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The comparison of computer generated protein structural models is an important element of protein structure prediction. It has many uses including model quality evaluation, selection of the final models from a large set of candidates or…
Foundation models are trained on increasingly immense and opaque datasets. Even while these models are now key in AI system building, it can be difficult to answer the straightforward question: has the model already encountered a given…
Medical image computing software is essential for identifying imaging biomarkers that can support diagnosis, prognosis, treatment planning, and clinical research. However, the lack of standardized, user-friendly, and reproducible software…
This paper is concerned with synthesizing programs based on black-box oracles: we are interested in the case where there exists an executable implementation of a component or library, but its internal structure is unknown. We are provided…
In this study, we explore advanced strategies for enhancing software quality by detecting and refactoring data clumps, special types of code smells. Our approach transcends the capabilities of integrated development environments, utilizing…
Bioinformatics pipelines depend on shared POSIX filesystems for its input, output and intermediate data storage. Containerization makes it more difficult for the workloads to access the shared file systems. In our previous study, we were…
We present the pulsar_spectra software repository, an open-source pulsar flux density catalogue and automated spectral fitting software that finds the best spectral model and produces publication-quality plots. The Python-based software…
The genome-scale metabolic model with protein constraint (PC-model) has been increasingly popular for microbial metabolic simulations. We present PROSO Toolbox, a unified and simple-to-use PC-model toolbox that takes any high-quality…
Dependency analysis is recognized as an important field of software engineering due to a variety of reasons. There exists a large pool of tools providing assistance to software developers and architects. Analysis of inter- and intra-project…
The SunPy Project is a community of scientists and software developers creating an ecosystem of Python packages for solar physics. The project includes the sunpy core package as well as a set of affiliated packages. The sunpy core package…
Nowadays the analysis of dynamics of and on networks represents a hot topic in the Social Network Analysis playground. To support students, teachers, developers and researchers in this work we introduce a novel framework, namely NDlib, an…
Background: The study of genome-scale metabolic models and their underlying networks is one of the most important fields in systems biology. The complexity of these models and their description makes the use of computational tools an…
Nowadays, engineers have to develop software often without even knowing which hardware it will eventually run on in numerous mobile phones, tablets, desktops, laptops, data centers, supercomputers and cloud services. Unfortunately,…
Cloud platforms allow users to execute tasks directly from their web browser and are a key enabling technology not only for commerce but also for computational science. Research software is often developed by scientists with limited…
In the field of image-based drug discovery, capturing the phenotypic response of cells to various drug treatments and perturbations is a crucial step. However, existing methods require computationally extensive and complex multi-step…
Fast, incremental evolution of physics instrumentation raises the question of efficient software abstraction and transferability of algorithms across similar technologies. This contribution aims to provide an answer by introducing Track…
This paper presents an open-source, lightweight, yet comprehensive software framework, named RPC, which integrates physics-based simulators, planning and control libraries, debugging tools, and a user-friendly operator interface. RPC…
Biopsy is commonly used to confirm cancer diagnosis when radiologically indicated. Given the ability of PET to localize malignancies in heterogeneous tumors and tumors that do not have a CT correlate, PET/CT guided biopsy may improve the…
A Materials Project based open-source Python tool, MPInterfaces, has been developed to automate the high-throughput computational screening and study of interfacial systems. The framework encompasses creation and manipulation of interface…
Self-assembly is a phenomenon observed in nature at all scales where autonomous entities build complex structures, without external influences nor centralised master plan. Modelling such entities and programming correct interactions among…