[throwawayjava]

There is no one answer. The answer will change drastically depending on the sort of research you're doing, and your role in that research.

Are you a mathematician simulating a dynamical system? A theoretical computer scientist exploring the effects of parameters that are difficult to nail down analytically?

Are you a computer scientist working on a new sort of system? Is the point of that system to support a long-running research agenda, or to demonstrate the feasibility of a general notion/idea?

Or are you a software engineer supporting a natural scientist (e.g., in a large bio/neuro/chem/physics lab)?

Are you the PhD student, the research scientist, the supporting engineer, or the PI?

But in any case, the correct answer will start with interrogating the purpose/role of the software in your research project. And that answer could range from "hack out the MATLAB and sanity check" all the way to "lives are on the line; practice extreme rigor". And certainly not excluding "convince your funding agency/PI that it's time to hire a professional"!