Lmst

The Institute - Chapter II: Tipping Points.

A discussion on systems, complexity, and tipping points.

https://open.substack.com/pub/pcnmartin/p/tipping-points?r=2k3tin&utm_campaign=post&utm_medium=web&showWelcomeOnShare=true

Getting structurally homogenous spatial samples is often challenging.

We developed a method to map the spatial context of cells between heterogenous samples gaining insights into development and patient sub-populations!

#SpatialBiology #scRNA #compbio

https://www.biorxiv.org/content/10.1101/2024.08.31.610638v1

Patrick Martin boosted:

I might as well have make a pinned post.

We published Vesalius a tool that uses Image analysis methods to analyze spatial-omics data.

A new version will be coming soon that will include multimodal analysis and alignment!

GitHub: https://patrickcnmartin.github.io/Vesalius/

MSB: https://www.embopress.org/doi/full/10.15252/msb.202211080

#SpatialTranscriptomics #ImageAnalysis

Patrick Martin boosted:

Introducing The Institute: A fictional research institute which explores things I find interesting in the fields of philosophy, society, and science. Mainly science.

Chapter I: Reorganize the social network.

https://open.substack.com/pub/pcnmartin/p/reorganize-the-social-network?r=2k3tin&utm_campaign=post&utm_medium=web&showWelcomeOnShare=true

Introducing The Institute: A fictional research institute which explores things I find interesting in the fields of philosophy, society, and science. Mainly science.

Chapter I: Reorganize the social network.

https://open.substack.com/pub/pcnmartin/p/reorganize-the-social-network?r=2k3tin&utm_campaign=post&utm_medium=web&showWelcomeOnShare=true

@researchbuzz

An interesting read and initiative!

@JMarkOckerbloom

Yes - preprint are very common in my field but they come with their own set of challenges. They often serves as ways to say: I was here first! A lot of papers come half baked.

I guess that the challenge is providing a better alternative in practice rather than just a "good idea".

I will at least contribute to wikipedia summary pages.

@JMarkOckerbloom

What are your thoughts as to why they haven't taken off?

@JMarkOckerbloom

Yes, the message went through and thank you for your feedback.

As I said over there, it's a shame since Wikipedia is already there and well known. I hope at least that a similar concept can emerge for new research.

@woozle @researchbuzz

By all means! But zero pressure.

I am currently at the stage of gaging interest and seeing who would be interested in this idea among academics in my field. It's not an easy sell for a lot people I know...

@woozle @researchbuzz

Tell me about it... I have been thinking about this for years as well.

Hopefully, one day, I can convince enough people to donate to get this off the ground

@woozle @researchbuzz

That is a good point. It is my worry as well. I have reviewed enough papers to know
that many constitute noise rather than findings.

With that said, the conclusions/consensus-reality part would be done in "higher order pages". The contribution of a single experiment - say a sequencing run of specific gene - does not need a conclusion to performed and linked to the platform.

The scientific process would remain similar but data presentation and access would change.

@independentpen @researchbuzz

My main hope is that none of this is set in stone. Wikipedia could play that role. Sure the current platform is not suitable for it but we can imagine that things would change.

@woozle @researchbuzz

It's a shame since it would have been nice to build upon what is already there. But if the software is easy enough to develop...

Yes the goal is to shift towards publication and peer-review of science in a more open way. And a more human centric way. Ultimately, the data would't need to be fully hosted by the website. Raw data can still be hosted by the usual repositories. As long as we can see what is underlying the finding

What if we contributed to Wikipedia instead of publishing papers?
An unhinged essay that I have finally put together!

#Academia #Publishing #Wikipedia #Research #academicWriting

https://pcnmartin.substack.com/p/what-if-we-contributed-to-wikipedia