24 papers · ranked by Valyu relevance
Bas Wijnen, Emily J. Hunt, Gerald C. Anzalone, Joshua M. Pearce + 1 more
'Giorgio F. Gilestro'] This article explores a new open-source method for developing and manufacturing high-quality scientific equipment suitable for use in virtually any laboratory. A syringe pump was designed using freely available open-source computer aided design (CAD) software and manufactured using an open-source…
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…
Jesus Gorroñogoitia Cruz, Andrey Sadovykh, Dragoş Truşcan, Hugo Brunelière + 2 more
'Hugo Brunelière' 'Pierluigi Pierini' 'Lara Lopez Muñiz'] Abstract. In this paper, we overview our experiences of developing large set of open source tools in ECSEL JU European project called MegaM@Rt2 whose main objective is to propose a scalable model-based framework incorporating methods and tools for the continuous…
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…
Paul Macklin, Samuel H. Friedman
To reach the full potential of multicellular systems biology, mathematical and computational modelers must pool their efforts to share and curate biophysical measurements, create and combine mathematical models, analyze and visualize model predictions, and validate and refine against shared data. An ecosystem of open…
Jon Ison, Hans Ienasescu, Piotr Chmura, Emil Rydza + 32 more
'Matúš Kalaš' 'Veit Schwämmle' 'Björn Grüning' 'Niall Beard' 'Rodrigo Lopez' 'Severine Duvaud' 'Heinz Stockinger' 'Bengt Persson' 'Radka Svobodová Vařeková' 'Tomáš Raček' 'Jiří Vondrášek' 'Hedi Peterson' 'Ahto Salumets' 'Inge Jonassen' 'Rob Hooft' 'Tommi Nyrönen' 'Alfonso Valencia' 'Salvador Capella' 'Josep Gelpí'…
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 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…
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…
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.…
Chengjie Chen, Hao Chen, Yi Zhang, Hannah R. Thomas + 3 more
The rapid development of high-throughput sequencing (HTS) techniques has led biology into the big-data era. Data analyses using various bioinformatics tools rely on programming and command-line environments, which are challenging and time-consuming for most wet-lab biologists. Here, we present TBtools (a Toolkit for…
Gagan Gupta, Tony Nowatzki, Vinay Gangadhar, Karthikeyan Sankaralingam
'Karthikeyan Sankaralingam'] Innovation in hardware is slowing due to rising costs of chip design and diminishing benefits from Moore's law and Dennard scaling. Software innovation, on the other hand, is flourishing, helped in good measure by a thriving open-source ecosystem. We believe that open source can similarly…
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…
Raya Al-Hajri, Ghada Al-Mukhaini, Rajasekar Ramalingam
- The adoption of Free and Open Source Software (FOSS) in educational institutions is increasing day by day. Many countries are insisting the use of FOSS in their government sectors and few are in the process of adopting FOSS strategies. The reasons for adopting FOSS are: total cost ownership, free to make copies and…
Sheng Liu, Huadong Xing, Mengying Han, Dachuan Zhang + 5 more
A large number of biomedical computational tools have spawned several tool registries. However, in the face of the rapid growth in the number of tools, existing tool registries, which are manually curated or community-driven, are difficult to keep up to date, resulting in inadequate tool repository data. In this paper…
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…
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…
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…
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…
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…
Katalin Ferenc, Konrad Otto, Francisco Gomes de Oliveira Neto, Marcela Dávila López + 2 more
Software quality in computational tools impacts research output in a variety of scientific disciplines. Biology is one of these fields, especially for High Throughput Sequencing (HTS) data, such tools play an important role. This study therefore characterises the overall quality of a selection of tools which are…
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…
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…