That’s a graph automatically generated by the cell signalling pathway simulation automation software I developed over the winter break. It’s a bit ugly — a quick and dirty CDF rendered in R of activation times of ERK in the TCR (T-Cell Receptor) pathway model for a particular endogenous pMHC ligand dosage. Fancy lingo, eh?
The past several weeks I participated in CMACS, an NSF-funded program intended to get undergrads to go on to grad school. You mean I’m not in grad school yet? Oh, right. More on CMACS later. I joined the Treespace research group at Lehman, where I’ll be expanding on my limited knowledge of phylogenetics and drawing some pretty graphs with Java, Python, and Cytoscape. I continue to be involved at Hunter with the EvoBioLab where I’m reading up on bacterial recombination and mutation and working on genomic visualization tools. The hackerspace I started back in September is thriving, with fifteen paying members, and we just filled up a 100 seat event we’re hosting at the NYPL. I’m working on organizing an iGEM team at Hunter and looking into starting some of that work at Genspace — we already have a rather nice team lineup. I hope to continue the work I started this past summer with my esteemed colleague James Estill. Yes, I’ll be taking some classes, too. Organic chemistry included. What, me nervous? Back to CMACS…
We looked at cell signalling pathways in cancer using stochastic simulations in BioNetGen. I got a bit carried away automating experiments and created ScanBatch. This new tool I whipped up runs arbitrary numbers of simulations over arbitrary numbers of models, species (molecule types), and concentrations of those species. To my delight, I’ve been asked to contribute ScanBatch to the BioNetGen project and continue work on it to expand the automated simulation capabilities. I’ll be working on accepting more complex parameter ranges, templating the simulation code, doing more complex combinations of parameters, validating model output, and making large batches of simulations scale. It’s an honor to be asked to help take such a cool piece of cutting edge research software to the next level. I look forward to working with Dr. Jim Faeder and co. on this. I’m digging Systems Biology!
If everything I’m working on pans out, I can expect to see my name on a few papers next year, which would be concrete proof that this whole scientist thing is really happening. I’ve been getting paid to do science related work since June 2011, and it’s a good feeling that this trend is ongoing. It was only months before that I threw down the gauntlet and challenged myself to do only science work. I’m feeling a strong pull towards systems and synthetic biology, but I may be biased since I’m a computer programmer, and the field seems to be especially welcoming towards my kind right now. I hope you, my friends, family, and colleagues, have had a wonderful and imagination-catalyzing winter so far.
PS. Convergence of ideas: Bacterial evolution simulation at EvoBioLab, Bacterial recombination as engine for computation in-vivo for combinatorial problems. Bacterial evolution of whole genomes plus gene expression simulation via BioNetGen. Visualization of genomic data, visualization of phylogenetic data, visualization of cell pathway data. DNA fingerprinting, DNA computing, cryptography and digital security. Okay, now I can sleep.
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[...] chemical diffusion as the engine of life since the workshop. CMACS has been amazing for me, between what I got to do last year, and all the people I met and ideas I was exposed to this [...]