efischer/BiGpairSEQ
1
0
Fork 0
Code Issues Pull Requests Projects Releases 13 Wiki Activity

Remove testing code, add garbage collection calls

Browse Source
This commit is contained in:
efischer
2022-02-20 20:06:45 -06:00
parent 1bc6a11545
commit 410f0ae547
3 changed files with 7 additions and 13 deletions
Download Patch File Download Diff File Expand all files Collapse all files

8
readme.md
View File

@@ -222,9 +222,10 @@ using the (2021 corrected) formula from the original pairSEQ paper. (Howie, et a
## TODO
* Try invoking GC at end of workloads to reduce paging to disk
* ~~Try invoking GC at end of workloads to reduce paging to disk~~ DONE
* ~~Hold graph data in memory until another graph is read-in?~~
* No, this won't work, because BiGpairSEQ simulations alter the underlying graph based on filtering constraints. Changes would cascade with multiple experiments.
* ~~See if there's a reasonable way to reformat Sample Plate files so that wells are columns instead of rows~~ DONE
* Enable GraphML output in addition to serialized object binaries, for data portability
* Custom vertex type with attribute for sequence occupancy?
* Re-implement CDR1 matching method
@@ -237,10 +238,7 @@ using the (2021 corrected) formula from the original pairSEQ paper. (Howie, et a
* 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.
* preliminary data suggests that BiGpairSEQ behaves roughly as though the whole plate had whatever the *average* well concentration is, but that's still speculative.
* See if there's a reasonable way to reformat Sample Plate files so that wells are columns instead of rows
* Problem is variable number of cells in a well
* Apache Commons CSV library writes entries a row at a time
* Can possibly sort the wells by length first, then construct entries
## 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)