diff --git a/readme.md b/readme.md
index 907bd6b..d6e5db4 100644
--- a/readme.md
+++ b/readme.md
@@ -12,7 +12,7 @@ Unlike pairSEQ, which calculates p-values for every TCR alpha/beta overlap and c
 against a null distribution, BiGpairSEQ does not do any statistical calculations
 directly.
 
-BiGpairSEQ creates a [simple bipartite weighted graph](https://en.wikipedia.org/wiki/Bipartite_graph) representing the sample plate.
+BiGpairSEQ creates a [weightd bipartite graph](https://en.wikipedia.org/wiki/Bipartite_graph) representing the sample plate.
 The distinct TCRA and TCRB sequences form the two sets of vertices. Every TCRA/TCRB pair that share a well
 are connected by an edge, with the edge weight set to the number of wells in which both sequences appear.
 (Sequences present in *all* wells are filtered out prior to creating the graph, as there is no signal in their occupancy pattern.)
@@ -69,16 +69,26 @@ Please select an option:
 0) Exit
 ```
 
-### OUTPUT
+### INPUT/OUTPUT
 
 To run the simulation, the program reads and writes 4 kinds of files:
 * Cell Sample files in CSV format
 * Sample Plate files in CSV format
-* Graph and Data files in binary object serialization format
+* Graph/Data files in binary object serialization format
 * Matching Results files in CSV format
 
+These files are often generated in sequence. To save file I/O time, the most recent instance of each of these four
+files either generated or read from disk is cached in program memory. This is especially important for Graph/Data files,
+which can be several gigabytes in size. Since some simulations may require running multiple, 
+differntly-configured BiGpairSEQ matchings on the same graph, keeping the most recent graph cached drastically reduces 
+execution time. 
+
+Subsequent uses of the same data file won't need to be read in again until another file of that type is used or generated.
+The program checks whether it needs to update its cached data by comparing filenames as entered by the user. On 
+encountering a new filename, the program flushes its cache and reads in the new file.
+
 When entering filenames, it is not necessary to include the file extension (.csv or .ser). When reading or
-writing files, the program will automatically add the correct extension to any filename without one.
+writing files, the program will automatically add the correct extension to any filename without one. 
 
 #### Cell Sample Files
 Cell Sample files consist of any number of distinct "T cells." Every cell contains 
@@ -121,7 +131,7 @@ Options when making a Sample Plate file:
     * Standard deviation size 
   * Exponential
     * Lambda value
-      * (Based on the slope of the graph in Figure 4C of the pairSEQ paper, the distribution of the original experiment was exponential with a lambda of approximately 0.6. (Howie, et al. 2015))
+      * *(Based on the slope of the graph in Figure 4C of the pairSEQ paper, the distribution of the original experiment was exponential with a lambda of approximately 0.6. (Howie, et al. 2015))*
 * Total number of wells on the plate
 * Number of sections on plate
 * Number of T cells per well
@@ -155,8 +165,8 @@ Structure:
 
 ---
 
-#### Graph and Data Files
-Graph and Data files are serialized binaries of a Java object containing the weigthed bipartite graph representation of a
+#### Graph/Data Files
+Graph/Data files are serialized binaries of a Java object containing the weigthed bipartite graph representation of a
 Sample Plate, along with the necessary metadata for matching and results output. Making them requires a Cell Sample file 
 (to construct a list of correct sequence pairs for checking the accuracy of BiGpairSEQ simulations) and a 
 Sample Plate file (to construct the associated occupancy graph).
@@ -164,7 +174,7 @@ Sample Plate file (to construct the associated occupancy graph).
 These files can be several gigabytes in size. Writing them to a file lets us generate a graph and its metadata once,
 then use it for multiple different BiGpairSEQ simulations.
 
-Options for creating a Graph and Data file:
+Options for creating a Graph/Data file:
 * The Cell Sample file to use
 * The Sample Plate file to use. (This must have been generated from the selected Cell Sample file.)
 
@@ -175,11 +185,7 @@ portable data format may be implemented in the future. The tricky part is encodi
 
 #### Matching Results Files 
 Matching results files consist of the results of a BiGpairSEQ matching simulation. Making them requires a Graph and 
-Data file. To save file I/O time, the data from the most recent Graph and Data file read or generated is cached
-by the simulator. Subsequent BiGpairSEQ simulations run with the same input filename will use the cached version
-rather than reading in again from disk.
-
-Files are in CSV format. Rows are sequence pairings with extra relevant data. Columns are pairing-specific details.
+Data file. Matching results files are in CSV format. Rows are sequence pairings with extra relevant data. Columns are pairing-specific details.
 Metadata about the matching simulation is included as comments. Comments are preceded by `#`.
 
 Options when running a BiGpairSEQ simulation of CDR3 alpha/beta matching: