15 papers · ranked by Valyu relevance
Yuma Ito, Masanori Hirose, Makio Tokunaga
Single-molecule imaging is a promising method for direct quantification of the dynamics and distribution of biomolecules in living cells. Although numerous methods have been developed to gain biological insights into molecular behavior, the high diversity of microscopes and single-molecule dynamics can result in…
Boris Yamrom, Yoon-ha Lee, Steven Marks, Lubomir Chorbadjiev + 2 more
Snakemake is one of the most popular workflow management systems, particularly in biological sciences. Snakemake workflows are highly portable, scalable, and transparent. Moreover, they enable the painless reproduction of published results and adaption to similar data processing and analysis projects. Here we present…
Mohamed Salim Nasser Al Hinai, Zakira Naureen, Syed Abdullah Gilani
Since, Bioinformatic research is getting attraction that can be seen with sudden increase in development of tools as well as publications. However, there are challenges in bioinformatics which are making the results difficult to obtain while facing reproducibility, scalability, and accessibility of computational…
Daniel J.B. Clarke, John Erol Evangelista, Zhuorui Xie, Giacomo B. Marino + 36 more
Many biomedical research projects produce large-scale datasets that may serve as resources for the research community for hypothesis generation, facilitating diverse use cases. Towards the goal of developing infrastructure to support the findability, accessibility, interoperability, and reusability (FAIR) of biomedical…
Malwina Kotowicz, Sven Fengler, Birgit Kurkowsky, Anja Meyer-Berhorn + 13 more
Data management and sample tracking in complex biological workflows are essential steps to ensure necessary documentation and guarantee the reusability of data and metadata. Currently, these steps pose challenges related to correct annotation and labeling, error detection, and safeguarding the quality of documentation.…
Shixiang Wang
Bioinformatics analyses depend on workflow engines to coordinate dozens of computational tools across complex dependency chains. The most widely adopted engines—Snakemake, Nextflow, the Common Workflow Language (CWL), and the Workflow Description Language (WDL)—run on interpreted or just-in-time (JIT) compiled language…
Andrew E. Webb, Scott W. Wolf, Ian M. Traniello, Sarah D. Kocher
The exponential growth in biological data generation has created an urgent need for efficient, reproducible computational analysis workflows. Here, we present pipemake, a computational platform designed to streamline the development and implementation of efficient and reproducible Snakemake workflows. pipemake creates…
C Domínguez-Dalmases, A Cañellas-Solé, R Lambea-Jané, M Municoy + 1 more
Horus is a versatile, multi-platform reproducible-workflow management system designed for biomolecular modelling and computational life sciences. Available as both a desktop application and a web-based service, Horus offers researchers an intuitive graphical interface alongside a robust Python API, democratising the…
Matt Burridge, Zhen Ou, Katherine James, Gizem Buldum + 4 more
Advances in laboratory automation and AI-driven experimental design have increased the scale and complexity of data generated in synthetic biology. Whilst biofoundries provide significant resources and infrastructure to execute these experiments, most laboratories rely on isolated automated instruments and software…
Helena L. Crowell, Yixing Dong, Ilaria Billato, Peiying Cai + 30 more
Spatial transcriptomics technologies provide spatially-resolved measurements of gene expression through assays that can either target selected genes or capture transcriptome-wide expression profiles. The complexity and variability of these technologies and their associated data necessitate multi-step workflows…
Paula Pena González, Dafne Lozano-Paredes, José Luis Rojo-Álvarez, Luis Bote-Curiel + 1 more
The efficient importation of quantified gene expression data is pivotal in transcriptomics. Historically, the R package Tximport addressed this need by enabling seamless data integration from various quantification tools. However, the Python community lacked a corresponding tool, restricting cross-platform…
Robert Neil McArthur, Thomas King-Fung Wong, Yapeng Lang, Richard Andrew Morris + 4 more
piqtree (pronounced pie-cue-tree) is an easy to use, open-source Python package that provides Python script based control of IQ-TREE’s phylogenetic inference engine. piqtree builds IQ-TREE as a Python package, presenting a library of Python functions for performing many of IQ-TREE’s capabilities including phylogenetic…
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…
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…
Mauro Silberberg, Henning Hermjakob, Rahuman S. Malik-Sheriff, Hernán E. Grecco
Chemical Reaction Networks (CRNs) play a pivotal role in diverse fields such as systems biology, biochemistry, chemical engineering, and epidemiology. High-level modelling of CRNs enables various simulation approaches, including deterministic and stochastic methods. However, existing Python tools for CRN modelling…