For simple organisms, we could probably consider what would happen if we put their DNA in the nucleas, letting it be transcribed by the 'standard' process. This is exactly what viruses do when they inject their DNA/RNA into a foreign cell so they will be cloned.
A few links for the interested: https://en.wikipedia.org/wiki/Developmental_biology http://en.wikipedia.org/wiki/Epigenetics
That said, there has been quite an exciting paper published around a year ago describing the first simulation of one life cycle of an in silico Mycoplasma genitalium (the smallest known bacteria). Here's a link to relevant HN discussion: https://news.ycombinator.com/item?id=4272039