My colleagues face fundamental problem with going from LaTeX to IPython notebook (=Markdown)

Plan.

I am used to write LaTeX paper/book-style with lots of cross-references and floating figures, code snippets, tables, algorithms, but now I want to convert to IPython notebooks.

Problem.

Must have fixed figures, code snippets, tables. No algorithm environment, cross-referencing, equation referencing. All code needed for a snippet to run must be included. It's a different writing style, but lots of new opportunities.