10 papers · ranked by Valyu relevance
Johnathan Pocock, Simon Graham, Quoc Dang Vu, Mostafa Jahanifar + 10 more
Computational Pathology (CPath) has seen rapid growth in recent years, driven by advanced deep learning (DL) algorithms. These algorithms typically share the same sequence of steps. However, due to the sheer size and complexity of handling large multi-gigapixel whole-slide images, there is no open-source software…
Laura Wiggins, Stuart Lacy, Graeme Park, Joanne Marrison + 5 more
We previously developed the CellPhe toolkit^1^, an open-source R package for automated cell phenotyping from ptychography time-lapse videos. To align with the growing adoption of python-based image analysis tools and to enhance interoperability with widely used software for cell segmentation and tracking, we developed…
Randy Heiland, Daniel Bergman, Blair Lyons, Julie Cass + 4 more
Defining a multicellular model can be challenging. There may be hundreds of parameters that specify the attributes and behaviors of objects. Hopefully the model will be defined using some format specification, e.g., a markup language, that will provide easy model sharing (and a minimal step toward reproducibility).…
Maximilien Colange, Guillaume Appé, Léa Meunier, Solène Weill + 3 more
We introduce InMoose, an open-source Python environment aimed at omic data analysis. We illustrate its capabilities for bulk transcriptomic data analysis. Due to its wide adoption, Python has grown as a de facto standard in fields increasingly important for bioinformatic pipelines, such as data science, machine…
Knut Rand, Ivar Grytten, Milena Pavlovic, Chakravarthi Kanduri + 1 more
Python is a popular and widespread programming language for scientific computing, in large part due to the powerful array programming library NumPy, which makes it easy to write clean, vectorized and efficient code for handling large datasets. A challenge with using array programming for biological data is that the…
Yangyang Li, Rendong Yang
We introduce PxBLAT, a Python library designed to enhance usability and efficiency in interacting with the BLAST-like alignment tool (BLAT). PxBLAT provides an intuitive application programming interface (API) design, allowing the incorporation of its functionality directly into Python-based bioinformatics workflows.…
François Moreews, Jean-Baptiste Bougaud, Emmanuelle Becker, Florence Gondret + 1 more
Biological Pathway Exchange (BioPAX) is a standard language, represented in OWL, that aims to enable the integration, exchange, visualization and analysis of biological pathway data. While public databanks increasingly provide datasets in BioPAX format, their use remains below potential. Users may encounter challenges…
Ryan Green, Xufeng Qu, Jinze Liu, Tingting Yu
The rapid expansion of Bioinformatics research has resulted in a vast array of computational tools utilized in the development of scientific analysis pipelines. However, constructing these pipelines is a laborious and intricate task, one which demands extensive domain knowledge and careful consideration at all stages.…
Erick Martins Ratamero, Kiya Govek, Julio Mateos Langerak, Fernando Cervantes Sanchez + 1 more
Many research laboratories need to manage, process, and analyze the increasingly large volumes and complexity of data being produced by state-of-the-art bioimaging platforms. OMERO is a popular open-source client-server application that provides a unified interface for managing and working with bioimages and their…
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…