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Some results from running MAGMA locally. Both gene based and gene-set analysis using the above method on each of the DecodeME GWAS subgroups against the full Molecular Signatures Database Human Collections release 2025.1 (MSigDB 2025.1.Hs). Please bear in mind this method differs from the way...

Something I’ve only really started to appreciate going through this process is quite what is being done and quite how clever and meaningful it is… and how those dismissing it are showing their own ignorance and how their ideas about genetics are decades out of date. I’m still pretty ignorant...

Looks interesting! Not sure what sort of computing power it would require… It does use a python library for doing liftover though, which looks interesting! https://pypi.org/project/pyliftover/

I’ve gained a whole new level of appreciation for what you and other people in bioinformatics do.…

As mentioned above, something @forestglip and I have been working on recently is running MAGMA locally on the DecodeME summary statistics. I wouldn’t necessarily recommend anyone do this or follow these instructions. There may be things wrong with this method and it seems to end up with only...

Thanks @Chris Ponting I look forward to seeing what more there is to come and echo @Hoopoe in thanking you and the rest of the team, for all you’ve done so far. The more I’m learning the more possibilities and scope there seems to be, exciting times! Really useful answers in general but also in...

Absolutely. The efficiency improvements have been huge. That small local models can do what huge models used to be needed for and that the big players are pushing on efficiency even on their larger models to reduce costs seems far more significant that any imagined progress towards AGI. But the...

I was reading this the other day and it is entertaining in some ways but highlights a number of the ways LLMs struggle. https://www.anthropic.com/research/project-vend-1 A positive read could be that they feel they can fix these issues. But I think it also shows how much the earlier points made...

I thought I made the distinction in my posts and think it’s pretty clear? It also seems most likely that LLMs will stick around in some form but perhaps as the human interface to other forms of AI/ML, that’s what they’re most suited to after all. The scaling stuff for LLMs has always been a...

I’m finding understanding the science and statistics of things like GWAS studies far from immediately intuitive so I can understand people getting it wrong. What I can’t understand is how confidently people speak on it or how little curiosity they have it trying to understand it. How did they...

Oh thanks for this! I was just listening to this one from the same institute MPG Primer: Genome-Wide Association Studies (GWAS): A Refreshed Perspective (2024)

Like @forestglip and @ME/CFS Science Blog I’ve spent some time digging into some tools including magma/fuma and annovar. And learnt a bit about the myriad hurdles and technical issues bioinformatics students and researchers must live with. After a week much of my understanding is likely way off...

Nope! It’s starting in September or October I think. There was some engagement from those running it on the members only advocacy planning forum.

Fever is definitely not part of my illness or PEM. I’ve sometimes (not frequently) felt like I may have a temperature, even had that same sort of weird feeling you can get when feverish, but whenever I’ve measured (digital thermometer under the tongue) my temperature has been around or under...

It’s my big concern for any drug trials. We don’t have any drs that can look after us now so trusting them to do in a trial seems… a hurdle we need to fix.

Not sure if this has been posted but PrecisionLife posted a response to the Delivery Plan https://precisionlife.com/blog-supporting-progress-in-mecfs-and-the-patients-still-waiting

A couple of links from PrecisionLife on this Details of their attendance at the World Congress on Endometriosis conference in May https://precisionlife.com/news-and-events/wce2025 And more informatively information on “Characterizing the genetic and biological differences between endometriosis...

I feel similarly to you @Sasha but then again companies like PrecisionLife seem to think otherwise. It will be interesting to see if their analysis of the DecodeME data backs up what they’ve said and found in the past or not.

I hadn’t heard about it and it seems pretty unmanageable for many. Especially over the summer months when many severe people struggle even more. Seems a long way from the great engagement from the people running the AfME survey.

These tools can make great leaps, and do things unexpected and new, the example of AlphaGo is a great one for this. As is I think things like protein folding or the maths challenges. It requires very specific domains with clear rules and concepts of what is ‘correct’ as well as the ability to...