BioInfograph: An Online Tool to Design and Display Multi-Panel Scientific Figure Interactively

Many fit-for-purpose bioinformatics tools generate plots to interpret complex biological data and illustrate findings. However, assembling individual plots in different formats from various sources into one high-resolution figure in the desired layout requires mastery of commercial tools or even programming skills. In addition, it is a time-consuming and sometimes frustrating process even for a computationally savvy scientist who frequently takes a trial-and-error iterative approach to get satisfactory results. To address the challenge, we developed bioInfograph, a web-based tool that allows users to interactively arrange high-resolution images in diversified formats, mainly Scalable Vector Graphics (SVG), to produce one multi-panel publication-quality composite figure in both PDF and HTML formats in a user-friendly manner, requiring no programming skills. It solves stylesheet conflicts of coexisting SVG plots, integrates a rich-text editor, and allows creative design by providing advanced functionalities like image transparency, controlled vertical stacking of plots, versatile image formats, and layout templates. To highlight, the sharable interactive HTML output with zoom-in function is a unique feature not seen in any other similar tools. In the end, we make the online tool publicly available at https://baohongz.github.io/bioInfograph while releasing the source code at https://github.com/baohongz/bioInfograph under MIT open-source license.

An Author’s Guide to Mastering Research Communication Skills: Introduction of a Medical Manuscript

Skilled academic/medical writing is critical to research communication. The fundamental sections of a scholarly manuscript are introduction, methods, results and discussion. The introduction of a medical manuscript is aimed at briefing readers on the clinical extent and public health context of the research problem. It must justify the essentialness of the research to the scientific community and reveal any underlying research novelty. Skillfully conceived, designed and performed research protocols that are unskillfully presented can lose scientific credibility and impact. Without research communication skills authors would not be able to display the usefulness of their research for the scientific community. Generally, research communication or medical writing training/skills is underrepresented in curricular systems of medical schools globally. This can challenge publication quality and quantity of early-career authors/researchers. The author presents the academic experience he accumulated through peer review and supervision of vast manuscripts and theses. This article aimed at presenting a comprehensive roadmap for academic writing of the introduction and at identifying its common pitfalls.

Mutagenesis-visualization: analysis of site saturation mutagenesis datasets in Python

Site saturation mutagenesis (SSM) experiments have been transformative in our study of protein function. Despite the rich data generated from such experiments, current tools for processing, analyzing, and visualizing the data offer only a limited set of static plots that are difficult to customize. Furthermore, usage of the tools requires extensive experience and programming. This slows the research process for those in the biological field who are unfamiliar with programming. Here, we introduce mutagenesis-visualization, a Python API for the creation of publication quality figures for SSM datasets which requires no prior Python or statistics experience. The plots can be rendered as native matplotlib objects (easy to stylize) or as Plotly objects (interactive graphs). Additionally, the software offers the possibility to visualize the datasets on Pymol. Availability and implementation: The software can be installed from PyPI or GitHub using the pip package manager and is compatible with Python ≥ 3.8. The documentation can be found at readthedocs and the source code can be found on GitHub.

StainedGlass: Interactive visualization of massive tandem repeat structures with identity heatmaps

Summary: Visualization and analysis of genomic repeats is typically accomplished through the use of dot plots; however, the emergence of telomere-to-telomere assemblies with multi-megabase repeats requires new visualization strategies. Here, we introduce StainedGlass which can generate publication quality figures and interactive visualizations that depict the identity and orientation of multi-megabase repeat structures at a genome-wide scale. The tool can rapidly reveal higher-order structures and improve the inference of evolutionary history for some of the most complex regions of genomes. Availability and implementation: StainedGlass is implemented using Snakemake and is available open source under the MIT license at https://mrvollger.github.io/StainedGlass/.

SteadyCellPhenotype: A web-based tool for the modeling of biological networks with ternary logic

We introduce SteadyCellPhenotype, a browser based interface for the analysis of ternary biological networks. It includes tools for deterministically finding all steady states of a network, as well as the simulation and visualization of trajectories with publication quality graphics. Stochastic simulations allow us to approximate the size of the basin for attractors and deterministic simulations of trajectories nearby specified points allow us to explore the behavior of the system in that neighborhood.

The Programme for International Student Assessment Research in Indonesia

Several Programme for International Student Assessment (PISA) research articles published in Indonesia have contributed to PISA research development in Indonesia, with mathematics as one of the PISA domains. However, there is no research to categorize the PISA research article to give future PISA researchers essential information. Therefore, this study aims to organize PISA research in Indonesia in the period 2016-2020. This study uses the Systematic Literature Review (SLR). The SLR method identifies, analyzes, evaluates, and categorizes specific topics related to PISA research in Indonesia. The research data comes from 27 articles published in thirteen accredited journals in the Sinta 1 and Sinta 2 category by the Ministry of Research, Technology and Higher Education of the Republic of Indonesia as an achievement for review journals, which have excellent management and publication quality. The findings indicated that nine categories were identified in this study, including the PISA articles dominance, the development of PISA model math problems, PISA research and subjects, the research methods, the content and context, students' abilities, and the level of the questions. Lastly, this research contribution also is intended to guide future PISA researchers in determining PISA research trends and the following PISA research opportunities in Indonesia.

RevGadgets: an R Package for visualizing Bayesian phylogenetic analyses from RevBayes

1. Statistical phylogenetic methods are the foundation for a wide range of evolutionary and epidemiological studies. However, as these methods grow increasingly complex, users often encounter significant challenges with summarizing, visualizing, and communicating their key results. 2. We present RevGadgets, an R package for creating publication-quality figures from the results of a large variety of phylogenetic analyses performed in RevBayes (and other phylogenetic software packages). 3. We demonstrate how to use RevGadgets through a set of vignettes that cover the most common use cases that researchers will encounter. 4. RevGadgets is an open-source, extensible package that will continue to evolve in parallel with RevBayes, helping researchers to make sense of and communicate the results of a diverse array of analyses.