25 papers · ranked by Valyu relevance
Penny Whiting, Robert Wolff, Susan Mallett, Iveta Simera + 1 more
'Jelena Savović'] Background Assessment of the quality of included studies is an essential component of any systematic review. A formal quality assessment is facilitated by using a structured tool. There are currently no guidelines available for researchers wanting to develop a new quality assessment tool. Methods This…
Simon Bray, Matthias Bernt, Nicola Soranzo, Marius van den Beek + 7 more
There are thousands of well-maintained high-quality open-source software utilities for all aspects of scientific data analysis. For over a decade, the Galaxy Project has been providing computational infrastructure and a unified user interface for these tools to make them accessible to a wide range of researchers. In…
Bethany Laursen, Bianca Vienni-Baptista, Gabriele Bammer, Antonietta Di Giulio + 3 more
'Antonietta Di Giulio' 'Theres Paulsen' 'Melissa Robson-Williams' 'Sibylle Studer'] A growing number of inter- and transdisciplinary (ITD) toolkits provide methods, processes, concepts, heuristics, frameworks, and other resources for designing and implementing ITD research. A brief overview of the currently fragmented…
Havan Yusuf, Alison Hillman, Jan Arend Stegeman, Angus Cameron + 1 more
'Skye Badger'] Introduction Digital clinical decision support (CDS) tools are of growing importance in supporting healthcare professionals in understanding complex clinical problems and arriving at decisions that improve patient outcomes. CDS tools are also increasingly used to improve antimicrobial stewardship (AMS)…
Zoë Goldsborough, Meredith Carlson, Leonie Reetz, Margaret C. Crofoot + 1 more
Percussive tool use for extractive foraging allows animals to access otherwise inaccessible resources and forage more efficiently, with potentially important implications for their fitness. The development of tool use proficiency has been well-documented in nut-cracking chimpanzees and robust capuchins, and in…
Zoë Goldsborough, Meredith K.W. Carlson, Leonie S. Reetz, Margaret C. Crofoot + 1 more
Percussive tool use for extractive foraging allows animals to access otherwise inaccessible resources and forage more efficiently, with potentially important implications for their fitness. The development of tool use proficiency has been well-documented in nut-cracking chimpanzees and robust capuchins, and in…
Max Wielsch, Raik Bieniek, Bernd Grams, Jörg Lässig
The paper describes the need for and goals of tool-integration within software development processes. In particular we focus on agile software development but are not limited to. The integration of tools and data between the different domains of the process is essential for an efficient, effective and customized…
Oscar Nierstrasz, Tudor Gîrba
Moldable development supports decision-making by making software systems explainable. This is done by making it cheap to add numerous custom tools to your software, turning it into a live, explorable domain model. Based on several years of experience of applying moldable development to both open-source and industrial…
Paul P. Gardner
The development of accurate bioinformatic software tools is crucial for the effective analysis of complex biological data. This study examines the relationship between the academic department affiliations of authors and the accuracy of the bioinformatic tools they develop. By analyzing a corpus of previously…
G. Fylaktopoulos, G. Goumas, M. Skolarikis, A. Sotiropoulos + 1 more
'I. Maglogiannis'] This paper provides an overview of the state of the art technologies for software development in cloud environments. The surveyed systems cover the whole spectrum of cloud-based development including integrated programming environments, code repositories, software modeling, composition and…
Anselm W. Hahn, Joseph Zsombor-Pindera, Pierre Kennepohl, Serena DeBeer
In chemistry, analyzing spectra through peak fitting is a crucial task that helps scientists extract useful quantitative information about a sample's chemical composition or electronic structure. To make this process more efficient, we have developed a new open-source software tool called SpectraFit. This tool allows…
Luis Bastiao Silva, Rafael C. Jimenez, Niklas Blomberg, José Luis Oliveira
Most bioinformatics tools available today were not written by professional software developers, but by people that wanted to solve their own problems, using computational solutions and spending the minimum time and effort possible, since these were just the means to an end. Consequently, a vast number of software…
Meiying Qin, Jake Brawer, Brian Scassellati
Using human tools can significantly benefit robots in many application domains. Such ability would allow robots to solve problems that they were unable to without tools. However, robot tool use is a challenging task. Tool use was initially considered to be the ability that distinguishes human beings from other animals.…
Pierre R. Mercuriali, Carlos Hernandez Corbato, Geeske H.J. Langejans
To contribute to current discussions on the complexity of extinct and modern non-human and human primate tasks, we explore if ontologies are helpful as a means of representing tool tasks. We thus hope to help illuminate how primates approach tool tasks internally, such as breaking open a nutshell between a wooden anvil…
Samantha Durdy, Cameron J. Hargreaves, Mark Dennison, Benjamin Wagg + 5 more
The discovery of new materials often requires collaboration between experimental and computational chemists. Web based platforms allow more flexibility in this collaboration by giving access to computational tools without the need for access to computational researchers. We present Liverpool Materials Discovery Server…
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…
Ivan Ruchkin, Vladimir Prus
— This paper addresses the problem of IDE interface complexity by introducing single-window graphical user interface. This approach lies in removing additional child windows from IDE, thus allowing a user to keep only text editor window open. We describe an abstract model of IDE GUI that is based on most popular modern…
Eric Deutsch, Luis Mendoza, David Shteynberg, Michael Hoopmann + 3 more
The Trans-Proteomic Pipeline mass spectrometry data analysis suite has been in continual development and refinement since its first tools PeptideProphet and ProteinProphet were published twenty years ago. The current release provides a large complement of tools for spectrum processing, spectrum searching, search…
Muhammad Aziz
Computational chemistry software designed to compute the chemical properties of compounds falls under the category of dry research. The computational calculation of chemicals is a broad term. In this current study, chemical properties are estimated through computational methods, which is valuable for newly synthesis…
Carolin Brandt, Andy Zaidman
Automatically generating test cases for software has been an active research topic for many years. While current tools can generate powerful regression or crash-reproducing test cases, these are often kept separately from the maintained test suite. In this paper, we leverage the developer's familiarity with test cases…
Glaucia Melo, Luis Fernando Lins, Paulo Alencar, Don A. Cowan
—Software Development (SD) is remarkably dynamic and is critically dependent on the knowledge acquired by the project's software developers as the project progresses. Software developers need to understand large amounts of information related to the tasks at hand. This information (context) is often not explicit, as it…
Christopher Southan
This report covers academic small-molecule drug development with a view to distilling guidelines. The first section covers research productivity feeding into commercial development before reviewing the literature on statistics of academic development It then considers differences between probes and drugs before…
Christopher Southan
This report covers academic small-molecule drug development with a view to distilling guidelines. The first section covers research productivity feeding into commercial development before reviewing the literature on statistics of academic development It then considers differences between probes and drugs before…
VP Nagraj, Stephen D Turner, Neal Magee
Containerization enables portable, reproducible, and scalable scientific computing. However, container development, documentation, and deployment practices can vary widely, even within a single domain. Understanding patterns of how containers are implemented in real-world settings can inform community guidelines…
Philippe Kruchten
We propose a conceptual model of software development that encompasses all approaches: traditional or agile, light and heavy, for large and small development efforts. The model identifies both the common aspects in all software development, i.e., elements found in some form or another in each and every software…