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Update readme to reflect caching changes

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efischer
2022-02-24 12:47:26 -06:00
parent 108b0ec13f
commit 2829b88689
1 changed files with 13 additions and 10 deletions
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readme.md
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@@ -58,13 +58,14 @@ main menu looks like this:
``` ```
--------BiGPairSEQ SIMULATOR-------- --------BiGPairSEQ SIMULATOR--------
ALPHA/BETA T CELL RECEPTOR MATCHING ALPHA/BETA T CELL RECEPTOR MATCHING
USING WEIGHTED BIPARTITE GRAPHS USING WEIGHTED BIPARTITE GRAPHS
------------------------------------ ------------------------------------
Please select an option: Please select an option:
1) Generate a population of distinct cells 1) Generate a population of distinct cells
2) Generate a sample plate of T cells 2) Generate a sample plate of T cells
3) Generate CDR3 alpha/beta occupancy data and overlap graph 3) Generate CDR3 alpha/beta occupancy data and overlap graph
4) Simulate bipartite graph CDR3 alpha/beta matching (BiGpairSEQ) 4) Simulate bipartite graph CDR3 alpha/beta matching (BiGpairSEQ)
8) Options
9) About/Acknowledgments 9) About/Acknowledgments
0) Exit 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 * Graph/Data files in binary object serialization format
* Matching Results files in CSV 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 These files are often generated in sequence. When entering filenames, it is not necessary to include the file extension
files either generated or read from disk is cached in program memory. This is especially important for Graph/Data files, (.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, 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 differently-configured BiGpairSEQ matchings on the same graph, keeping the most recent graph cached can reduce execution time
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. 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 or caching is turned off for that file type. The program checks whether it needs to update its cached data by comparing
encountering a new filename, the program flushes its cache and reads in the new file. 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 The program's caching behavior can be controlled in the Options menu. By default, caching for cell sample and
writing files, the program will automatically add the correct extension to any filename without one. sample plate files is OFF, and caching for graph/data files is ON.
#### Cell Sample Files #### Cell Sample Files
Cell Sample files consist of any number of distinct "T cells." Every cell contains Cell Sample files consist of any number of distinct "T cells." Every cell contains