https://github.com/IQSS/dataverse
phy: Interactive electrophysiological data analysis package
slurm-magic: IPython magic for SLURM.
skluma-local-deploy: A file-level metadata extraction service that interfaces with zero cloud services.
MobilECG-II: Open source ECG holter
SciCrunch-Portal: SciCrunch Portal
c-blosc: A blocking, shuffling and loss-less compression library that can be faster than memcpy().
SimpleITK: SimpleITK: a simplified layer build on top of the Insight Toolkit (ITK), intended to facilitate its use in rapid prototyping, education and interpreted languages.
pipe_tasks: LSST Data Management: astronomical data processing tasks
bisweb: This is the repository for the BioImage Suite Web Project
osf.io: Facilitating Open Science
cet_toolbox: None
mpm: Simple Matlab package management inspired by pip
jupyter-omeroanalysis-desktop: Run OMERO clients in a Linux desktop using Jupyter
diss: Influence apart from Adoption: How Interaction between Programming and Scientific Practices Shapes Modes of Inquiry in Four Oceanography Teams
birthdaycard: Program to generate birthday cards from structural brain scans.
pubpub: Open Community Publishing
shablona: A template for small scientific python projects
awesome-open-science: some links to projects/tools related to "open science".
atmosphere: Where cloud lives.
good-enough-practices-in-scientific-computing: Minimalist alternatives to "best practices" paper
globus-search-cli: Globus Search CLI Tool
irods: Open Source Data Management Software
pangeo: Pangeo website + discussion of general issues related to the project.
neuroglancer: WebGL-based viewer for volumetric data
datacrate: Bagit-based data packaging specification for dissemination of research data with useful human and machine readable metadata: "Make Data Crate Again!"
jsPsych: A JavaScript library for creating and running behavioral experiments in a web browser
criu: Checkpoint/Restore tool
sycl-blas: An implementation of BLAS using the SYCL open standard for acceleration on OpenCL devices
psiTurk: An open platform for science on Amazon Mechanical Turk.
Dery_HBM_ClubsOfScience: Dery_HBM_ClubsOfScience
jupyterlab_iframe: JupyterLab iframe widget
TaxonX: TaxonX XML Schema
puppet-ganglia: Manages ganglia gmond & gmetad daemons + web front end
awesome-research: :seedling: a curated list of tools to help you with your research/life; I built a front end around this repo, please use the link
neurospinqc: None
homefarm: Tools for deploying and managing a BOINC compute farm
pyhrf: PyHRF is a set of tools to analyze fMRI data and specifically study hemodynamics.
FastQt: FastQC port to Qt5: A quality control tool for high throughput sequence data.
visbrain: A multi-purpose GPU-accelerated open-source suite for brain data visualization
funcX: funcX: High Performance Function Serving for Science
psychopy: For running psychology and neuroscience experiments
2016-phil-openscience: None
CUBLAS.jl: Julia interface to CUBLAS
ICA-AROMA: ICA-AROMA Software Package: a data-driven method to identify and remove head motion-related artefacts from functional MRI data.
A-Psychologists-Guide-to-R: A repository containing the course notes and worked examples for a six week course in the R statistical programming language aimed at helping psychology students and faculty to learn R. This course was taught live at the University of Melbourne, Australia in 2016.
dmtcp: DMTCP: Distributed MultiThreaded CheckPointing
clesperanto.github.io: clEsperanto - GPU-accelerated image processing across languages and platforms
real-life: None
WhitakerLabProjectManagement: This repository contains issues related to the management of all Whitaker Lab projects
managing-research-software-projects: Managing small to medium-sized research software projects.
reprozip: ReproZip is a tool that simplifies the process of creating reproducible experiments from command-line executions, a frequently-used common denominator in computational science.
ssm: Bayesian learning and inference for state space models
stencila: Stencila
what-is-computational-reproducibility: What is computational reproducibility?
2017-09-science-foia: The FOIA logs referenced in the Sep. 2, 2017 BuzzFeed News article, "These Scientists Got To See Their Competitors’ Research Through Public Records Requests." https://www.buzzfeed.com/teresalcarey/when-scientists-foia
UKRSE.github.io: Old website for the UK Society of Research Software Engineers - not the source for the live site at rse.ac.uk. To suggest changes to that, contact [email protected]
yacs: YACS -- Yet Another Configuration System
projectMatlab: Interface R, Matlab, SPM
sustaining-research-projects: sustainability models for research software projects
convert_matlab73_hdf5: Convert Matlab v7.3 '.mat' files (i.e. HDF5 file format) into Python's pickle or numpy format.
sciencegraph: A comprehensive knowledge graph of scientific concepts
convert-eprime: Python functions to convert E-Prime files to csvs. Not currently being developed, but issues and PRs welcome!
scipy: Scipy library main repository
raw-data-repository: PMI DRC data repositories and APIs
exploratory_computing_with_python: None
pyfilesec: File-oriented privacy and integrity tools for research with human subjects
awesome-scientific-python: A curated list of awesome scientific Python resources
QUIT: A set of tools for processing Quantitative MR Images
bioqa: QA pipeline based on BaseQA and designed for biomedical related QA problems, like TREC Genomics tasks.
binderhub: Run your code in the cloud, with technology so advanced, it feels like magic!
jupyter-desktop-server: Run a Linux Desktop on a JupyterHub
thunder: scalable analysis of images and time series
texture: A visual editor for research.
python-blosc: A Python wrapper for the extremely fast Blosc compression library
leibniz: A Digital Scientific Notation
scitests: Provide tests and test runner harnesses to test scientific artifacts
binder: reproducible executable environments
citizen-science: 🔬 A repository of resources related to citizen, community-based and/or non-institutional science
BioSolr: A project aiming "to significantly advance the state of the art with regard to indexing and querying biomedical data with freely available open source software"
scibot: curation workflow automation and coordination
MAT.jl: Julia module for reading MATLAB files
OpenSpace: This is the official GitHub repository for OpenSpace: an open source astrovisualization project. For instructions on how to build and run OpenSpace, see the Getting Started Guides on the wiki page at http://wiki.openspaceproject.com
enterprise_gateway: A lightweight, multi-tenant, scalable and secure gateway that enables Jupyter Notebooks to share resources across distributed clusters such as Apache Spark, Kubernetes and others.
matlab-dockerfile: Create a docker container that contains a MATLAB install
GPU-DFC: None
fastqz: Compression library for FastQ files, code from http://mattmahoney.net/dc/fastqz/
jupyterlab_html: (Merged into JupyterLab Core!) JupyterLab extension for displaying HTML files