25 papers · ranked by Valyu relevance
Zhouming Wu, Dakota Murray
Science advances not only through the accumulation of facts but also through the evolution of tools. Crucially, tools are rarely used in isolation. They form tool portfolios, combinations shaped by a discipline's workflows and analytical demands. Software, near-ubiquitous in modern research and traceable across the…
Christian Lovis, Negin Eslamiamirabadi, Andrew Brown, Kathryn Cowie + 4 more
'Asad Rahmatullah' 'Nicole Hardy' 'Karl Holub' 'Kevin Kallmes'] Background Systematic reviews (SRs) are central to evaluating therapies but have high costs in terms of both time and money. Many software tools exist to assist with SRs, but most tools do not support the full process, and transparency and replicability of…
Haseeb A Khan
Biomedical scientists and clinicians often require customized and user-friendly software tools due to the unavailability of specific software, complexity of existing software or high cost of commercial software. This editorial provides a short update on recently published task-oriented biomedical software tools. The…
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…
Adrian Zapletal, Dimitri Höhler, Carsten Sinz, Alexandros Stamatakis
Scientific software from all areas of scientific research is pivotal to obtaining novel insights. Yet the quality of scientific software is rarely assessed, even though it might lead to incorrect scientific results in the worst case. Therefore, we have developed an open source tool and benchmark called SoftWipe, that…
Elizabeth Bjarnason, Patrik Åberg, Nauman bin Ali
Context Software selection in large-scale software development continues to be ad hoc and ill-structured. Previous proposals for software component selection tend to be technology-specific and/or do not consider business or ecosystem concerns. Objective Our main aim is to develop an industrially relevant…
Georgi Danovski, Teodora Dyankova, Stoyno Stoynov
We present CellTool, a stand-alone open source software with a Graphical User Interface for image analysis, optimized for measurement of time-lapse microscopy images. It combines data management, image processing, mathematical modeling and graphical presentation of data in a single package. Multiple image filters…
Marc-Oliver Gewaltig, Robert Cannon, Sean Hill
Almost all research work in computational neuroscience involves software. As researchers try to understand ever more complex systems, there is a continual need for software with new capabilities. Because of the wide range of questions being investigated, new software is often developed rapidly by individuals or small…
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…
Adrian Zapletal, Dimitri Höhler, Carsten Sinz, Alexandros Stamatakis
Scientific software from all areas of scientific research is pivotal to obtaining novel insights. Yet the coding standards adherence of scientific software is rarely assessed, even though it might lead to incorrect scientific results in the worst case. Therefore, we have developed an open source tool and benchmark…
Mahendra Reddy Bhumula
- The dissertation provides a comparative analysis of a number of variability tools currently in use. It serves as a catalogue for practitioners interested in the topic. We compare a range of modelling, configuring, and management tools for product line engineering. The tools surveyed are compared against the following…
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…
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…
Manar Abu Talib
Versatility, flexibility and robustness are essential requirements for software forensic tools. Researchers and practitioners need to put more effort into assessing this type of tool. A Markov model is a robust means for analyzing and anticipating the functioning of an advanced component based system. It is used, for…
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.…
Oliver Lee, Malte Gather, Eli Zysman-Colman
We describe a new tool for the efficient management of computational chemistry. Digichem is a program that automates and simplifies nearly the entire computational pipeline, including large-scale batch submission of calculations, analysis and results parsing, the generation of 3D density plots and 2D graphs of…
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…
Ra’Fat Al-Msie’deen
—Software artifacts visualization helps software developers to manage the size and complexity of the software system. The tag cloud technique visualizes tags within the cloud according to their frequencies in software artifacts. A font size of the tag within the cloud indicates its frequency within a software artifact…
Juan Andrés Carruthers, Jorge Andrés Díaz Pace, Emanuel Irrazábal
Resumen. Contexto: los proyectos software son insumos comunes en los experimentos de la Ingeniería del Software, aunque estos muchas veces sean seleccionados sin seguir una estrategia específica, lo cual disminuye la representatividad y replicación de los resultados. Una opción es el uso de colecciones preservadas de…
Raphaël Robidas, Claude Legault
Computational chemistry is an increasingly active field due to the improvement of computing resources and theoretical tools. However, its use remains usually limited to technically-inclined users due to the technical challenges of preparing, launching and analyzing calculations. In this context, we have developed…
Authors not listed
Mass spectrometric analysis of inorganic materials is widely used. However, no major advances were made in this area compared to the significant progress in the analysis of biological materials. This work introduces a novel open-source R workflow that efficiently processes and models isotopic distributions in LDI-TOF…
Stephen R. Piccolo, Zachary E. Ence, Elizabeth C. Anderson, Jeffrey T. Chang + 1 more
Command-line software plays a critical role in biology research. However, processes for installing and executing software differ widely. The Common Workflow Language (CWL) is a community standard that addresses this problem. Using CWL, tool developers can formally describe a tool’s inputs, outputs, and other execution…
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…
Mens, Tom, De Roover, Coen
This chapter defines and presents different kinds of software ecosystems. The focus is on the development, tooling and analytics aspects of "software ecosystems", i.e., communities of software developers and the interconnected software components (e.g., projects, libraries, packages, repositories, plug-ins, apps) they…