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  • 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

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