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…
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…
Virginia T. Scarlett, Renata Gonçalves Curty, Juanita Gomez, Laura Langdon + 3 more
Academic open source contributors face a wide array of challenges, making it difficult for universities, support staff, and funders to determine which needs they should prioritize. To help address this problem, the University of California (UC) Open Source Program Office (OSPO) Network conducted a multi-campus survey…
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…
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…
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…
Stan Zajdel, Diego Elias Costa, Hafedh Mili
The Open Source Software movement has been growing exponentially for a number of years with no signs of slowing. Driving this growth is the wide-spread availability of libraries and frameworks that provide many functionalities. Developers are saving time and money incorporating this functionality into their…
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…
Chris Macek, Brad Cunningham, Nicolas Boillot
Global health has been historically committed to adopting open-source software in health applications globally. This is due to a well-intentioned commitment to capacity-building and the belief that open-source systems enable in-country capacity to take over technology implementations without being locked into specific…
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…
Izuchukwu Azuka Okafor, Smart Ikechukwu Mbagwu, Terkuma Chia, Zuwati Hasim + 2 more
The advancement of scientific research and raising the next-generation scientists in Africa depend largely on science access. The COVID-19 pandemic has caused discussions around open science (OS) to reemerge globally, especially in resource-poor settings like Africa, where the practice of OS is low. The authors…
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…
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…
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…
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…
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…
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…
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…
Suzanne A. Aleksander, Anna V. Anagnostopoulos, Giulia Antonazzo, Valerio Arnaboldi + 97 more
The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively-studied model organisms. The Alliance is organized as individual knowledge centers with strong connections to their research communities and a centralized software infrastructure…
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…