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In this chapter we first outline some of the popular computing environments used for analysing neural data, followed by a brief discussion of 'software carpentry', basic tools and skills from software engineering that can be of great use to…
Almost all research work in computational neuroscience involves software. As researchers try to understand ever more complex systems, there is a continual need for software with new capabilities. Because of the wide range of questions being…
Across the life sciences, an ongoing effort over the last 50 years has made data and methods more reproducible and transparent. This openness has led to transformative insights and vastly accelerated scientific progress. For example,…
Free and open source software (FOSS) is considered by many, along with Wikipedia, the proof of an ongoing paradigm shift from hierarchically-managed and market-driven production of knowledge to heterarchical, collaborative and commons-based…
Sustainable software ecosystems are difficult to build, and require concerted effort, community norms and collaborations. In science it is especially important to establish communities in which faculty, staff, students and open-source…
In recent years, deep learning revolutionized machine learning and its applications, producing results comparable to human experts in several domains, including neuroscience. Each year, hundreds of scientific publications present…
Journalists, public policy analysts, and economists have called attention to the growing importance that high-performance and scientific computing have to national security and industrial leadership. As computing continues to power…
Open science describes the movement of making any research artefact available to the public and includes, but is not limited to, open access, open data, and open source. While open science is becoming generally accepted as a norm in other…
Software is the key crosscutting technology that enables advances in mathematics, computer science, and domain-specific science and engineering to achieve robust simulations and analysis for science, engineering, and other research fields.…
The reproducibility of scientific research has become a point of critical concern. We argue that openness and transparency are critical for reproducibility, and we outline an ecosystem for open and transparent science that has emerged…
Scientific open-source software (OSS) has greatly benefited research communities through its transparent and collaborative nature. Given its critical role in scientific research, ensuring the sustainability of such software has become…
Open source software is a rapidly evolving center for distributed work, and understanding the characteristics of this work across its different contexts is vital for informing policy, economics, and the design of enabling software. The…
Software plays a central role in scientific discovery. Improving how we develop and use software for research can have both broad and deep impacts on a spectrum of challenges and opportunities society faces today. The emergence of Research…
Neuroscience research has evolved to generate increasingly large and complex experimental data sets, and advanced data science tools are taking on central roles in neuroscience research. Neurodata Without Borders (NWB), a standard language…
Open Science aims to foster openness and collaboration in research, leading to more significant scientific and social impact. However, practicing Open Science comes with several challenges and is currently not properly rewarded. In this…
Digital services such as repositories and science gateways have become key resources for the neuroscience community, but users often have a hard time orienting themselves in the service landscape to find the best fit for their particular…
The brain is a complex system comprising a myriad of interacting elements, posing significant challenges in understanding its structure, function, and dynamics. Network science has emerged as a powerful tool for studying such intricate…
Modern tools for biological research, especially microscopy, have rapidly advanced in recent years, which has led to the generation of increasingly large amounts of data on a regular basis. The result is that scientists desperately need…
In computational science and in computer science, research software is a central asset for research. Computational science is the application of computer science and software engineering principles to solving scientific problems, whereas…
Software is now a vital scientific instrument, providing the tools for data collection and analysis across disciplines from bioinformatics and computational physics, to the humanities. The software used in research is often home-grown and…