Abstract : A rigorous scientific methodology has to follow a number of supposedly well-known principles. These principles come from as far as the ancient Greece where they started to be established by Philosophers like Aristotle; later noticeable contributions include principles edicted by Descartes, and more recently Karl Popper. All disciplines of modern Science do manage to comply with those principles with quite some rigor. All ... Except maybe when they come to computer-based Science. Computer-based Science should not to be confused with the Computer Science discipline (a large part of which is not computer-based); It designates the corpus of scientific results obtained, in all disciplines, by means of computers, using in-silico experiments, and in particular computer simulations. Issues and flaws in computer-based Science started to be regularly pointed out in the scientific community during the last decade. In this talk, after a brief historical perspective, I will review some of these major issues and flaws, such as reproducibility of results or reusability and traceability of scientific software material and data. Finally I will discuss a number of ideas and techniques that are currently investigated or could possibly serve as part of candidate solutions to solve those issues and flaws.