# HG changeset patch # User tduigou # Date 1636982434 0 # Node ID a9e9eb8a392cecc5b84e48239ff92110df52f008 # Parent 37185c8a8f469dfb934d03f9be1bd6e4d0342c45 Uploaded diff -r 37185c8a8f46 -r a9e9eb8a392c rpbasicdesign/rpbasicdesign.xml --- a/rpbasicdesign/rpbasicdesign.xml Tue Oct 12 15:24:00 2021 +0000 +++ b/rpbasicdesign/rpbasicdesign.xml Mon Nov 15 13:20:34 2021 +0000 @@ -1,7 +1,7 @@ - + Build DNA-BOT input files from rpSBML - rpbasicdesign + rpbasicdesign - - - - + + + + - + - - + + `_ + +License +------- + +* `MIT `_ ]]> diff -r 37185c8a8f46 -r a9e9eb8a392c rpbasicdesign/test-data/BASIC_construct_A1.xml --- a/rpbasicdesign/test-data/BASIC_construct_A1.xml Tue Oct 12 15:24:00 2021 +0000 +++ b/rpbasicdesign/test-data/BASIC_construct_A1.xml Mon Nov 15 13:20:34 2021 +0000 @@ -1,339 +1,339 @@ + 1 + - 1 LMS - + - BASIC_SEVA_37_CmR_p15A_1 + 1 - - + BASIC_SEVA_37_CmR_p15A_1 + LMP + 1 - + - - LMP + 1 + + PJ23119_BASIC - - 1 - PJ23119_BASIC - - - - - 1 + + - U3_RBS3 - - - - - P31019 - 1 - - - - - - U2_RBS3 - - 1 - - - - - - - - Q84BZ3 + U1_RBS1 + 1 - - + + + 1 - U1_RBS2 - + + P21684 + + + U2_RBS1 + + 1 + + - - - Q8FB35 + + P21683 + 1 + + + - + + + 1 - + + U3_RBS2 + + + + + + + P21685 + + + 1 - - - - - constraint_7 - - - 1 - - - - - - - constraint_1 - - - - 1 - - - - 1 - - Q8FB35_0 - - - - - - - - constraint_6 - - - + + U3_RBS2_0 + + 1 - - - - - constraint_8 - 1 - - - - - - - - - constraint_4 - - - - 1 - - - - - - Q84BZ3_0 - - 1 - - - - - - - - - 1 - PJ23119_BASIC_0 - - - - - constraint_0 - 1 - - - - - - U2_RBS3_0 + 1 - - - - - - - - - - U3_RBS3_0 - - - 1 - - - - - + + constraint_5 + - - - constraint_3 - - 1 + - - + + + constraint_7 - - constraint_2 - 1 + + + 1 + + + 1 + + + + U1_RBS1_0 + + + + + + + BASIC_SEVA_37_CmR_p15A_1_0 + 1 + + + + + + 1 + + P21684_0 + + + + - + LMS_0 - - 1 - - - - - - - constraint_5 - - 1 - - - - - - LMP_0 - - - 1 - - - BASIC_construct_A1 - 1 - - - - U1_RBS2_0 - 1 - - + + + 1 + LMP_0 - - - BASIC_SEVA_37_CmR_p15A_1_0 - 1 + - - + 1 - P31019_0 - + + P21683_0 + + + + + + + + + + 1 + constraint_8 + + + + + constraint_2 + + + 1 + + + + + + BASIC_construct_A1 + + + constraint_0 + 1 + + + + + + + + + + + constraint_6 + + 1 + + + + + + + 1 + PJ23119_BASIC_0 + + + + + + + + + 1 + U2_RBS1_0 + + + + + + + 1 + + + constraint_3 + + + + + + + 1 + + P21685_0 + + + + + + + + + + constraint_1 + 1 + + + + + + + + 1 + + constraint_4 + + + + 1 + LMS - 1 - - BASIC_SEVA_37_CmR_p15A_1 + 1 - 1 + LMP - LMP - - - 1 - PJ23119_BASIC - - - - U3_RBS3 - 1 + + PJ23119_BASIC - - 1 - - atgc - - P31019 - - - U2_RBS3 - 1 + - + U1_RBS1 + 1 + - + + atgc - Q84BZ3 + 1 + + P21684 + + + U2_RBS1 + + + 1 - + + + + P21683 + atgc + 1 - + 1 + + U3_RBS2 - - U1_RBS2 - + + + atgc 1 + P21685 - - atgc - Q8FB35 diff -r 37185c8a8f46 -r a9e9eb8a392c rpbasicdesign/test-data/BASIC_construct_A2.xml --- a/rpbasicdesign/test-data/BASIC_construct_A2.xml Tue Oct 12 15:24:00 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,339 +0,0 @@ - - - - - - 1 - LMS - - - - - BASIC_SEVA_37_CmR_p15A_1 - - 1 - - - - - - 1 - - - - LMP - - - - - - PJ23101_BASIC - - 1 - - - - 1 - - U2_RBS1 - - - - - - - O85674 - - 1 - - - - - U3_RBS2 - - 1 - - - - - - - - 1 - Q43984 - - - - 1 - - U1_RBS3 - - - - - - - Q3KIF2 - - 1 - - - - - - - - - - - - 1 - constraint_3 - - - - - - - - 1 - - U1_RBS3_0 - - - - - - 1 - Q3KIF2_0 - - - - - - - - 1 - - U2_RBS1_0 - - - - - - - - - BASIC_SEVA_37_CmR_p15A_1_0 - 1 - - - - - constraint_4 - - - - - 1 - - - - - - - - - constraint_6 - 1 - - - - - LMS_0 - - - 1 - - - - - - 1 - - - - constraint_7 - - - - - - - - U3_RBS2_0 - 1 - - - - - - 1 - - - constraint_0 - - - - - - - - - - 1 - constraint_1 - - - - - - - - 1 - Q43984_0 - - - - - - - - - constraint_2 - 1 - - - - - BASIC_construct_A2 - - - 1 - PJ23101_BASIC_0 - - - - - - - - - constraint_8 - - - 1 - - - - - - - O85674_0 - - - 1 - - - 1 - - - 1 - LMP_0 - - - - - - - - 1 - - - - constraint_5 - - - - - - LMS - 1 - - - - - - BASIC_SEVA_37_CmR_p15A_1 - - - 1 - - - - - 1 - - LMP - - - - PJ23101_BASIC - - - - 1 - - - - 1 - U2_RBS1 - - - - - atgc - 1 - - O85674 - - - - 1 - - U3_RBS2 - - - - - - - atgc - Q43984 - 1 - - - 1 - - - U1_RBS3 - - - - - 1 - - Q3KIF2 - atgc - - diff -r 37185c8a8f46 -r a9e9eb8a392c rpbasicdesign/test-data/BASIC_construct_A3.xml --- a/rpbasicdesign/test-data/BASIC_construct_A3.xml Tue Oct 12 15:24:00 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,339 +0,0 @@ - - - - - - 1 - LMS - - - - - BASIC_SEVA_37_CmR_p15A_1 - - 1 - - - - - - 1 - - - - LMP - - - - - - PJ23101_BASIC - - 1 - - - - - - 1 - - U3_RBS3 - - - P95607 - - - - 1 - - - - 1 - U2_RBS2 - - - - - - - - - - 1 - - P23262 - - - U1_RBS1 - - - 1 - - - - - 1 - Q5QUP2 - - - - - - - - - - 1 - Q5QUP2_0 - - - - - - - constraint_8 - - - - - 1 - - - 1 - - - - 1 - constraint_1 - - - - - - - - 1 - - - - - constraint_7 - - - - - - - - constraint_5 - - 1 - - - - - 1 - - - LMS_0 - - - - - - - - - BASIC_SEVA_37_CmR_p15A_1_0 - 1 - - - - - P23262_0 - 1 - - - - - - - - - 1 - - - - constraint_3 - - - - - U2_RBS2_0 - - 1 - - - - - - - U3_RBS3_0 - 1 - - - - - - - - - 1 - PJ23101_BASIC_0 - - - - - - - - - constraint_6 - - 1 - - - - - - 1 - constraint_4 - - - - - - - - - 1 - - - - U1_RBS1_0 - - - - BASIC_construct_A3 - - - 1 - - - - constraint_2 - - - - - - - 1 - - constraint_0 - - - - - - - 1 - LMP_0 - - - - - - - - - 1 - - P95607_0 - - - - - - - - LMS - 1 - - - - - - BASIC_SEVA_37_CmR_p15A_1 - - - 1 - - - - - 1 - - LMP - - - - PJ23101_BASIC - - - - 1 - - - U3_RBS3 - - - 1 - - - - 1 - - P95607 - - atgc - - - - 1 - U2_RBS2 - - - - - - - P23262 - atgc - 1 - - - U1_RBS1 - - - 1 - - - - 1 - Q5QUP2 - - - atgc - - diff -r 37185c8a8f46 -r a9e9eb8a392c rpbasicdesign/test-data/BASIC_construct_B1.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpbasicdesign/test-data/BASIC_construct_B1.xml Mon Nov 15 13:20:34 2021 +0000 @@ -0,0 +1,339 @@ + + + + 1 + + + + LMS + + + + + + + 1 + BASIC_SEVA_37_CmR_p15A_1 + + + + LMP + + 1 + + + + + + PJ23101_BASIC + + + + 1 + + + U1_RBS3 + + 1 + + + + + + + + 1 + + + P21684 + + + U2_RBS1 + + 1 + + + + + + P21683 + 1 + + + + + + + + 1 + + U3_RBS2 + + + + + + + P21685 + + + 1 + + + + + + 1 + + + constraint_1 + + + + + + + P21684_0 + 1 + + + + + + + + + 1 + constraint_7 + + + + + + + + + + 1 + + U2_RBS1_0 + + + + + BASIC_SEVA_37_CmR_p15A_1_0 + + 1 + + + + + + + constraint_3 + + + 1 + + + + + + + + + constraint_6 + + 1 + + + + + + + U3_RBS2_0 + 1 + + + + + + + + + constraint_4 + + 1 + + + + + + + 1 + + + + U1_RBS3_0 + + + + + + constraint_5 + 1 + + + + + + + + + 1 + LMP_0 + + + + + + + + + 1 + + LMS_0 + + + + BASIC_construct_B1 + + + P21685_0 + + + + 1 + + + + + 1 + + + PJ23101_BASIC_0 + + + + + + + + + 1 + constraint_8 + + + + + + + P21683_0 + + + 1 + + + + + + 1 + + constraint_0 + + + + + 1 + + + 1 + + + + constraint_2 + + + + + + + 1 + + LMS + + + + BASIC_SEVA_37_CmR_p15A_1 + + + + 1 + + + + 1 + LMP + + + + + + PJ23101_BASIC + + + 1 + + + + + + 1 + U1_RBS3 + + + + atgc + 1 + + P21684 + + + U2_RBS1 + + + + 1 + + + + + P21683 + atgc + 1 + + + + 1 + + U3_RBS2 + + + + + atgc + 1 + P21685 + + + diff -r 37185c8a8f46 -r a9e9eb8a392c rpbasicdesign/test-data/BASIC_construct_C1.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpbasicdesign/test-data/BASIC_construct_C1.xml Mon Nov 15 13:20:34 2021 +0000 @@ -0,0 +1,339 @@ + + + + 1 + + + + LMS + + + + + + + 1 + BASIC_SEVA_37_CmR_p15A_1 + + + + LMP + + 1 + + + + + + PJ23101_BASIC + + + + 1 + + + + + U1_RBS1 + + 1 + + + + + + 1 + + + P21684 + + + + 1 + + U3_RBS2 + + + + + + + P21685 + + + 1 + + + + + U2_RBS2 + + + 1 + + + P21683 + 1 + + + + + + + + + + + 1 + + + P21685_0 + + + + + BASIC_SEVA_37_CmR_p15A_1_0 + + 1 + + + + + + + + 1 + + + P21684_0 + + + 1 + + + + + + constraint_6 + 1 + + + + + + constraint_4 + + + + 1 + + + + + + + 1 + LMP_0 + + + + + + + + P21683_0 + + 1 + + + + + + + + U2_RBS2_0 + 1 + + + + + + + + + + + 1 + constraint_5 + + + + + + constraint_8 + + 1 + + + + + + + constraint_2 + + + + + 1 + + + + + 1 + + + + constraint_3 + + + + + + LMS_0 + 1 + + + + + + + + + U1_RBS1_0 + 1 + + + + + + + + + + 1 + + constraint_1 + + + + + + U3_RBS2_0 + 1 + + + + + + + + + + constraint_7 + + + 1 + + + BASIC_construct_C1 + + + + + constraint_0 + + 1 + + + + + + + + + PJ23101_BASIC_0 + 1 + + + + + + 1 + + LMS + + + + BASIC_SEVA_37_CmR_p15A_1 + + + + 1 + + + + 1 + LMP + + + + + + PJ23101_BASIC + + + 1 + + + + + U1_RBS1 + 1 + + + + + atgc + 1 + + P21684 + + + + 1 + + U3_RBS2 + + + + + atgc + 1 + P21685 + + + + U2_RBS2 + + 1 + + + + + + + P21683 + atgc + 1 + + diff -r 37185c8a8f46 -r a9e9eb8a392c rpbasicdesign/test-data/constructs.csv --- a/rpbasicdesign/test-data/constructs.csv Tue Oct 12 15:24:00 2021 +0000 +++ b/rpbasicdesign/test-data/constructs.csv Mon Nov 15 13:20:34 2021 +0000 @@ -1,4 +1,4 @@ Well,Linker 1,Part 1,Linker 2,Part 2,Linker 3,Part 3,Linker 4,Part 4,Linker 5,Part 5,Linker 6,Part 6,Linker 7,Part 7,Linker 8,Part 8,Linker 9,Part 9,Linker 10,Part 10 -A1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U3-RBS3,P31019,U2-RBS3,Q84BZ3,U1-RBS2,Q8FB35,,,,,,,,,, -A2,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U2-RBS1,O85674,U3-RBS2,Q43984,U1-RBS3,Q3KIF2,,,,,,,,,, -A3,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U3-RBS3,P95607,U2-RBS2,P23262,U1-RBS1,Q5QUP2,,,,,,,,,, +A1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U1-RBS1,P21684,U2-RBS1,P21683,U3-RBS2,P21685,,,,,,,,,, +B1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U1-RBS3,P21684,U2-RBS1,P21683,U3-RBS2,P21685,,,,,,,,,, +C1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U1-RBS1,P21684,U3-RBS2,P21685,U2-RBS2,P21683,,,,,,,,,, diff -r 37185c8a8f46 -r a9e9eb8a392c rpbasicdesign/test-data/lycopene_CrtEBI_from_selenzy.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpbasicdesign/test-data/lycopene_CrtEBI_from_selenzy.xml Mon Nov 15 13:20:34 2021 +0000 @@ -0,0 +1,393 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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diff -r 37185c8a8f46 -r a9e9eb8a392c rpbasicdesign/test-data/user_parts_plate.csv --- a/rpbasicdesign/test-data/user_parts_plate.csv Tue Oct 12 15:24:00 2021 +0000 +++ b/rpbasicdesign/test-data/user_parts_plate.csv Mon Nov 15 13:20:34 2021 +0000 @@ -1,13 +1,7 @@ Part/linker,Well,Part concentration (ng/uL) BASIC_SEVA_37_CmR-p15A.1,A1, -O85674,A2, -P23262,A3, -P31019,A4, -P95607,A5, -PJ23101_BASIC,A6, -PJ23119_BASIC,A7, -Q3KIF2,A8, -Q43984,A9, -Q5QUP2,A10, -Q84BZ3,A11, -Q8FB35,A12, +P21683,B1, +P21684,C1, +P21685,D1, +PJ23101_BASIC,E1, +PJ23119_BASIC,F1,