I am a bit unclear about what exactly you want to do, though I am sure that something that fits what I think you are wanting can be done.
Do you want some code that runs outside of the specified notebook to do the processing or do you want the code to be within the notebook itself?
Either way, this might not be trivial (but see my final comments below where a simplified approach may be workable depending on the particular workflow you have). It generally involves using notebook programming constructs to move around in the notebook and to execute the particular cells as desired. To execute cells from code that is controlling that execution you will need the function NotebookEvaluate and one would then find particular cells in the original notebook, create a temporary notebook with those cells, and execute the temporary notebook with NotebookEvaluate. Finding those cells may involve using NotebookFind using CellTags and having the original notebook's cells properly tagged. (See http://library.wolfram.com/infocenter/Conferences/7246/ for more than you may ever want to know about tagging.... ).
Another approach is to, at the end of each Input cell in your notebook, have code that uses NotebookFind and then SelectionEvaluate as the final expressions in that cell which points (via CellTags) to the next cell in the notebook (wherever it is) that should be executed.
Perhaps there are other approaches which may work, depending on the detailed particulars of what you want to do.
Finally, it may simply be that you want to (a) specify the data source that you want to access prior to each time you want to fully execute the notebook and then (b) execute the notebook. If this is the case then, if we call the notebook's NotebookObject nb(assumed for this discussion to be an open notebook), the form of the code you would create and which would be executed from a different notebook would be
Do[
(
assignExternalDataSourceParameters[i];
NotebookEvaluate[nb];
),
{i, 1, nIterations}]
where assignExternalDataSourceParameters[i] just represents the code that does the assignment of the needed data source locations (e.e., file names) in order for your notebook to run for those.
