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Expand Up @@ -373,6 +373,33 @@ Written by astrophysicists, but since applied to many other domains.
The spiritual successor to spyder, in that it is designed specifically for scientists.
* [papermill](https://papermill.readthedocs.io/en/latest/) - A tool for parameterizing, executing, and analyzing multiple Jupyter Notebooks.

##Other

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1. **ASCEND** - ([Repo](http://code.ascend4.org/ascend/trunk), [Home](http://ascend4.org/Main_Page), [WP](https://en.wikipedia.org/wiki/ASCEND)) Mathematical chemical process modelling system developed at Carnegie Mellon University since late 1978. `(linux, windows, mac, gtk)`
1. **CellProfiler** - ([Repo](https://github.com/CellProfiler/CellProfiler), [Home](http://cellprofiler.org/), [Manual](https://cellprofiler.org/cpa), [Docs](https://github.com/CellProfiler/CellProfiler/wiki)) Interactive data exploration, analysis, and classification of biological image sets. `(linux, windows, mac)`
1. **cellxgene** - ([Repo](https://github.com/chanzuckerberg/cellxgene), [Home](https://chanzuckerberg.github.io/cellxgene)) Web-based interactive explorer for single-cell transcriptomics data. `(linux, windows, mac, fnd)`
1. **CKAN** - ([Repo](https://github.com/ckan/ckan), [Home](https://ckan.org/)) Data management system (DMS) which makes it easy to publish, share, and use data. Data hubs powered by CKAN include [datahub.io](https://datahub.io), [catalog.data.gov](https://catalog.data.gov), and [europeandataportal.eu](https://europeandataportal.eu/data/en/dataset), among many other sites. `(server, flask)`
1. **CoCalc** - ([Repo](https://github.com/sagemathinc/cocalc), [Home](https://cocalc.com/), [WP](https://en.wikipedia.org/wiki/CoCalc)) Collaborative calculation in the cloud, with support for the scientific Python stack, SageMath, R, LaTeX, Markdown, and more. Also features chat, course management, and other supporting functionality. `(server)`
1. **Dissem.in** - ([Repo](https://github.com/dissemin/dissemin), [Home](https://dissem.in/), [Docs](https://dev.dissem.in/)) Web platform to help researchers upload their papers to open-access repositories. `(server, django)`
1. **Galaxy** - ([Repo](https://github.com/galaxyproject/galaxy), [Home](https://galaxyproject.org/), [Docs](https://galaxyproject.org/docs)) Web-based platform for reproducible and transparent computational research, with a focus on bioinformatics. `(server)`
1. **InVesalius** - ([Repo](https://github.com/invesalius/invesalius3), [Home](https://invesalius.github.io/), [WP](https://en.wikipedia.org/wiki/InVesalius)) Generates virtual reconstructions of structures in the human body for medical purposes, including CT and MRI scans. `(linux, windows, mac, gtk)`
1. **Manim** - ([Repo](https://github.com/3b1b/manim), [Docs](https://manim.readthedocs.io/)) Animation engine for explanatory math videos, primarily designed for [works by 3blue1brown](https://www.youtube.com/channel/UCYO_jab_esuFRV4b17AJtAw). `(linux)`
1. **Mayavi** - ([Repo](https://github.com/enthought/mayavi), [Home](http://docs.enthought.com/mayavi/mayavi)) General purpose, cross-platform tool for 2-D and 3-D scientific data visualization. `(linux, windows, mac, qt4)`
1. **Mosaic** - ([Repo](https://github.com/usnistgov/mosaic), [Home](https://pages.nist.gov/mosaic), [Docs](https://pages.nist.gov/mosaic/html/index.html)) Desktop-based single molecule analysis toolbox that automatically decodes multi-state nanopore data. `(linux, windows, mac, gov)`
1. **odemis** - ([Repo](https://github.com/delmic/odemis), [Home](https://www.delmic.com/microscopy-software-odemis)) Desktop imaging workflow software for Delmic microscopes, supporting autofocus, coordinate history, and OME-TIFF and HDF5 export. `(linux)`
1. **OPEM** - ([Repo](https://github.com/ECSIM/opem), [Docs](https://www.ecsim.ir/opem/doc)) A modeling tool for evaluating the performance of [proton exchange membrane (PEM) fuel cells](https://en.wikipedia.org/wiki/Proton-exchange_membrane_fuel_cell). `(linux, windows, mac)`
1. **Orange** - ([Repo](https://github.com/biolab/orange3), [Home](https://orange.biolab.si/), [WP](https://en.wikipedia.org/wiki/Orange_%28software%29)) Component-based data mining software for graphical interactive data analysis and visualization. `(linux, windows, mac, qt4, qt5)`
1. **Pybliographer** - ([Repo](https://github.com/GNOME/pybliographer), [Home](https://pybliographer.org/)) Bibliographic database manager with a user-friendly desktop UI. `(linux, gtk)`
1. **ReproZip** - ([Repo](https://github.com/VIDA-NYU/reprozip), [Home](https://www.reprozip.org/), [Demo](https://examples.reprozip.org/), [PyPI](https://pypi.org/project/reprozip), [Docs](https://docs.reprozip.org/)) Command-line tool which automatically builds reproducible experiments archives from console commands, designed for use in computational science. `(productivity, linux)`
1. **Sage Math** - ([Repo](https://git.sagemath.org/sage.git), [Home](http://www.sagemath.org/), [WP](https://en.wikipedia.org/wiki/SageMath)) Cross-platform computer algebra system with features covering many aspects of mathematics, including algebra, combinatorics, graph theory, numerical analysis, number theory, calculus, and statistics. `(linux, windows, mac)`
1. **Scholia** - ([Repo](https://github.com/fnielsen/scholia), [Home](https://scholia.toolforge.org/), [Docs](https://www.wikidata.org/wiki/Wikidata%3AScholia)) Python package and web application for interacting with scholarly information on [Wikidata](https://www.wikidata.org/). `(organization, server)`
1. **SOFA Statistics** - ([Repo](https://code.launchpad.net/sofastatistics), [Home](http://www.sofastatistics.com/)) User-friendly statistics and analysis with a learn-as-you-go approach. `(linux, windows, mac, wx)`
1. **Spack** - ([Repo](https://github.com/spack/spack), [Home](https://spack.io/), [Docs](https://spack.readthedocs.io/en/latest)) Language-independent package manager for supercomputers, Mac, and Linux, designed for scientific computing. `(pkg_mgr, linux, mac)`
1. **Taguette** - ([Repo](https://gitlab.com/remram44/taguette), [Home](https://www.taguette.org/), [gh](https://github.com/remram44/taguette), [PyPI](https://pypi.org/project/taguette), [Docs](https://www.taguette.org/getting-started.html)) Web-based qualitative research tool supporting importing, tagging, highlighting, and exporting many document formats. `(server)`
1. **Veusz** - ([Repo](https://github.com/veusz/veusz), [Home](https://veusz.github.io/)) 2D and 3D scientific plotting, designed to produce publication-ready PDF or SVG graphs. `(linux, windows, mac, qt)`


# Beginner Recommendations

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