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…
Raphael Sonabend, Hugo Gruson, Leo Wolansky, Agnes Kiragga + 2 more
'Daniel S. Katz' 'Jason A. Papin'] This paper extends the FAIR (Findable, Accessible, Interoperable, Reusable) guidelines to provide criteria for assessing if software conforms to best practices in open source. By adding “USE” (User-Centered, Sustainable, Equitable), software development can adhere to open source best…
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…
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…
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…
Andrew L. Hufton
In [this month’s issue]() of Patterns, we take a special look at open-source software. Data science is a field that is defined more by a set of common tools and approaches than any other factor. These tools-statistical and databasing techniques, machine learning methods, etc.-are frequently embedded within and shared…
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…
Joshua Tan, Nicholas Vincent, Katherine Elkins, Magnus Sahlgren
Open source projects have made incredible progress in producing transparent and widely usable machine learning models and systems, but open source alone will face challenges in fully democratizing access to AI. Unlike software, AI models require substantial resources for activation—compute, post-training, deployment…
Yasset Perez-Riverol, Wout Bittremieux, William S. Noble, Lennart Martens + 16 more
and FAIR Research Software for Proteomics Authors: ['Yasset Perez-Riverol' 'Wout Bittremieux' 'William S. Noble' 'Lennart Martens' 'Aivett Bilbao' 'Michael R. Lazear' 'Bjorn Grüning' 'Daniel S. Katz' 'Michael J. MacCoss' 'Chengxin Dai' 'Jimmy K. Eng' 'Robbin Bouwmeester' 'Michael R. Shortreed' 'Enrique Audain' 'Timo…
Marco Gaido, Sara Papi, Luisa Bentivogli, Alessio Brutti + 5 more
Model Training on EU Languages Authors: ['Marco Gaido' 'Sara Papi' 'Luisa Bentivogli' 'Alessio Brutti' 'Mauro Cettolo' 'Roberto Gretter' 'Marco Matassoni' 'Mohamed Nabih' 'Matteo Negri'] The rise of foundation models (FMs), coupled with regulatory efforts addressing their risks and impacts, has sparked significant…
Mohamed Ouf, Rowan Hussein
Open source software (OSS) is not homogeneous. A project's purpose, governance, and funding shape how its community forms, who contributes, and how the software is maintained, yet empirical research often samples OSS broadly and reports findings as if they held for open source as a whole. We argue that OSS comprises…
Yue Yang, Wang Yi, David Redmiles
Encompassing a diverse population of developers, non-technical users, organizations, and many other stakeholders, open source software (OSS) development has expanded to broader social movements from the initial product development aims. Ideology, as a coherent system of ideas, offers value commitments and normative…
Yang Luo, Yongsheng Jin, Yuanmao Ji, Silvia Escribano Cubas
Open-source communities(OSCs) are gaining significant attention in the current business environment of information technology(IT). More and more IT companies and individuals are exploring how to achieve innovation through open-source collaboration, and value co-creation(VCC) in the OSCs has become a trend. Therefore…
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…
Thomas Roder, Simone Oberhänsli, Noam Shani, Rémy Bruggmann
OpenGenomeBrowser is a self-hostable open-source platform that manages access to genomic data and drastically simplifies comparative genomics analyses. It enables users to interactively generate phylogenetic trees, compare gene loci, browse biochemical pathways, perform gene trait matching, create dot plots, execute…
Rodolfo Keesey, Armi Tiihonen, Alexander E. Siemenn, Thomas W. Colburn + 18 more
Rodolfo Keesey , Armi Tiihonen3,1 , Alexander E. Siemenn 1 , Thomas W. Colburn 4 , Shijing Sun 1 , Noor Titan Putri Hartono 1 , James Serdy 1 , Margaret Zeile 2 , Keqing He 2 , Cole A. Gurtner 4 , Austin C. Flick 4 , Clio Batali 1 , Alex Encinas 1 , Richa R. Naik 1 , Zhe Liu 1 , Felipe Oviedo 1 , I. Marius Peters 1 …
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…
Nicola Bernabò, Luca Valbonetti, Alessandra Ordinelli, Rosa Ciccarelli + 1 more
The widespread use of internet has had enormous consequences in changing the way of accessing to scientific literature in all domains of knowledge and, in particular, in medicine. One of the most important related factors is the idea of making research output freely available: the so-called Open Access (OA) option. OA…
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…
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…
Tomas Rees, Valérie Philippon, Andrew Liew, Slávka Baróniková + 6 more
In biomedical and health sciences, many articles are published open access (OA). Rates of OA publications continue to grow, including for research carried out by pharmaceutical companies. To help drive more openness in the pharmaceutical industry, we aimed to compare the OA publication rates of pharmaceutical companies…
Simon Boothroyd, Pavan Kumar Behara, Owen Madin, David Hahn + 15 more
Simon Boothroyd 2 , Pavan Kumar Behara 1 , Owen Madin 3 , David Hahn 4 , Hyesu Jang5,6 , Vytautas Gapsys4,7 , Jeffrey Wagner 1,8 , Joshua Horton 9 , David Dotson10,8 , Matthew Thompson3,8 , Jessica Maat 1 , Trevor Gokey 1 , Lee-Ping Wang 5 , Daniel Cole 9 , Michael Gilson 11 , John Chodera 12 , Christopher Bayly 6 …