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Analyzed about 2 months ago. based on code collected about 2 months ago.

Commit Message	Contributor	Files Modified	Lines Added	Lines Removed	Code Location	Date
Mar 01, 2023 — Mar 01, 2024 Showing page 1 of 4 Search / Filter on:
minor cleaning	notadoctor	More...				about 13 years ago
Merge branch 'steffi' of desdemona.ebalto.jhmi.edu:/Users/Shared/GeneDesign agh	notadoctor	More...				over 13 years ago
Making two copies of the pms. Will fix it in a later release	notadoctor	More...				over 13 years ago
Updated to be less platform specific	notadoctor	More...				over 13 years ago
added more advanced apache configuration help	notadoctor	More...				over 13 years ago
updated to actually work on windows (i hope)	notadoctor	More...				over 13 years ago
added perl library installer	notadoctor	More...				over 13 years ago
Slight modifications, cleaning up	Steffi Liu	More...				over 13 years ago
Lock fully works for both SSRem and OliRem! OliRem works off of the SSS pl fully too! YAY! :D	Steffi Liu	More...				over 13 years ago
gdSSRem is now fully running off of Restriction_Site_Subtraction, and the lock sequence option is added in, minor changes to GeneDesign.pm to ensure that lock sequence works, GeneDesignTest and pl changed to clean up code	Steffi Liu	More...				over 13 years ago
RSS subtraction is running off of the bin, slight modifications to GeneDesignML.pm to add a random organism choice (That has not been tested with RSS yet though), GeneDesign.pm got array_writer, slight changes in Reverse_Translate.pl and gdRevTrans for better code. Placeholder.txt to hold the permissions of the tmp folder	Steffi Liu	More...				over 13 years ago
Deleted these files (They were for testing purposes, now the script cleans up)	Steffi Liu	More...				over 13 years ago
Fully working! Now with error messages and everything. gdRevTrans.cgi runs off of Reverse_Translate.pl, finally. Some of Reverse_Translate.pl was changed in order to adapt for the CGI.	Steffi Liu	More...				over 13 years ago
Updated the SSS and RSS to work with the changed lock subroutine, Reverse_Translate.pl had minor changes to make it compatible with the cgi-bin, CGI-BIN somewhat works, but definitely needs to be debugged. GeneDesign was changed with corrections and changed lock sub.	Steffi Liu	More...				over 13 years ago
Oops, forgot to upload these with the last batch	Steffi Liu	More...				over 13 years ago
Prepped Reverse_Translate.pl for CGI compatibility, need to work out bugs with gdRevTrans.cgi, added tmp directory	Steffi Liu	More...				over 13 years ago
Error message breaks code :[	Steffi Liu	More...				over 13 years ago
Added lock_parser to GeneDesign, fixed RSS and SSS accordingly. Also fixed some stylistic stuff	Steffi Liu	More...				over 13 years ago
Count subroutine was modified	Steffi Liu	More...				over 13 years ago
Added tests for the new subroutines, fixed some formatting in the other files.	Steffi Liu	More...				over 13 years ago
Lock subroutine is fully working, fully functional in both RSS and SSS. Able to read locked sequences from txt files or user input. Sample txt file provided.	Steffi Liu	More...				over 13 years ago
Lock fully works, just need to clean up the code and copy it over to restriction enzyme file.	Steffi Liu	More...				over 13 years ago
Lock sub is fully working! Working on writing an error message though, for short sequence...	Steffi Liu	More...				almost 14 years ago
Worked out a few bugs with the two pl files. However, locking sequences is encountering some hiccups, will be debugging after commiting this.	Steffi Liu	More...				almost 14 years ago
Also added the different/multiple short sequences function to SSS (similar to the RSS one), here is the sample text file	Steffi Liu	More...				almost 14 years ago
Cleaned up code in RSS, modified sub check_lock in GeneDesign, added lock to SSS, but needs to test	Steffi Liu	More...				almost 14 years ago
Code cleanup	Steffi Liu	More...				almost 14 years ago
Added another way of providing restriction sites to that file, allowing for removal of different restriction sites for each nucleotide sequence. Provided another sample input file for that. Added new GeneDesign subroutines in preparation for similar situations as above and for locking sequences.	Steffi Liu	More...				almost 14 years ago
Modified the mask sub and added check_lock sub, still working out the logic of it	Steffi Liu	More...				almost 14 years ago
Changed a minor typo in the Restriction_Site file, adding Short_Sequence_Subtraction file and test short_sequences txt file.	Steffi Liu	More...				almost 14 years ago

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