What tools exactly are you using in Node and Python? Python has a nice data analysis tool Pandas(http://pandas.pydata.org/) which would help with your task of generating multiple permutations of your data. Check out plot.ly to visualize the data (it integrates well with a pandas pipeline from experience); It would also help if you mentioned exactly what kind of visualizations you're looking to create from the data.
I had similar issues when doing research in computer science, and I feel a lot of researchers working with data have this headache of organizing, visualizing and scaling their infrastructure along with versioning data and coupling their data with code. Also adding more collaborators to this workflow would be very time consuming...
With regards to your issue of scale, this might help: http://stackoverflow.com/questions/14262433/large-data-work-...
I had similar issues when doing research in computer science, and I feel a lot of researchers working with data have this headache of organizing, visualizing and scaling their infrastructure along with versioning data and coupling their data with code. Also adding more collaborators to this workflow would be very time consuming...