ArticleBriefings in bioinformatics2018
Top considerations for creating bioinformatics software documentation.
Article in Briefings in bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
30 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Assessment of the functionality and usability of open-source rare variant analysis pipelines.Briefings in bioinformatics · 2025Pooled it
- Evaluating LC-HRMS metabolomics data processing software using FAIR principles for research software.Metabolomics : Official journal of the Metabolomic Society · 2023Pooled it
- Nine quick tips for trustworthy machine learning in the biomedical sciences.PLoS computational biology · 2025Article
- Open-Source and FAIR Research Software for Proteomics.Journal of proteome research · 2025Review
- Harnessing artificial intelligence for engineering extracellular vesicles.Extracellular vesicles and circulating nucleic acids · 2025Review
- Gene signatures for cancer research: A 25-year retrospective and future avenues.PLoS computational biology · 2024Article
- ENCORE: a practical implementation to improve reproducibility and transparency of computational research.Nature communications · 2024Article
- Systematic evaluation with practical guidelines for single-cell and spatially resolved transcriptomics data simulation under multiple scenarios.Genome biology · 2024Article
- Ten quick tips for clinical electroencephalographic (EEG) data acquisition and signal processing.PeerJ. Computer science · 2024Article
- The good, the bad and the ugly of transposable elements annotation tools.Genetics and molecular biology · 2024Article
- Ten quick tips for fuzzy logic modeling of biomedical systems.PLoS computational biology · 2023Article
- Ten quick tips for harnessing the power of ChatGPT in computational biology.PLoS computational biology · 2023Article
- Ten quick tips for avoiding pitfalls in multi-omics data integration analyses.PLoS computational biology · 2023Article
- Ten quick tips for bioinformatics analyses using an Apache Spark distributed computing environment.PLoS computational biology · 2023Article
- Eleven quick tips for data cleaning and feature engineering.PLoS computational biology · 2022Article
- Nine quick tips for pathway enrichment analysis.PLoS computational biology · 2022Article
- Assessing and assuring interoperability of a genomics file format.Bioinformatics (Oxford, England) · 2022Article
- Documenting research software in engineering science.Scientific reports · 2022Review
- Software testing in microbial bioinformatics: a call to action.Microbial genomics · 2022Article
- Improving bioinformatics software quality through incorporation of software engineering practices.PeerJ. Computer science · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.