Most bioinformatics tools put software first and data second. GLUE does the opposite.
In this blog post (link in reply), I provide a plain-language explanation of its data-oriented philosophy, and why that matters for reproducible virology.
gluetools.substack.com/p/data-orien...
Genomics has a data rot problem.
Pipelines change. Alignments are regenerated. Assumptions disappear. Context is lost.
This post explains why GLUE was built around data immutability and durable scientific objects.
gluetools.substack.com/p/data-immut...
Comparative genomics generates results fast - but preserving the context needed to understand them over time is much harder.
I’ve written a perspective on GLUE as a long-lived, data-oriented knowledge base: projects as persistent scientific objects rather than disposable pipelines.
sl1nk.com/Y0O4H
Studying immune gene evolution is rarely about a lack of data, it’s about keeping data, biology, and interpretation aligned as everything changes.
New GLUE Genomics post: from viral genomes to immune genes, using interferon lambda as a case study.
gluetools.substack.com/p/glue-resou...
Recovery of viral RNA from centuries old human tissue is genuinely exciting.
This changes the horizons for recovery of ancient virus genomes.
Studying immune gene evolution is rarely about a lack of data, it’s about keeping data, biology, and interpretation aligned as everything changes.
New GLUE Genomics post: from viral genomes to immune genes, using interferon lambda as a case study.
gluetools.substack.com/p/glue-resou...
MLCA genotyping in GLUE is currently available for a range of viruses, including:
HCV, HBV, HEV, dengue, chikungunya, West Nile virus, yellow fever virus, rabies virus, and lentiviruses (SRLVs, EIAV).
I’ve just published a new Substack post explaining how MLCA genotyping works in GLUE, and how to run it yourself locally using Docker.
It covers the evolutionary logic behind MLCA and the practical workflow for using it.
gluetools.substack.com/p/how-mlca-g...
Great read! Congratulations @katarinazimmer.bsky.social on your insightful @knowablemag.bsky.social piece exploring the remarkable biology of the Aedes aegypti #mosquito knowablemagazine.org/content/arti...
As virus discovery accelerates, integrating new sequences meaningfully is becoming a central challenge.
Flavivirus-GLUE provides an open framework for multi-scale comparative genomic analyses of flaviviruses.
gluetools.substack.com/p/flavivirus...
HCV-GLUE is best known as a web-based tool for HCV genotyping and drug resistance analysis.
Less well known is that the same analysis can be run entirely offline and integrated into pipelines.
I’ve written a short guide on running HCV-GLUE offline using Docker and GLUE scripts.
shorturl.at/bvm3d
HCV-GLUE is best known as a web-based tool for HCV genotyping and drug resistance analysis.
Less well known is that the same analysis can be run entirely offline and integrated into pipelines.
I’ve written a short guide on running HCV-GLUE offline using Docker and GLUE scripts.
shorturl.at/bvm3d
Virus taxonomy increasingly rests on phylogenetic hypotheses, but the trees, alignments, and assumptions behind them are often ephemeral.
This post explores what it might look like to make that phylogenetic basis transparent and reproducible, using retroviruses as a case study.
shorturl.at/s9aft
The translational potential of bat immune traits is wildly overstated.
These aren’t modular switches we can port into humans;
They’re parts of tightly integrated systems that don’t travel.
www.sciencedirect.com/science/arti...
The Guardian frames a timing change for very low-risk infants as “limiting” vaccines.
ACIP didn’t restrict access or question safety, it shifted a universal 24-hour rule to shared decision-making.
When public-health advocates misstate the facts, it doesn’t protect trust. It erodes it.
These scary numbers appear to come from a maximalist population model, based on delaying the birth dose to exactly 2 months for all infants.
ACIP did not recommend:
- eliminating the vaccine
- delaying until 2 months
- delaying universally
- denying the birth dose to parents who want it
Gardening in the Viral Genome Wilderness:
Why virus genomics needs structure, not pipelines.
gluetools.substack.com/p/the-sequen...
Stellenbosch University Botanical Garden
- Presents a false paradox
- Recycles unsupported, unfalsifiable bat immunology narratives
- Conflates association with causation in outbreaks
- Relies on a small circle of experts
- Omits massive negative evidence
- Treats rumour as fact
- Applies mythic spectacle (bats as villains and saviours)
This article by Linda Geddes reproduces every structural flaw I described in my recent Substack essay.
Every narrative device, every logical inconsistency, and every evidentiary shortcut that sustains the ‘bat specialness’ story.
www.gavi.org/vaccineswork...
Most viral workflows are fragile pipelines.
GLUE turns them into structured, shareable projects: curated sequences, alignments, features, phylogenies, metadata & scripts all in one reproducible environment.
gluetools.substack.com/p/glue-a-fle...
"The hyperreal bat: more vivid, more coherent, and more narratively satisfying than any bat in nature."
Why does the idea of bats as special viral reservoirs endure?
New Substack post:
robertjgifford.substack.com/p/bats-and-v...
Grounded and thought-provoking reflections on LLMs.
Do you think that would also be the case here?
Weekly symptoms of infection doesn't sound particularly appealing to me.
www.newscientist.com/article/2492...
Complete ape genomes! 🦍🦧 Our closest relatives get the deluxe sequencing treatment, resolving the most complex & often most interesting parts of the genome.
Happy to make a tiny contribution alongside @panpan100.bsky.social to awesome teamwork & fantastic resource.
www.nature.com/articles/s41...
There is currently no approved vaccine for scarlet fever.
It appears my error was in devoting decades to virology rather than mastering Victorian literature and kitchen remedies. A humbling revelation—thank you for your service to science.
I don't think you're capable of a reasonable discussion.
Bye!!!
