You can also easily add it to existing chatbots like Claude Desktop, VS Code and others. Find out how in our README: github.com/biocontext-a...

If you would like to explore how MCP servers might be helpful for your work, we provide a reference server called "Knowledgebase MCP" that integrates UniProt, STRING, PRIDE, InterPro, ClinicalTrials, EuropePMC and many more sources. You can start chatting at: biocontext.ai/chat

Preprint alert 🚨 Do you use chatbots in your work or even build MCP servers and agentic systems yourself?

Or would you like to find a way to use biomedical tools using natural language?

Then check out biocontext.ai, now out on bioRxiv: www.biorxiv.org/content/10.1...

And even before histologically or clinically detectable disease, PathoPlex was able to detect several changes at the molecular level in young adults with early-onset type 2 diabetes and profile the effect of SGLT2i administration on renal metabolism and signalling.

In a cohort of patients with advanced diabetic kidney disease, our antibody panel of 61 markers led to the identification of tubular calcium signalling as a potential target for pharmacological intervention 💊

In a multimodal cross species validation experiment guided by PathoPlex, we were able to characterize pJUN mediated signalling in PECs as a key feature of disease.

A key use case unlocked by spatiomic is pixel-level clustering of protein co-expression patterns. This not only looks beautiful, but combined with confocal microscopy also enables truly subcellular image analysis 🖥️

On the image analysis side, we developed a new GPU-accelerated Python package termed "spatiomic". It is available through PyPi with documentation and a full example notebook available at: spatiomic.org
Code is available at: github.com/complextissu...

Our imaging protocol builds on 4i (Gut et al., 2018) but scales it to > 100 proteins in pathology specimens. We optimise tissue stability through the use of APTES as a coating agent and achieve high throughput through 3D-printed tissue chambers that can fit 40+ samples and prevent pipetting errors.

PathoPlex represents a flexible framework that leverages off-the-shelf antibodies and covers both multiplex imaging as well as image analysis at a subcellular resolution.
Let's go through the parts 🚀

Of course, you can also use pytximport from within Python with an easy-to-learn API. (8/12)

With pytximport and tools like fastp by Shifu Chen, kallisto by the @lpachter.bsky.social lab and gget by @lauraluebbert.com et al, running a bulk RNA-sequencing analysis is now a 10 line bash script. (7/12)

Coding in Python and looking to perform bulk RNA sequencing analysis? With pytximport recently published in Bioinformatics and version 0.11.0 out today with many improvements, it’s time for my first Bluetorial!

A thread 🧵 (1/12)