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I am adding another answer here since this is the kind of resource I was originally looking for. The Journal of Inquiry Based Learning has a book on mathematical modelling. The abstract says the following: This is a set of notes for a one semester course in Mathematical Modeling. The topics covered are difference equations, Markov chains, Monte Carlo ...


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A great example in this vein is Lorena Barba's CFDPython also known as "12 Steps to Navier Stokes", which consists of a sequence of jupyter notebooks that go from really basic numerical analysis up through more complex problems.


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One project I have discovered since I initially asked this question is the following: https://projectlovelace.net/ It is still a work in progress, but is building up a set of problems that can aid in learning computational science. For a similar resource that focuses primarily on bioinformatics we have Rosalind: http://rosalind.info/problems/locations/


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