Discover the most talked about and latest scientific content & concepts.

Concept: Software documentation


Investing in documenting your bioinformatics software well can increase its impact and save your time. To maximize the effectiveness of your documentation, we suggest following a few guidelines we propose here. We recommend providing multiple avenues for users to use your research software, including a navigable HTML interface with a quick start, useful help messages with detailed explanation and thorough examples for each feature of your software. By following these guidelines, you can assure that your hard work maximally benefits yourself and others.

Concepts: Technical communication, Documentation, Software documentation


To explore how communication failures occur in documents and documentations across the perioperative pathway in nurses' interactions with other nurses, surgeons and anaesthetists.

Concepts: Surgery, Information science, Documentation, Software documentation


Endoscopic documentation software can generate research data on large numbers of subjects automatically. There are increasing numbers of published studies based on endoscopic databases such as the Clinical Outcomes Research Initiative. However, no study has yet validated such data. We compared colonoscopic findings reported by an endoscopic documentation software (Provation) against manually collected medical records data from two similar patient cohorts in the same endoscopy unit.

Concepts: Database, Validation, Colonoscopy, Cultural studies, Rectum, Endoscopy, Computer software, Software documentation


pViz.js is a visualization library for displaying protein sequence features in a web browser. By simply providing a sequence and the locations of its features, this lightweight yet versatile JavaScript library renders an interactive view of the protein features. Interactive exploration of protein sequence features over the web is a common need in Bioinformatics. Although many websites have developed viewers to display these features, their implementations are usually focused on data from a specific source or use case. Some of these viewers can be adapted to fit other use cases but are not designed to be reusable. pViz makes it very easy to display features as boxes aligned to a protein sequence with zooming functionality but also includes predefined renderings for secondary structure and post-translational modifications. The library is designed to further customize this view. We demonstrate such applications of pViz using two examples: a proteomic data visualization tool with an embedded viewer for displaying features on protein structure, and a tool to visualize the results of the variant_effect_predictor tool from Ensembl. Availability: pViz.js is a JavaScript library, available on github at This site includes examples and functional applications, installation instructions and usage documentation. A Readme file, which explains how to use pViz with examples, is available as Supplementary Material A.

Concepts: Protein, Protein structure, Bioinformatics, Amino acid, Primary structure, World Wide Web, Web browser, Software documentation


ProVation Medical documentation software was introduced in our Department of Gastroenterology (GI). We evaluated the use of a simulation module to improve the introduction of new documentation software into a tertiary care center GI department.

Concepts: Health care, Medicine, Engineering, Tertiary referral hospital, Introduction, Computer software, Software, Software documentation