They will look at your cumulative GPA including all the courses you took while in undergrad, including community college. This is why they have you send in each transcript from every institution you have attended. I had taken 5 courses at a community college,(dual enrollment during high school, courses that were too full or at an inconvenient time at my home institution)two of which were science prerequisites.They asked me about them during my interview at Nova.. but because I had gotten A's in both Biology I and II it was not an issue.
Science GPA is also typically cumulative because almost all of the major prerequisite courses, save biochem, are 2000 level courses. Assuming you took some of your pre-req's at the community college on behalf of their intro-level course numbering, they will definitely be factored into your science GPA.
