Discussion by Manu Leonetti at Chan Zuckerberg hub.
Self driving cars are taught in simulation. Similar biology should be also done as simulations. The cell needs to be thought as devices. How does information flow within a cell and do that in cells. Use GFP to tag the cells but also later use it for finding protein – protein interaction.
Opencell.czbiohub.org
organelle.czbiohub.org
This is a wiring diagram of the proteome. These experiments take a long time to do…since they are done 1 t a time. Coarse graining cellular representations with organelle profiling: mesoclale polifilng ath the organelle level.
The organelle becomes biomarkers of the cellular state.
Later do morphological analysis of whole organelle by Mass Spectrometry…
Pan-cellular organelle collection. This generalizes 30 different protein markers for different organelles.
Human stem cell generalization is in progress.
Analysis by Graph based analytical strategy (cf scRNASeq). Clusters correspond to organelles. This is UMAP version that can be browsed on the web and can show a graph with relationships and complexes and proteins that are next to each other are close together on the graph.
This can be seen remodeled in a OC43B-coronavirus infection. (infection vsn noon-infected).
Cells either move things around or by abundance changes. Subcellular remodeling reveals cellular responses not captured by abundance changes. They found link between ferroptosis and viral infection.
This data is AI ready.
czbiohub-sf/grassp. MAX FRANK. AI-ready subcellular proteomics. All the code is on github.
How is cell a basic unit of biological computation – They are non-linear dynamic system. Need to know the starting state – to use dynamic data.
In imaging – interpretability is hard (Imagine if we could watch cells think).
Multi-modality – imaging as a foundation for all the omics. Project all the molecular information to live cells.
AI interpreter for images that is learnt from omics embeddings.
High throughput optical screening platform…
How do you build generalizability? How do we go from cells → tissues ?
Imaging on the RNA molecules may also be possible.
