7 papers · ranked by Valyu relevance
Venus N. Sherathiya, Michael D. Schaid, Jillian L. Seiler, Gabriela C. Lopez + 1 more
Fiber photometry (FP) is an adaptable method for recording in vivo neural activity in freely behaving animals. It has become a popular tool in neuroscience due to its ease of use, low cost, the ability to combine FP with freely moving behavior, among other advantages. However, analysis of FP data can be challenging for…
Thomas Donoghue, Sandra Maesta-Pereira, Claire Zhixian Han, Salman Ehtesham Qasim + 1 more
A common method of collecting and analyzing neural activity is to implant electrodes that record the electrical activity of the brain, from which action potentials of individual neurons can be recorded (). After pre-processing to detect spike waveforms and cluster them into groups representing putative single neurons…
Benjamin M. Gyori, Charles Tapley Hoyt
Understanding the complex molecular processes governing how cells respond to external stimuli crucially relies on prior knowledge about signaling, regulatory, and metabolic pathways. Standardized representations are necessary to exchange such pathway knowledge and allow interoperability between tools. BioPAX () is a…
Daewon Lee, Pier Luigi Martelli
A variety of real-world phenomena such as biological pathways, communication networks and social relationships can be represented as networks (). An insightful visualization of networks facilitates understanding of the analyzed networks and leads to important discoveries. Therefore, open-source software for analyzing…
Mohammed Zniber, Youssef Fatihi, Tan-Phat Huynh, Sofia Forslund
Metabolomics is an emerging field within systems biology and represents the final step in the ‘omics’ cascade (, ). As a technology-driven discipline, metabolomics utilizes advancements in analytical chemistry and computational techniques to improve data collection, analysis, and interpretation (). Key platforms in…
Jan Janssen, Janine George, Julian Geiger, Marnik Bercx + 7 more
Numerous Workflow Management Systems (WfMS) have been developed in the field of computational materials science with different workflow formats, hindering interoperability and reproducibility of workflows in the field. To address this challenge, we introduce here the Python Workflow Definition (PWD) as a workflow…
Wubin Ding, David Goldberg, Wanding Zhou
PyComplexHeatmap was designed to visualize matrix data and associated metadata through sophisticated, richly annotated heatmap layouts. We have integrated the R grammar-of-graphics semantics with the Python-native matplotlib/Pandas-based data science ecosystem, allowing users to utilize built-in matplotlib colormaps…