Transcriptome assembly and functional annotation are essential for understanding gene expression and biological function. Nevertheless, many existing tools lack the flexibility to integrate both short- and long-read sequencing data or fail to provide a complete, customizable workflow for transcriptome analysis. Here, we present TrAnnoScope, a comprehensive transcriptome analysis pipeline that provides a complete, customizable workflow capable of efficiently processing and integrating short- and long-read sequencing data to generate high-quality, full-length transcripts with detailed functional annotation. The pipeline encompasses steps from quality control to functional annotation, employing a range of tools and established databases, such as SwissProt, Pfam, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes. As a case study, TrAnnoScope was applied to RNA-Seq data from zebra finch brain, ovary, and testis tissues. TrAnnoScope produced comprehensive transcriptome, demonstrating strong alignment with the reference genome (99.63%) and capturing a significant proportion of nearly complete protein sequences (92.7%). The functional annotation process yielded extensive matches to known protein databases and successfully assigned relevant functional terms to majority of the transcripts. As such, TrAnnoScope successfully integrates multiple sequencing technologies to generate comprehensive transcriptomes with minimal user input. Its modular design, flexibility, and ease of use make it a valuable tool for researchers working with complex datasets, particularly for non-model organisms.

A contrasting empirical evaluation will be provided with the aim of suggesting that the reductionist approach results in experiments that are not reproducible.

Stock assessment determines the status of fishery stock to support manage- ment decision making. Considering the iterations between exploratory cal- culations and the need to compare outputs to elicit better model settings, we should focus on not only the accuracy of abundance estimation and the toler- ance of uncertainty but also the efficiency of the project workflow. Although in Japan, a stock assessment model was introduced written in the R language in 2012, the workflow did not sufficiently adjust, creating problems because the current workflow is contrary to the principles of effective value creation. To make our project sustainable, we propose adopting the agile methodol- ogy, an iterative development method used by software developers, for stock assessment. Therefore, we wrote an example report as a package document in the R language. Developed under a continuous integration environment, the report remains up to date, with every modification on component files. This method enabled our work to be efficient and transparent by allowing and documenting scenario branching, error corrections, and annual updates. We show that the iterative development cycle benefit us by allowing us to focus on the essential business problem of the assessment project.

Recently the increased cost-effectiveness of high-throughput technologies has made available a large number of RNA sequencing datasets to identify circular RNAs (circRNAs). However, despite many computational tools were developed to predict circRNAs, a limited number of workflows exists to predict and to characterize circRNAs. Moreover, to the best of our knowledge, these available workflows do not ensure computational reproducibility and require advanced bash scripting skills to be correctly installed and used. To cope with these critical aspects we present Docker4Circ, a new computational framework designed for a comprehensive analysis of circRNAs composed of: circRNAs prediction, classification and annotation using public databases, the back-splicing sequence reconstruction; the internal alternative splicing of circularizing exons; the alignment-free circRNAs quantification from RNA-Seq reads, and, finally, their differential expression analysis. Docker4Circ was specifically designed for making easier and more accessible circRNAs analysis thanks to the following features: (i) its R interface; (ii) the encapsulation of its computational tasks into a docker image; (iii) an available user-friendly Java GUI Interface. Furthermore, Docker4Circ ensures a reproducible analysis because all its tasks were embedded into a docker image following the guidelines provided by Reproducible Bioinformatics Project (RBP, http://reproducible-bioinformatics.org/). The effectiveness of Docker4Circ was demonstrated on a real case study whose goal is to characterize the circRNAs predicted in colorectal cancer cell lines and quantified in public RNA-Seq experiments performed on primary tumor tissues. In conclusion, we propose Docker4Circ as a framework for reproducible and comprehensive analyses of circRNAs to efficiently exploit their biological role.

Modern research applies the Open Science approach that fosters the production and sharing of Open Data according to the FAIR (Findable, Accessible, Interoperable, Reusable) principles. In the geospatial context this is generally achieved through the setup of OGC Web services that implements open standards that satisfies the FAIR requirements. Nevertheless, the requirement of Findability is not fully satisfied by those services since there’s no use of persistent identifiers and no guarantee that the same dataset used for a study can be immutably accessed in a later period: a fact that hinders the replicability of research. This is particularly true in recent years where data-driven research and technological advances have boosted frequent updates of datasets. Here, we review needs and practices, supported by some real case examples, on frequent data or metadata updates in geo-datasets of different data types. Additionally we assess the currently available tools that support data versioning for databases, files and log-structured tables. Finally we discuss challenges and opportunities to enable geospatial web services that are fully FAIR: a fact that would provide, due to the massive use and increasing availability of geospatial data, a great push toward open science compliance with ultimately impacts on the science transparency and credibility.

Hyaluronic acid, in the form of a gel or viscoelastic colloidal solution, is currently used for viscosupplementation of joints affected by osteoarthritis, but its effectiveness is under debate in relation to newer alternatives. Based on meta-analytical arguments, the present article reinforces the opinion that there are still no decisive arguments for its complete replacement, but for its use adapted to the peculiarities of the disease manifestation and of the patients. A “broad” comparison is first made with almost all alternatives studied in the last decade, and then a meta-regression study is performed to compare and predict the effect size induced by viscosupplementation and platelet-rich plasma therapies. If they are computerized, the developed models can represent tools for clinicians in determining the appropriateness of the option or not for viscosupplementation, in a manner adapted to the pain felt by the patients, to their age, or to other clinical circumstances. The models were generated using the latest algorithms for meta-analysis and meta-regression implemented in the R language and assembled in different R packages. All primary data and necessary R scripts are provided in accordance with the philosophy of reproducible research. Finally, HA-based products, currently under circumspection, are still clinically useful.