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Challenges and recommendations to improve installability and archival stability of omics computational tools

https://doi.org/10.1101/452532
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/bmb.2003.494031010165openalex-snapshot
“Link rot” limits the usefulness of web‐based educational materials in biochemistry and molecular biology*
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Challenges and promises for translating computational tools into clinical practice
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The life and death of URLs in five biomedical informatics journals
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How to make replication the norm
inferredcites →https://doi.org/10.1038/nbt.2721openalex-snapshot
The anatomy of successful computational biology software
inferredcites →https://doi.org/10.1038/nmeth.2073openalex-snapshot
A call for bioimaging software usability
inferredcites →https://doi.org/10.1038/nmeth.3996openalex-snapshot
Database under maintenance
inferredcites →https://doi.org/10.1038/s41592-018-0046-7openalex-snapshot
Bioconda: sustainable and comprehensive software distribution for the life sciences
inferredcites →https://doi.org/10.1073/pnas.1708290115openalex-snapshot
An empirical analysis of journal policy effectiveness for computational reproducibility
inferredcites →https://doi.org/10.1080/10438590290004555openalex-snapshot
The impact of public R&D expenditure on business R&D*
inferredcites →https://doi.org/10.1080/10919390701294012openalex-snapshot
Digital Preservation: Organizational Commitment, Archival Stability, and Technological Continuity
inferredcites →https://doi.org/10.1093/bib/bbs086openalex-snapshot
A survey of tools for variant analysis of next-generation genome sequencing data
inferredcites →https://doi.org/10.1093/bib/bbv018openalex-snapshot
Adapting bioinformatics curricula for big data
inferredcites →https://doi.org/10.1093/bib/bbw134openalex-snapshot
Top considerations for creating bioinformatics software documentation
inferredcites →https://doi.org/10.1093/bib/bbx159openalex-snapshot
A snapshot of 3649 Web-based services published between 1994 and 2017 shows a decrease in availability after 2 years
inferredcites →https://doi.org/10.1093/bioinformatics/btn127openalex-snapshot
URL decay in MEDLINE—a 4-year follow-up study
inferredcites →https://doi.org/10.1093/bioinformatics/bts605openalex-snapshot
Tools for mapping high-throughput sequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/btw284openalex-snapshot
Bioinformatics programs are 31-fold over-represented among the highest impact scientific papers of the past two decades
inferredcites →https://doi.org/10.1093/bioinformatics/btx192openalex-snapshot
BioContainers: an open-source and community-driven framework for software standardization
inferredcites →https://doi.org/10.1093/nar/gkx182openalex-snapshot
Use it or lose it: citations predict the continued online availability of published bioinformatics resources
inferredcites →https://doi.org/10.1098/rsos.170344openalex-snapshot
Task allocation and site fidelity jointly influence foraging regulation in honeybee colonies
inferredcites →https://doi.org/10.1126/science.1088234openalex-snapshot
Going, Going, Gone: Lost Internet References
inferredcites →https://doi.org/10.1186/1472-6947-8-23openalex-snapshot
An update on Uniform Resource Locator (URL) decay in MEDLINE abstracts and measures for its mitigation
inferredcites →https://doi.org/10.1186/gb-2004-5-10-r80openalex-snapshot
Bioconductor: open software development for computational biology and bioinformatics
inferredcites →https://doi.org/10.1186/gb-2014-15-3-r42openalex-snapshot
A comprehensive evaluation of assembly scaffolding tools
inferredcites →https://doi.org/10.1186/s13059-015-0702-5openalex-snapshot
Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data
inferredcites →https://doi.org/10.12688/f1000research.11407.1openalex-snapshot
Four simple recommendations to encourage best practices in research software
inferredcites →https://doi.org/10.12688/f1000research.3681.1openalex-snapshot
Developing sustainable software solutions for bioinformatics by the “Butterfly” paradigm
inferredcites →https://doi.org/10.1371/journal.pbio.1002195openalex-snapshot
Big Data: Astronomical or Genomical?
inferredcites →https://doi.org/10.1371/journal.pbio.2002050openalex-snapshot
All biology is computational biology
inferredcites →https://doi.org/10.1371/journal.pcbi.0020087openalex-snapshot
Scientific Software Development Is Not an Oxymoron
inferredcites →https://doi.org/10.1371/journal.pcbi.1002802openalex-snapshot
Ten Simple Rules for the Open Development of Scientific Software
inferredcites →https://doi.org/10.1371/journal.pcbi.1003376openalex-snapshot
Current Practice in Software Development for Computational Neuroscience and How to Improve It
inferredcites →https://doi.org/10.1371/journal.pcbi.1004947openalex-snapshot
Ten Simple Rules for Taking Advantage of Git and GitHub
inferredcites →https://doi.org/10.1371/journal.pcbi.1005265openalex-snapshot
Ten Simple Rules for Developing Usable Software in Computational Biology
inferredcites →https://doi.org/10.3389/fgene.2014.00199openalex-snapshot
On best practices in the development of bioinformatics software
inferredcites →https://doi.org/10.6028/nist.fips.202openalex-snapshot
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What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/978-981-16-7893-6_11openalex-snapshot
Management of Next-Generation Sequencing in Precision Medicine
inferred← citeshttps://doi.org/10.1007/s12038-019-9930-2openalex-snapshot
Microbiome data science
inferred← citeshttps://doi.org/10.1038/s41587-019-0071-9openalex-snapshot
A comparison of single-cell trajectory inference methods
inferred← citeshttps://doi.org/10.1057/s41599-025-04716-zopenalex-snapshot
Predicting the longevity of resources shared in scientific publications
inferred← citeshttps://doi.org/10.1101/482380openalex-snapshot
PUMA: A tool for processing 16S rRNA taxonomy data for analysis and visualization
inferred← citeshttps://doi.org/10.1101/649368openalex-snapshot
Exautomate: A user-friendly tool for region-based rare variant association analysis (RVAA)
inferred← citeshttps://doi.org/10.1109/ccgrid.2019.00028openalex-snapshot
Reproducible Scientific Workflows for High Performance and Cloud Computing
inferred← citeshttps://doi.org/10.11606/t.55.2019.tde-15102019-145225openalex-snapshot
Computational methods in Biology: cancer biomarkers, protein networks and lateral gene transfer
inferred← citeshttps://doi.org/10.1186/s12859-019-2781-xopenalex-snapshot
Computational enhancer prediction: evaluation and improvements
inferred← citeshttps://doi.org/10.1186/s13059-019-1649-8openalex-snapshot
Improving the usability and archival stability of bioinformatics software
inferred← citeshttps://doi.org/10.1186/s13059-019-1738-8openalex-snapshot
Essential guidelines for computational method benchmarking
inferred← citeshttps://doi.org/10.1186/s13059-019-1763-7openalex-snapshot
Challenges in funding and developing genomic software: roots and remedies
inferred← citeshttps://doi.org/10.14806/ej.29.0.1037openalex-snapshot
Ds-Seq: an integrated pipeline for in silico small RNA sequence analysis for host-pathogen interaction studies
inferred← citeshttps://doi.org/10.3389/fbioe.2018.00198openalex-snapshot
GitHub Statistics as a Measure of the Impact of Open-Source Bioinformatics Software
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