diff --git a/readme.md b/readme.md index d6e5db4..b56f128 100644 --- a/readme.md +++ b/readme.md @@ -58,13 +58,14 @@ main menu looks like this: ``` --------BiGPairSEQ SIMULATOR-------- ALPHA/BETA T CELL RECEPTOR MATCHING - USING WEIGHTED BIPARTITE GRAPHS + USING WEIGHTED BIPARTITE GRAPHS ------------------------------------ Please select an option: 1) Generate a population of distinct cells 2) Generate a sample plate of T cells 3) Generate CDR3 alpha/beta occupancy data and overlap graph 4) Simulate bipartite graph CDR3 alpha/beta matching (BiGpairSEQ) +8) Options 9) About/Acknowledgments 0) Exit ``` @@ -77,18 +78,20 @@ To run the simulation, the program reads and writes 4 kinds of files: * 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, +These files are often generated in sequence. 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. + +To save file I/O time, the most recent instance of each of these four +files either generated or read from disk can be 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. +differently-configured BiGpairSEQ matchings on the same graph, keeping the most recent graph cached can reduce 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. +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, +or caching is turned off for that file type. 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. +The program's caching behavior can be controlled in the Options menu. By default, caching for cell sample and +sample plate files is OFF, and caching for graph/data files is ON. #### Cell Sample Files Cell Sample files consist of any number of distinct "T cells." Every cell contains