Step 9: Write the thesis.
If you have written one or more publications, with minor modifications you likely already have one or more thesis chapters. Go back to your rough thesis outline and fill it in with the methods you used and the results you have now. Write it similarly to the papers, starting with the rough outline, filling in rough drawn versions of figures, replacing drawn figures with preliminary versions of real figures, writing subsection outlines. Decide on any gaps that you'd like to fill. Fill in text - figure captions, introduction, abstract, text, references, acknowledgements, conclusions. Edit and reedit. Keep track of methods, data, and analysis used in the thesis. Submit to committee, defend, and graduate.