Teachers seek to create moments when students demonstrate their understanding of knowledge or skills and teachers provide feedback, known as formative assessment. Pen and touch input, in combination with apps that support digital ink and virtual manipulation, allow students to express their knowledge in more varied and natural ways, improving formative assessment and subsequent differentiation of instruction. Teachers and students at University Prep (Seattle) have used digital ink and virtual manipulation to increase the flexibility of formative assessment in a variety of subject areas. General purpose apps for writing, drawing, and making explainer videos have gained adoption more quickly at U Prep than subject specific learning apps that use a very specific pedagogical model. This paper describes the conceptual basis for our work with formative assessment, shares examples of student use of digital ink and virtual manipulation, and identifies themes among these examples.