- 
- ActivePapers
- aims to make computational science more open and more reliable by
- making computations reproducible and publishable. It is a file
- format for storing computations, consisting of both code and data,
- and it is also a software infrastructure for working with this
- file format.
-
- Contact:
- Konrad Hinsen
-
- 
- ARCHER
- is the UK National Supercomputing Service, providing a world-class
- supercomputer and invaluable computational resources, consultancy
- and training for researchers who study problems with a global
- impact.
-
- Contact:
- Mike Jackson
-
- 
- Astropy
- is a community-driven package intended to contain much of the core
- functionality and some common tools needed for performing
- astronomy and astrophysics with Python.
-
- Contact:
- Erik Bray
-
- 
- Biostars
- is a bioinformatics, computational genomics and biological data
- analysis question and answer forum. It is most used by biological
- computational scientists and it addresses all levels of questions
- regarding biological and computational data analysis. Biostars was
- started by Istvan Albert in 2010 and has since grown to more than
- 16,000 contributors with more than 120,000 posts on bioinformatics
- and genomics.
-
- Contact:
- Josh Herr
-
- 
- Cyclus,
- the Next Generation Nuclear Fuel Cycle Simulator, is the
- next-generation agent-based nuclear fuel cycle simulator,
- providing flexibility to users and developers through a dynamic
- resource exchange solver and plug-in, user-developed agent
- framework. The goal of Cyclus is to enable a broad spectrum of
- fuel cycle simulation while providing a low barrier to entry for
- new users and agent developers.
-
- Contact:
- Katy Huff,
- Paul Wilson,
- Anthony Scopatz
-
- 
- The EcoData Retriever
- automates finding, downloading and cleaning up ecological datasets.
-
- Contact:
- Ethan White,
- Ben Morris
-
- 
- Effective Computation in
- Physics is a manual of programming and software skills aimed at
- researchers in the physical sciences and engineering. This field guide to
- effective scientific computing in Python covers: programming in Python,
- important Python packages such as NumPy and Pandas, interaction with the
- command line, software testing, version control, build systems,
- documentation, publishing using LaTeX, how to manage collaborative
- software development with GitHub, and even how to license your software.
-
- Contact:
- Katy Huff, Anthony Scopatz
-
- 
- GAP is a free, open and
- extensible system for discrete computational algebra, with
- particular emphasis on Computational Group Theory. GAP provides a
- programming language, a library of thousands of functions
- implementing algebraic algorithms written in the GAP language as
- well as large data libraries of algebraic objects.
-
- Contact:
- Alexander Konovalov
-
- 
- The Genomics Virtual Lab
- provides analysis tutorials and protocols, and scalable research
- platforms on the cloud with easy access to reference data and
- tools on demand. Tools include Galaxy, IPython Notebook, RStudio,
- and environment modules for command-line users.
-
- Contact:
- Clare Sloggett
-
-
- Git-RDM
- is a Research Data Management (RDM) plugin for the Git version control
- system. It interfaces Git with data hosting services to manage the
- curation of version controlled files using persistent, citable
- repositories.
-
- Contact:
- Christian Jacobs
-
- 
- IPFS
- is a system for managing generic content-addressable data in
- a generalized
- Markle graph and mutable references to that data over a
- distributed, peer-to-peer network. For example, you could use the
- same system to manage both your source code and your huge binary
- datasets, transferring changes efficiently between any set of
- nodes, and archiving past versions for as long as you like.
-
- Contact:
- W. Trevor King
-
- 
- The iPlant Collaborative
- is cyberinfrastructure for scientists, educators, and students
- working in all domains of life sciences. iPlant resources allow
- users to analyze, manage, and store data and experiments, access
- high-performance computing, and share results with colleagues.
- iPlant is open source and funded by the National Science
- Foundation.
-
- Contact:
- Jason Williams
-
- 
- The Journal of Open Research Software is an Open
- Access journal featuring peer reviewed software metapapers
- describing research software with high reuse potential and
- full-length papers that cover different aspects of
- creating, maintaining and evaluating open source research
- software.
Contact:
- Neil Chue Hong
-
-
- The khmer project
- provides scripts and a library for analyzing,
- filtering, and correcting DNA sequencing data. The project
- implements efficient probabilistic data structures and lossy
- compression algorithms for working with very large DNA sequencing
- data sets.
-
- Contact:
- Titus Brown
-
- 
- Macroeco
- provides a comprehensive set of functions for analyzing empirical
- patterns in ecological data, predicting patterns using theory and
- models, and comparing empirical patterns to theory. Many major
- macroecological patterns can be analyzed using this package,
- including the species abundance distribution, the species and
- endemics area relationships, several measures of beta diversity,
- and many others.
-
- Contact:
- Mark Wilber,
- Justin Kitzes
-
-
- MAGeTBrain
- Given a set of anatomically labelled MR images (atlases) and
- unlabeled images (subjects), MAGeT (Multiple Automatically
- Generated Templates Brain Segmentation) produces a segmentation
- (automatic labeling) for each subject using a multi-atlas voting
- procedure based on a template library made up of images from the
- subject set.
-
- Contact:
- Gabriel A. Devenyi
-
-
- Mahotas
- is a computer vision and image processing library for Python based
- on NumPy.
-
- Contact:
- Luis Pedro Coelho
-
-
- The Math Education Resources
- is a volunteer-run project that provides substantial learning
- resources to undergraduate students taking math courses at UBC or
- elsewhere. Our wiki provides free hints and peer-reviewed
- solutions to previous final exam questions from UBC's math
- courses. Students can search questions by topic, watch mini video
- lectures for each topic, or use the difficulty ratings from their
- peers to guide their studies.
-
- Contact:
- Bernhard Konrad
-
- 
- mothur is an open source and
- portable software package that meets the bioinformatics needs of
- the microbial ecology research community. It is particularly
- useful for analyzing 16S rRNA gene sequences that have been
- generated using a variety of sequencing platforms. We emphasize
- making the software as easy to use as possible through our efforts
- in maintaining a wiki, blog, and user forum.
-
- Contact:
- Pat Schloss
-
- 
- The Mozilla
- Science Lab is helping a global network of researchers, tool
- developers, librarians and publishers collaborate to further
- science on the web, via collaboration, prototyping and educational
- projects. Check
- out projects they're
- working on with the open science community, and join the
- dicsussion on their
- forum or their
- community calls.
-
- Contact:
- Abby Cabunoc,
- Arliss Collins,
- Bill Mills
-
- 
- NIPY (Neuroimaging in
- Python) is making it easier to do better brain imaging research, by designing
- and implementing free and open-source algorithms and pipelines for the
- analysis of data from neuroimaging experiments, and teaching neuroscientists
- how to use them.
-
- Contact:
- Ariel Rokem
-
- 
- The Open Tree of Life
- is building a comprehensive tree of all life. By enabling
- community contribution of phylogenies (estimates of species or
- other group relationships), and combining these phylogenies into a
- single tree-of-life we capturing the depth of knowledge about
- biodiversity on Earth, encouraging community comment and
- refinement and preserving phylogenetic data in a readily reusable
- way.
-
- Contact:
- Emily Jane McTavish,
- Karen Cranston
-
- 
- The Predictive Ecosystem Analyzer (PEcAn)
- is an integrated ecological bioinformatics toolbox that provides tools to synthesize
- plant and ecosystem data with mechanistic understanding encoded in ecosystem models.
- PEcAn is not a model itself, but a platform for model parameterization and calibration
- that wraps simulation models within a Bayesian framework. The PEcAn Project is an open
- community of scientists, programmers, and educators and we welcome new contributions
- and applications.
-
- Contact:
- David LeBauer
-
- 
- Practical Computing for Biologists
- aims to teach scientists of all types essential computational
- skills for data analysis. It assumes no pre-requisites other than
- motivation, features the most useful tools that can benefit
- researchers almost immediately, and explains how to use these
- tools together. With a background level of comfort, researchers
- can then go on to reap even more benefit from Software Carpentry
- and other educational sites and courses.
-
- Contact:
- Steve Haddock
-
- 
- PyMC
- is a Python module that implements Bayesian statistical models and fitting algorithms,
- including Markov chain Monte Carlo.
- Its flexibility and extensibility make it applicable to a large suite of problems.
- Along with core sampling functionality,
- PyMC includes methods for summarizing output, plotting, goodness-of-fit and convergence diagnostics.
-
- Contact:
- Chris Fonnesbeck
-
- 
- PyNE,
- the Nuclear Engineering Toolkit, is a suite of tools to aid in
- computational nuclear science and engineering. PyNE seeks to provide
- native implementations of common nuclear algorithms, as well as
- Python bindings and I/O support for other industry standard
- nuclear codes.
-
- Contact:
- Katy Huff,
- Rachel Slaybaugh,
- Paul Wilson,
- Anthony Scopatz
-
- 
- PyRDM
- is a Python-based library for research data management (RDM).
- It facilitates the automated management and publication of software
- source code and data via online, citable repositories hosted by
- Figshare, Zenodo, or a DSpace-based service. The library
- is open-source
- and can be readily incorporated into scientific workflows to allow
- research outputs to be curated and shared in a straight-forward manner.
-
- Contact:
- Christian Jacobs
-
- 
- rOpenSci
- is a software collective that provides R based tools to enable
- access to scientific data repositories, full-text of articles, and
- science metrics and also facilitate a culture shift in the
- scientific community towards reproducible research practices.
-
- Contact:
- Karthik Ram
-
- 
- scikit-bio
- is a Python bioinformatics library based on the standard Python
- scientific computing stack that implements core bioinformatics
- data structures, algorithms, parsers, and formatters. scikit-bio
- is the first bioinformatics-centric scikit, and arises from over
- ten years of development efforts on PyCogent and QIIME, It is
- intended to be useful both for students, who can use it in
- conjunction with the accompanying interactive
- textbook,
- An Introduction to Applied Bioinformatics,
- and for real-world bioinformatics developers.
-
- Contact:
- Greg Caporaso
-
- 
- scikit-image
- is a collection of algorithms for image processing. It is available free of
- charge and free of restriction. We pride ourselves on high-quality,
- peer-reviewed code, written by an active community of volunteers.
-
- Contact:
- Juan Nunez-Iglesias
-
- 
- ShareLaTeX
- is an online collaborative LaTeX editor designed to make LaTeX
- more accessible to newcomers, and to make collaboration easier
- between co-authors. Everyone can access the latest version, see a
- full change history, and work with the same compatible LaTeX
- environment. ShareLaTeX is available
- hosted,
- and is open source.
-
- Contact:
- James Allen
-
- 
- STAT 545
- at the University of British Columbia teaches students how to
- explore, groom, visualize, and analyze data, and how to make all
- of that reproducible, reusable, and shareable using R.
-
- Contact:
- Jenny Bryan
-
-
- tec
- provides utilities for a uniform and extensible API for easily
- simulating vacuum thermionic energy conversion (TEC) devices. A few
- models are supplied with the tec package, but others can be easily
- added.
-
- Contact: Joshua Ryan Smith
-