Documents

This document is adapted from the 16S tutorials available at Galaxy [https://training.galaxyproject.org/training-material/topics/metagenomics/ tutorials/mothur-miseq-sop-short/tutorial.html] and [https://training.galaxyproject.org/training-material/ topics/metagenomics/tutorials/mothur-miseq-sop/tutorial.html]. Please also go through these tutorials for better understandings. Note: The steps mentioned in this document are well suited for V3-V4 regions. However the parameters could be varied if ...

This workflow is part of the EJP RD case study on CAKUT published here: Bayjanov, J.R., Doornbos, C., Ozisik, O. et al. Integrative analysis of multi-omics data reveals importance of collagen and the PI3K AKT signalling pathway in CAKUT. Sci Rep 14, 20731 (2024). https://doi.org/10.1038/s41598-024-71721-8

Beyond Topology: Deterministic and Order-Preserving Graph Visualization with the Keçeci Layout

Mehmet Keçeci1 1ORCID : https://orcid.org/0000-0001-9937-9839, İstanbul, Türkiye

Received: 03.07.2025

Özet/Abstract:

The visualization of scientific data is a fundamental step in uncovering hidden patterns and relationships within complex systems. While conventional force-directed graph layout algorithms (e.g., spring layout) are effective at displaying the general topology and clustering tendencies of ...

This BioExcel best practice guide discusses the workflow engines available for the Common Workflow Language (CWL).

Protein domains can be viewed as building blocks, essential for understanding structure-function relationships in proteins. However, each domain database classifies protein domains using its own methodology. Thus, in many cases, boundaries between different domains or families differ from one domain database to the other, raising the question of domain definition and enumeration. The answer to this question cannot be found in a single database. Rather, expert integration and curation of various ...

In the recent years, the improvement of software and hardware performance has made biomolecular simulations a mature tool for the study of biological processes. Simulation length and the size and complexity of the analyzed systems make simulations both complementary and compatible with other bioinformatics disciplines. However, the characteristics of the software packages used for simulation have prevented the adoption of the technologies accepted in other bioinformatics fields ...

The results of the mentimeter for the FAIR workflows section of the EOSC-Life 3rd Open Call projects pre-hackathon induction