In undergraduate theses, a good methodology section should describe the series of steps that were followed in performing the research. To assist students in this task, we develop machine-learning models and an app that uses them to provide feedback while students write. We construct an annotated corpus that identifies sentences representing methodological steps and labels when a methodology contains a logical sequence of such steps. We train machine-learning models based on language modeling and lexical features that can identify sentences representing methodological steps with 0.939 f-measure, and identify methodology sections containing a logical sequence of steps with an accuracy of 87%. We incorporate these models into a Microsoft Office Add-in, and show that students who improved their methodologies according to the model feedback received better grades on their methodologies.