ArticlePLoS biology2019
Challenges and recommendations to improve the installability and archival stability of omics computational tools.
Article in PLoS biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 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
54 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Packaging and containerization of computational methods.Nature protocols · 2024Pooled it
- Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability.Genome biology · 2023Pooled it
- OpenChallenges: A FAIR-aligned, centralized platform for crowdsourced challenges in biomedical research.Patterns (New York, N.Y.) · 2026Article
- Designing reproducible large-language-model-assisted scientific analyses.Patterns (New York, N.Y.) · 2026Review
- A scoping review of approaches to evaluating workflow management systems for bioinformatics users.Briefings in bioinformatics · 2026Article
- Towards a decentralized future for open-science databases.Nature genetics · 2026Article
- ScriptManager: a platform for scalable and reproducible high-resolution analysis of genomics datasets.bioRxiv : the preprint server for biology · 2026Article
- Fifteen Years of the Genome Analysis Toolkit as the De Facto Standard in Short-Read Variant Calling.International journal of molecular sciences · 2026Review
- A multi-agent platform for assessment and improvement of bioinformatics software documentation.bioRxiv : the preprint server for biology · 2026Article
- Profiler: an open web platform for multi-omics analysis.Bioinformatics (Oxford, England) · 2026Article
- How benchmarking of bioinformatics tools is essential for informed workflow selection: a case study on SARS-CoV-2 subgenomic RNA detection.Frontiers in bioinformatics · 2026Article
- BIWT: a bioinformatics walkthrough for embedding spatial multiomics in agent-based models for virtual cells.Bioinformatics (Oxford, England) · 2025Article
- FitFoldData: A Web-Based Toolkit for Circular Dichroism and Differential Scanning Calorimetry Data Analysis of Protein Thermal Denaturation.ACS omega · 2025Article
- clonevdjseq: A workflow and bioinformatics management system for sequencing, archiving, and analysis of VDJ sequences from clonal libraries.BMC bioinformatics · 2025Article
- Causeway: a pipeline for genome-wide effector gene screening with Mendelian Randomization and colocalization.Bioinformatics advances · 2025Article
- findWormz is a user-friendly automated fluorescence quantification method formicroPublication biology · 2025Article
- A how-to guide for code sharing in biology.PLoS biology · 2024Review
- Review
- Genomic reproducibility in the bioinformatics era.Genome biology · 2024Review
- A comparative benchmarking and evaluation framework for heterogeneous network-based drug repositioning methods.Briefings in bioinformatics · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
17 authors.
Funding
Abstract
Developing new software tools for analysis of large-scale biological data is a key component of advancing modern biomedical research. Scientific reproduction of published findings requires running computational tools on data generated by such studies, yet little attention is presently allocated to the installability and archival stability of computational software tools. Scientific journals require data and code sharing, but none currently require authors to guarantee the continuing functionality of newly published tools. We have estimated the archival stability of computational biology software tools by performing an empirical analysis of the internet presence for 36,702 omics software resources published from 2005 to 2017. We found that almost 28% of all resources are currently not accessible through uniform resource locators (URLs) published in the paper they first appeared in. Among the 98 software tools selected for our installability test, 51% were deemed "easy to install," and 28% of the tools failed to be installed at all because of problems in the implementation. Moreover, for papers introducing new software, we found that the number of citations significantly increased when authors provided an easy installation process. We propose for incorporation into journal policy several practical solutions for increasing the widespread installability and archival stability of published bioinformatics software.
Indexed as
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What OpenQuestion holds
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.