23 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…
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…
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…
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…
Clark D. Asay
The software industry's history is also its future. Its history has been defined by both abundance and scarcity, and its future will be, too. In the 1970s and 80s, perceived software scarcity led U.S. legislators to formally grant intellectual property protections to software creators. Later, a different kind of…
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…
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…
Mohammad Nabil Almunawar
Open source software is free software that provides user freedom to use, replicate, modify, and distribute for any purpose. The quality of well-known open source software is very high and they are used by big companies such as IBM, Google and Amazon.com. Recently the number of open source software project growing very…
Jason R. Swedlow, Kevin W. Eliceiri
Significant technical advances in imaging, molecular biology and genomics have fueled a revolution in cell biology, in that the molecular and structural processes of the cell are now visualized and measured routinely. Driving much of this recent development has been the advent of computational tools for the…
Rita Kukafka, Neil Chue Hong, Simon Hettrick, Ye Ye + 21 more
Background The National Cancer Institute Informatics Technology for Cancer Research (ITCR) program provides a series of funding mechanisms to create an ecosystem of open-source software (OSS) that serves the needs of cancer research. As the ITCR ecosystem substantially grows, it faces the challenge of the long-term…
Andrew Morin, Jennifer Urban, Piotr Sliz, Fran Lewitter
Colloquially speaking, the spectrum of software licensing strategies can be divided into three categories: “proprietary,” “free and open source,” or a hybrid of the two. This strategy is familiar from the “click-thru” agreements that govern commercial software packages. The primary purpose of a proprietary software…
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…
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…
Martin Coleman
There is a multitude of licenses out there for a software developer to choose from, but a lot of programmers would prefer to not have to have a legal degree in order to understand them and would rather just have their code out in the public being used. This paper examines a few of the more popular and common software…
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…
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…
Authors not listed
The widespread adoption of open-source cheminformatics toolkits remains constrained by technical implementation barriers, including complex installation procedures, dependency management, and integration challenges. Here, we present Cheminformatics Microservice V3, a significant update to the existing platform that…
Venkata Chandrasekhar, Nisha Sharma, Jonas Schaub, Christoph Steinbeck + 1 more
In recent years, cheminformatics has experienced significant advancements through the development of new open-source software tools based on various cheminformatics programming toolkits. However, adopting these toolkits presents challenges, including proper installation, setup, deployment, and compatibility management.…
Eva Martín del Pico, Josep Lluis Gelpi, Salvador Capella-Gutiérrez
Software plays a crucial and growing role in research. Unfortunately, the computational component in Life Sciences research is challenging to reproduce and verify most of the time. It could be undocumented, opaque, may even contain unknown errors that affect the outcome, or be directly unavailable, and impossible to…
Adrian Zapletal, Dimitri Höhler, Carsten Sinz, Alexandros Stamatakis
Scientific software from all areas of scientific research is pivotal to obtaining novel insights. Yet the quality of scientific software is rarely assessed, even though it might lead to incorrect scientific results in the worst case. Therefore, we have developed an open source tool and benchmark called SoftWipe, that…
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…
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…
Serghei Mangul, Thiago Mosqueiro, Dat Duong, Keith Mitchell + 12 more
Developing new software tools for analysis of large-scale, biological data is a key component of advancing computational, data-enabled research. Scientific reproduction of published findings requires running computational tools on data generated by such studies, yet little attention is presently allocated to the…