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Typos in documentation

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efischer
2022-02-21 11:19:54 -06:00
parent 5c75c1ac09
commit aec7e3016f
2 changed files with 9 additions and 9 deletions
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16
readme.md
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@@ -55,7 +55,7 @@ main menu looks like this:
```
--------BiGPairSEQ SIMULATOR--------
ALPHA/BETA T-CELL RECEPTOR MATCHING
ALPHA/BETA T CELL RECEPTOR MATCHING
USING WEIGHTED BIPARTITE GRAPHS
------------------------------------
Please select an option:
@@ -215,7 +215,7 @@ Example output:
---
**NOTE: The p-values in the output are not used for matching**—they aren't part of the BiGpairSEQ algorithm at all.
P-values are calculated *after* BiGpairSEQ matching is completed, for purposes of comparison,
P-values are calculated *after* BiGpairSEQ matching is completed, for purposes of comparison only,
using the (2021 corrected) formula from the original pairSEQ paper. (Howie, et al. 2015)
### PERFORMANCE
@@ -230,9 +230,9 @@ correct pairings and 18 incorrect pairings, for an accuracy of 99.652%.
The simulation time was 14'22". If intermediate results were held in memory, this would be equivalent to the total elapsed time.
Since this implementation of BiGpairSEQ writes intermediate results to disk (to improve the efficiency of *repeated* simulations),
the actual elapsed time was greater. File I/O time was not measured, but took slightly less time than the simulation itself.
Real elapsed time from start to finish was under 30 minutes.
Since this implementation of BiGpairSEQ writes intermediate results to disk (to improve the efficiency of *repeated* simulations
with different filtering options), the actual elapsed time was greater. File I/O time was not measured, but took
slightly less time than the simulation itself. Real elapsed time from start to finish was under 30 minutes.
## TODO
@@ -245,7 +245,7 @@ Real elapsed time from start to finish was under 30 minutes.
* _Got this working, but at the cost of a profoundly strange bug in graph occupancy filtering. Have reverted the repo until I can figure out what caused that. Given how easily Thingiverse transposes CSV matrices in R, might not even be worth fixing._
* Re-implement command line arguments, to enable scripting and statistical simulation studies
* Implement sample plates with random numbers of T cells per well.
* Possible BiGpairSEQ advantage over pairSEQ: BiGpairSEQ is resilient to variations in well populations; pairSEQ is not.
* Possible BiGpairSEQ advantage over pairSEQ: BiGpairSEQ is resilient to variations in well population sizes on a sample plate; pairSEQ is not.
* preliminary data suggests that BiGpairSEQ behaves roughly as though the whole plate had whatever the *average* well concentration is, but that's still speculative.
* Enable GraphML output in addition to serialized object binaries, for data portability
* Custom vertex type with attribute for sequence occupancy?
@@ -261,8 +261,8 @@ Real elapsed time from start to finish was under 30 minutes.
## CITATIONS
* Howie, B., Sherwood, A. M., et al. ["High-throughput pairing of T cell receptor alpha and beta sequences."](https://pubmed.ncbi.nlm.nih.gov/26290413/) Sci. Transl. Med. 7, 301ra131 (2015)
* Duan, R., Su H. ["A Scaling Algorithm for Maximum Weight Matching in Bipartite Graphs."](https://web.eecs.umich.edu/~pettie/matching/Duan-Su-scaling-bipartite-matching.pdf) Proceedings of the Twenty-Third Annual ACM-SIAM Symposium on Discrete Algorithms, p. 1413-1424. (2012)
* K. Melhorn, St. Näher. [The LEDA Platform of Combinatorial and Geometric Computing.](https://people.mpi-inf.mpg.de/~mehlhorn/LEDAbook.html) Cambridge University Press. Chapter 7, Graph Algorithms; p. 132-162 (1999)
* M. Fredman, R. Tarjan. ["Fibonacci heaps and their uses in improved network optimization algorithms."](https://www.cl.cam.ac.uk/teaching/1011/AlgorithII/1987-FredmanTar-fibonacci.pdf) J. ACM, 34(3):596–615 (1987))
* Melhorn, K., Näher, St. [The LEDA Platform of Combinatorial and Geometric Computing.](https://people.mpi-inf.mpg.de/~mehlhorn/LEDAbook.html) Cambridge University Press. Chapter 7, Graph Algorithms; p. 132-162 (1999)
* Fredman, M., Tarjan, R. ["Fibonacci heaps and their uses in improved network optimization algorithms."](https://www.cl.cam.ac.uk/teaching/1011/AlgorithII/1987-FredmanTar-fibonacci.pdf) J. ACM, 34(3):596–615 (1987))
## EXTERNAL LIBRARIES USED
* [JGraphT](https://jgrapht.org) -- Graph theory data structures and algorithms

2
src/main/java/UserInterface.java
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@@ -258,7 +258,7 @@ public class UserInterface {
while (!quit) {
System.out.println();
System.out.println("--------BiGPairSEQ SIMULATOR--------");
System.out.println("ALPHA/BETA T-CELL RECEPTOR MATCHING");
System.out.println("ALPHA/BETA T CELL RECEPTOR MATCHING");
System.out.println(" USING WEIGHTED BIPARTITE GRAPHS ");
System.out.println("------------------------------------");
System.out.println("Please select an option:");