Use these instances as templates for running breedHS. They are organized by institution and pairing protocol:
hsw: Use this code for in-house pairing at HS West (using only rats produced at HSW)wfu: Use this code for in-house pairing at Wake Forest (using only rats produced at WFU)hsw_exchange: Use this code for pairing exchange generations at HS West (when HSW receives breeders from WFU)wfu_exchange: Use this code for pairing exchange generations at Wake Forest (when WFU receives breeders from HSW)
Code in hsw uploaded 1/21/26 after HSW gen108_109 pairing. This code should work as-is (after filling out the arguments file).
Code in hsw uploaded 3/2/26 after WFU gen53_54 pairing. This code should work as-is (after filling out the arguments file).
Code in hsw_exchange should be stable and usable as-is after filling out the arguments file. Uploaded 1/26/26 following HSW gen108_109 pairings.
This code base pairs HSW rats during exchanges, from the perspective of HS West. Use this code only when HS West receives breeders from Wake Forest. Note that script 03_propose_pairs lacks steps for identifying alternative/replacement pairs, due to complications imposed by WFU IDs.
Code uploaded 1/21/26 using code from WFU gen51_52 pairings. This might not be 100% usable as-is.
WFU exchanges require an early special step, 02_fams_to_ship, which identifies best-candidate families to send from HSW to WFU based on shared kinship with the previous WFU generation. This is because HSW animals must be shipped to WFU before all WFU rats are born, thus current kinship can't be estimated. The previous generation's kinship is used as a proxy for prioritizing low-kinship HSW rats to ship.
During WFU exchanges, execute 01_make_id_maps and 02_fams_to_ship to identify breeders to provide from HSW. When beginning official pairing, re-run 01_make_id_maps, then proceed to 03_setup_peds.