24 papers · ranked by Valyu relevance
Authors not listed
Scientific discovery relies on innovative software as much as experimental methods, especially in proteomics, where computational tools are essential for mass spectrometer setup, data analysis, and interpretation. Since the introduction of SEQUEST, proteomics software has grown into a complex ecosystem of algorithms…
Gunther Eysenbach, Ignacio Valdes, Neil Ernst, Hans Oh + 3 more
'Yuanyi Zhang' 'Carl J Reynolds' 'Jeremy C Wyatt'] Recognition of the improvements in patient safety, quality of patient care, and efficiency that health care information systems have the potential to bring has led to significant investment. Globally the sale of health care information systems now represents a…
Matthias Knoll
Wer offene Lösungen einsetzen möchte, sieht sich einer Reihe von Fragen und Herausforderungen gegenüber. Nicht nur technische Aspekte, sondern vor allem zwischenmenschliche Faktoren und passende Regelungen sind dabei zu berücksichtigen. Das richtige „Mindset“ spielt eine zentrale Rolle. Mit ihm einher geht eine…
Mark Fingerhuth, Tomáš Babej, Peter Wittek, Leonie Anna Mueck
Open source software is becoming crucial in the design and testing of quantum algorithms. Many of the tools are backed by major commercial vendors with the goal to make it easier to develop quantum software: this mirrors how well-funded open machine learning frameworks enabled the development of complex models and…
Christine Årdal, Annette Alstadsæter, John-Arne Røttingen
Background Innovation through an open source model has proven to be successful for software development. This success has led many to speculate if open source can be applied to other industries with similar success. We attempt to provide an understanding of open source software development characteristics for…
Matthew H Todd
Scientific data are being generated and shared at ever-increasing rates. Two new mechanisms for doing this have developed: open access publishing and open source research. We discuss both, with recent examples, highlighting the differences between the two, and the strengths of both.
Giorgio F. Signorini
One important goal in sustainability is making technologies available to the maximum possible number of individuals, and especially to those living in less developed areas (Goal 9 of SDG). However, the diffusion of technical knowledge is hindered by a number of factors, among which the Intellectual Property Rights…
John J. Sherlock, Manoj Muniswamaiah, Lauren Clarke, Shawn Cicoria
-Open Source Software (OSS) history is traced to initial efforts in 1971 at Massachusetts Institute of Technology (MIT) Artificial Intelligence (AI) Lab, the initial goals of OSS around Free vs. Freedom, and its evolution and impact on commercial and custom applications. Through OSS history, much of the research and…
Madiha Zahrah Choksi, Ilan Mandel, David Goedicke, Yan Shvartzshnaider
'Yan Shvartzshnaider'] Centralization in code hosting and package management in the 2010s created fundamental shifts in the social arrangements of open source ecosystems. In a regime of centralized open source, platform effects can both empower and detract from communities depending on underlying technical…
Authors not listed
The increasing importance and predictive power of modern molecular modeling, driven by physics- and machine learning-based methods, necessitates a new collaborative architecture to replace the isolated, traditional model of software development. The traditional approach often led to redundant engineering effort, high…
Yo Yehudi, Carole Goble, Caroline Jay
The global value of open source software is estimated to be in the billions or trillions worldwide 1 , but despite this, it is often under-resourced and subject to high-impact security vulnerabilities and stability failures 2,3 . In order to investigate factors contributing to open source community longevity, we…
Murtaza Hussain Shaikh
According to different opponents and commercial giants in software industries, the open source style software development has enough capacity to complete successfully the large scale projects. But we have seen many flaws and loops in collaboration and handling of mega scale projects in open source environment. Perhaps…
Salman Qayyum Mian, José Teixeira, Eija Koskivaara
The era of the PC platform left a legacy of competitive strategies for the future technologies to follow. However, this notion became more complicated, once the future grew out to be a present with huge bundle of innovative technologies, Internet capabilities, communication possibilities, and ease in life. A major step…
João Pedro Moraes, Ivanilton Polato, Igor Wiese, Filipe Saraiva + 1 more
'Gustavo Pinto'] Abstract Open source licenses create a legal framework that plays a crucial role in the widespread adoption of open source projects. Without a license, any source code available on the internet could not be openly (re)distributed. Although recent studies provide evidence that most popular open source…
Eric Deibel
The introduction of open source in the life sciences is increasingly being suggested as an alternative to patenting. This is an alternative, however, that takes its shape at the intersection of the life sciences and informatics. Numerous examples can be identified wherein open source in the life sciences refers to…
Tiqing Liu, Linda Hwang, Stephen K Burley, Carmen I Nitsche + 3 more
BindingDB (bindingdb.org) is a public, web-accessible database of experimentally measured binding affinities between small molecules and proteins, which supports diverse applications including medicinal chemistry, biochemical pathway annotation, training of artificial intelligence models, and computational chemistry…
Christopher Woods, Lester Hedges, Adrian Mulholland, Maturos Malaisree + 10 more
Sire is a Python/C++ library that is used to both prototype new algorithms and as an interoperability engine for exchanging information between molecular simulation programs. It provides a collection of file parsers and information converters that together make it easier to combine and leverage the functionality of…
Yasset Perez-Riverol, Laurent Gatto, Rui Wang, Timo Sachsenberg + 11 more
A ‘Ten Simple Rules’ guide to git and GitHub. We describe and provide examples on how to use these software to track projects, as users, teams and organizations. We document collaborative development using branching and forking, interaction between collaborators using issues and continuous integration and automation…
Authors not listed
Raman spectroscopy is an increasingly powerful and fast-growing analytical technique across diverse disciplines, from materials science and chemistry to biology and medicine, thanks to advances in Raman instrumentation and greatly supported by the flourishing of chemometrics and artificial intelligence (AI). However…
Pamela H Russell, Rachel L Johnson, Shreyas Ananthan, Benjamin Harnke + 1 more
In recent years, the explosion of genomic data and bioinformatic tools has been accompanied by a growing conversation around reproducibility of results and usability of software. However, the actual state of the body of bioinformatics software remains largely unknown. The purpose of this paper is to investigate the…
Christian B. Strømme, A. Kelly Lane, Aud H. Halbritter, Elizabeth Law + 7 more
Open Science (OS) comprises a variety of practices and principles that are broadly intended to improve the quality and transparency of research, and the concept is gaining traction. Since OS has multiple facets and still lacks a unifying definition, it may be interpreted quite differently among practitioners. Moreover…
Nico Riedel, Miriam Kip, Evgeny Bobrov
Open research data are increasingly recognized as a quality indicator and an important resource to increase transparency, robustness and collaboration in science. However, no standardized way of reporting Open Data in publications exists, making it difficult to find shared datasets and assess the prevalence of Open…
Piyush Agrawal, Rajesh Kumar, Salman Sadullah Usmani, Anjali Dhall + 9 more
In past number of web-based resources has been developed in the field of Bioinformatics. These resources are heavily used by scientific community to provide solution for challenges faced by experimental researchers particularly in the field of biomedical sciences. There are number of challenges in utilizing full…
Authors not listed
Accurately measuring compound binding affinities is key to driving the pharmaceutical development process. Rigorous physics-based in silico approaches, particularly alchemical free energy methods, have become a gold standard tool for estimating compound affinity changes. Here we present the results of a large-scale…