24 papers · ranked by Valyu relevance
Héctor D. García-Verdugo, Cristian Román-Palacios, Francis Ouellette
Effective collaboration, essential for success in academic environments, often requires efficient team communication and access to a team-oriented digital infrastructure. Despite the significance of efficient and effective collaboration within the academy, a standardized and structured suite for collaboration remains…
Mario Zuliani, C. J. Lortie
Open science, work and knowledge that are developed in full, offers critical resources that provide students with insights into the process of research in many fields. There are extensive opportunities within environmental sciences to incorporate open science into undergraduate level courses. There are seven major open…
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…
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.…
Andrea Janes, Xiaozhou Li, Valentina Lenarduzzi
Background. Coping with the rapid growing complexity in contemporary software architecture, tracing has become an increasingly critical practice and been adopted widely by software engineers. By adopting tracing tools, practitioners are able to monitor, debug, and optimize distributed software architectures easily.…
Rebecca Sophia Lais, Julia Fitzner, Yeon-Kyeng Lee, Verena Struckmann
'Verena Struckmann'] Introduction The COVID-19 pandemic had devastating effects on health systems globally. Emerging infectious diseases and pandemics will persist as a global health threat and preparedness for an evidence based response becomes challenging for decision makers. Epidemiological modeling can and has…
Hugo Caro, Sulyvan Dollin, Bryan Brancotte, Dimitri Desvillechabrol + 10 more
Bioinformatics is a field known for the numerous standards and formats that have been developed over the years. This plethora of formats, sometimes complementary, and often redundant, poses many challenges to bioinformatics data analysts. They constantly need to find the best tool to convert their data into the…
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…
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…
Roberto Di Cosmo, Sabrina Granger, Konrad Hinsen, Nicolas Jullien + 6 more
FAIR principles are a set of guidelines aiming at simplifying the distribution of scientific data to enhance reuse and reproducibility. This article focuses on research software, which significantly differs from data in its living nature, and its relationship with free and open-source software. We provide a tiered…
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…
Felix Bach, Jochen Klar, Axel Loewe, Jorge Sánchez + 3 more
collaborative development environment for research software Authors: ['Felix Bach' 'Jochen Klar' 'Axel Loewe' 'Jorge Sánchez' 'Gunnar Seemann' 'Yung-Lin Huang' 'Robert Ulrich'] 1Steinbuch Centre for Computing, Karlsruhe Institute of Technology (KIT), Germany 2 Institute of Biomedical Engineering, Karlsruhe Institute of…
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…
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…
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…
Evangelia Panourgia, Theodoros Plessas, Diomidis Spinellis
The rising popularity of deep learning (DL) methods and techniques has invigorated interest in the topic of SE4DL (Software Engineering for Deep Learning), the application of software engineering (SE) practices on deep learning software. Despite the novel engineering challenges brought on by the data-driven and…
Julie Skoven Hinge, Micha Moskovic, Axel Naumann, Noemi Calace + 1 more
We present a methodology to systematically assess the scale and impact of an organization's contributions to open source software (OSS). The methodology combines the archival data of Software Heritage with usage metrics, dependency analysis, economic valuation models, and interviews to comprehensively understand…
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…
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…
Bhavesh Patel, Sanjay Soundarajan, Zicheng Hu
Findable, Accessible, Interoperable, and Reusable (FAIR) guiding principles tailored for research software have been proposed by the FAIR for Research Software (FAIR4RS) Working Group. They provide a foundation for optimizing the reuse of research software. The FAIR4RS principles are, however, aspirational and do not…
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…