Reproducibility, closely related to replicability and repeatability, is a major principle underpinning the scientific method. For the findings of a study to be reproducible means that results obtained by an experiment or an observational study or in a statistical analysis of a data set should be achieved again with a high degree of reliability when the study is replicated. There are different kinds of replication but typically replication studies involve different researchers using the same methodology. Only after one or several such successful replications should a result be recognized as scientific knowledge.
Source-available software is software released through a source code distribution model that includes arrangements where the source can be viewed, and in some cases modified, but without necessarily meeting the criteria to be called open-source. The licenses associated with the offerings range from allowing code to be viewed for reference to allowing code to be modified and redistributed for both commercial and non-commercial purposes.
Psi is an ab initio computational chemistry package originally written by the research group of Henry F. Schaefer, III. Utilizing Psi, one can perform a calculation on a molecular system with various kinds of methods such as Hartree-Fock, Post-Hartree–Fock electron correlation methods, and density functional theory. The program can compute energies, optimize molecular geometries, and compute vibrational frequencies. The major part of the program is written in C++, while Python API is also available, which allows users to perform complex computations or automate tasks easily.
A source-code-hosting facility is a file archive and web hosting facility for source code of software, documentation, web pages, and other works, accessible either publicly or privately. They are often used by open-source software projects and other multi-developer projects to maintain revision and version history, or version control. Many repositories provide a bug tracking system, and offer release management, mailing lists, and wiki-based project documentation. Software authors generally retain their copyright when software is posted to a code hosting facilities.
CellProfiler is free, open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. Advanced algorithms for image analysis are available as individual modules that can be placed in sequential order together to form a pipeline; the pipeline is then used to identify and measure biological objects and features in images, particularly those obtained through fluorescence microscopy.
qBittorrent is a cross-platform free and open-source BitTorrent client written in native C++. It relies on Boost, OpenSSL, zlib, Qt 6 toolkit and the libtorrent-rasterbar library, with an optional search engine written in Python.
Computer-assistedqualitative data analysis software (CAQDAS) offers tools that assist with qualitative research such as transcription analysis, coding and text interpretation, recursive abstraction, content analysis, discourse analysis, grounded theory methodology, etc.
Authorea is an online collaborative writing tool that allows researchers to write, cite, collaborate, host data and publish. It has been described as "Google Docs for Scientists". It has been owned by the commercial publishing company Wiley through Atypon since 2018.
Reproducible builds, also known as deterministic compilation, is a process of compiling software which ensures the resulting binary code can be reproduced. Source code compiled using deterministic compilation will always output the same binary.
A notebook interface or computational notebook is a virtual notebook environment used for literate programming, a method of writing computer programs. Some notebooks are WYSIWYG environments including executable calculations embedded in formatted documents; others separate calculations and text into separate sections. Notebooks share some goals and features with spreadsheets and word processors but go beyond their limited data models.
Project Jupyter is a project to develop open-source software, open standards, and services for interactive computing across multiple programming languages.
The Journal of Open Source Software is a peer-reviewed open-access scientific journal covering open-source software from any research discipline. The journal was founded in 2016 by editors Arfon Smith, Kyle Niemeyer, Dan Katz, Kevin Moerman, and Karthik Ram. The editor-in-chief is Arfon Smith, and associate editors-in-chief: Dan Foreman-Mackey, Olivia Guest, Daniel Katz, Kevin Moerman, Kyle Niemeyer, George Thiruvathukal, and Krysten Thyng. The journal is a sponsored project of NumFOCUS and an affiliate of the Open Source Initiative. The journal uses GitHub as publishing platform.
Jennifer "Jenny" Bryan is a data scientist and an associate professor of statistics at the University of British Columbia where she developed the Master in Data Science Program. She is a statistician and software engineer at RStudio from Vancouver, Canada and is known for creating open source tools which connect R to Google Sheets and Google Drive.
The Carpentries is a nonprofit organization that teaches software engineering and data science skills to researchers through instructional workshops. The Carpentries is made up of three programs areas: Software Carpentry, Data Carpentry and Library Carpentry.
CovidSim is an epidemiological model for COVID-19 developed by Imperial College COVID-19 Response Team, led by Neil Ferguson. The Imperial College study addresses the question: If complete suppression is not feasible, what is the best strategy combining incomplete suppression and control that is feasible and leads to acceptable outcomes?
Originally developed in 2019 by Microsoft under the name Coco and later rebranded to Confidential Consortium Framework (CCF), it is an open-source framework for the development of a new category of performant applications that focuses on the optimization of secure multi-party computation and data availability. Intended to accelerate the adoption of blockchain technology by enterprises, CCF can enable a variety of high-scale, confidential permissioned distributed ledger networks that meet key enterprise requirements.
Karthik Ram is a research scientist at the Berkeley Institute for Data Science and member of the Initiative for Global Change Biology at the University of California, Berkeley. He is best known for being the co-founder of rOpenSci. Ram's work focuses on global change, data science, and open research software.
Research transparency is a major aspect of scientific research. It covers a variety of scientific principles and practices: reproducibility, data and code sharing, citation standards or verifiability.
