Model the Cell? A Cell API

I have been thinking of a way to programatically model the human cell for a while now and my thoughts were recently reignited after I read this post.

At a very basic level, I imagine an interface where a cell object can be initialized and passed various methods – to modify cellular components or run cellular functions. Consider the following code snippet:

SkinCell cell = new Cell();

    protein_A = cell.translate(chromosome 12, gene 56);
    visualize protein_A;


//load protein_A via HTML5 App


   protein_A.phosphorylate(C56); //Phosphorylate at carbon 56
   visualize protein_A;

Imagine inducing a genetic mutation at a specific loci via code instead of going through the difficulty of doing such in a lab on actual cells. Then, calling a function to visualize the modified, translated protein or calling a function to see how this new molecule reacts with other molecules.

Instead of turning to the lab to understand cellular functions, we could turn to our computers. Of course, to model the cell completely or accurately would be arguably impossible. There are too many unknown unknowns in cellular biology currently and probably will be in the foreseeable future. Further, calculating the result of interactions between n molecules would become extremely resource intensive once the number of molecules in this cell became larger than n – without making certain assumptions. We still can’t accurately model the folding of proteins, let alone the complex interactions of multiple proteins.

But nonetheless, let’s start somewhere. And I understand that these kind of domain-specific languages already exist – actually probably a ton already exist. But I don’t see any web API’s where we could leverage the increasing number of HTML5 webapps available for biologists. Further, a web API would call for a more centralized cloud-based development effort and increased open source contributions. Watch out for a future post for a prototype of this API.

Oh yeah – an awesome post of DNA seen through the eyes of a coder.

- Ariq