CREDO: a friendly Customizable, REproducible, DOcker file generator for bioinformatics applications.

BACKGROUND: The analysis of large and complex biological datasets in bioinformatics poses a significant challenge to achieving reproducible research outcomes due to inconsistencies and the lack of standardization in the analysis process. These issues can lead to discrepancies in results, undermining the credibility and impact of bioinformatics research and creating mistrust in the scientific process. To address these challenges, open science practices such as sharing data, code, and methods have been encouraged. RESULTS: CREDO, a Customizable, REproducible, DOcker file generator for bioinformatics applications, has been developed as a tool to moderate reproducibility issues by building and distributing docker containers with embedded bioinformatics tools. CREDO simplifies the process of generating Docker images, facilitating reproducibility and efficient research in bioinformatics. The crucial step in generating a Docker image is creating the Dockerfile, which requires incorporating heterogeneous packages and environments such as Bioconductor and Conda. CREDO stores all required package information and dependencies in a Github-compatible format to enhance Docker image reproducibility, allowing easy image creation from scratch. The user-friendly GUI and CREDO's ability to generate modular Docker images make it an ideal tool for life scientists to efficiently create Docker images. Overall, CREDO is a valuable tool for addressing reproducibility issues in bioinformatics research and promoting open science practices.

A single cell RNAseq benchmark experiment embedding "controlled" cancer heterogeneity.

Single-cell RNA sequencing (scRNA-seq) has emerged as a vital tool in tumour research, enabling the exploration of molecular complexities at the individual cell level. It offers new technical possibilities for advancing tumour research with the potential to yield significant breakthroughs. However, deciphering meaningful insights from scRNA-seq data poses challenges, particularly in cell annotation and tumour subpopulation identification. Efficient algorithms are therefore needed to unravel the intricate biological processes of cancer. To address these challenges, benchmarking datasets are essential to validate bioinformatics methodologies for analysing single-cell omics in oncology. Here, we present a 10XGenomics scRNA-seq experiment, providing a controlled heterogeneous environment using lung cancer cell lines characterised by the expression of seven different driver genes (EGFR, ALK, MET, ERBB2, KRAS, BRAF, ROS1), leading to partially overlapping functional pathways. Our dataset provides a comprehensive framework for the development and validation of methodologies for analysing cancer heterogeneity by means of scRNA-seq.

Microparticles from dental calculus disclose paleoenvironmental and palaeoecological records.

Plants have always represented a key element in landscape delineation. Indeed, plant diversity, whose distribution is influenced by geographic/climatic variability, has affected both environmental and human ecology. The present contribution represents a multi-proxy study focused on the detection of starch, pollen and non-pollen palynomorphs in ancient dental calculus collected from pre-historical individuals buried at La Sassa and Pila archaeological sites (Central Italy). The collected record suggested the potential use of plant taxa by the people living in Central Italy during the Copper-Middle Bronze Age and expanded the body of evidence reported by previous palynological and palaeoecological studies. The application of a microscopic approach provided information about domesticated crops and/or gathered wild plants and inferred considerations on ancient environments, water sources, and past health and diseases. Moreover, the research supplied data to define the natural resources (e.g., C4-plant intake) and the social use of the space during that period. Another important aspect was the finding of plant clues referable to woody habitats, characterised by broad-leaved deciduous taxa and generally indicative of a warm-temperate climate and grassy vegetation. Other unusual records (e.g., diatoms, brachysclereids) participated in defining the prehistoric ecological framework. Thus, this work provides an overview on the potential of the human dental calculus analysis to delineate some features of the ancient plant ecology and biodiversity.