# HG changeset patch
# User tduigou
# Date 1637241422 0
# Node ID e8e8050e9997ccf5412d0484ecbece5bb297b9b2
Uploaded rpbasicdesign 0.3.4
diff -r 000000000000 -r e8e8050e9997 rpbasicdesign/rpbasicdesign.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rpbasicdesign/rpbasicdesign.xml Thu Nov 18 13:17:02 2021 +0000
@@ -0,0 +1,121 @@
+
+ Build DNA-BOT input files from rpSBML
+
+ rpbasicdesign
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
+
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+
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+ `_
+
+License
+-------
+
+* `MIT `_
+
+ ]]>
+
+
+ @article{10.1093/synbio/ysaa010,
+ author = {Storch, Marko and Haines, Matthew C and Baldwin, Geoff S},
+ title = {DNA-BOT: a low-cost, automated DNA assembly platform for synthetic biology},
+ journal = {Synthetic Biology},
+ volume = {5},
+ number = {1},
+ year = {2020},
+ month = {07},
+ issn = {2397-7000},
+ doi = {10.1093/synbio/ysaa010},
+ url = {https://doi.org/10.1093/synbio/ysaa010},
+ note = {ysaa010},
+ eprint = {https://academic.oup.com/synbio/article-pdf/5/1/ysaa010/33722340/ysaa010.pdf},
+ }
+
+
+
\ No newline at end of file
diff -r 000000000000 -r e8e8050e9997 rpbasicdesign/test-data/BASIC_construct_A1.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rpbasicdesign/test-data/BASIC_construct_A1.xml Thu Nov 18 13:17:02 2021 +0000
@@ -0,0 +1,339 @@
+
+
+
+ 1
+
+
+
+ LMS
+
+
+
+
+
+
+ 1
+ BASIC_SEVA_37_CmR_p15A_1
+
+
+
+ LMP
+
+ 1
+
+
+
+
+ 1
+
+
+ PJ23119_BASIC
+
+
+
+
+
+
+ U1_RBS1
+
+ 1
+
+
+
+
+
+ 1
+
+
+ P21684
+
+
+ U2_RBS1
+
+ 1
+
+
+
+
+
+ P21683
+ 1
+
+
+
+
+
+
+
+ 1
+
+ U3_RBS2
+
+
+
+
+
+
+ P21685
+
+
+ 1
+
+
+
+
+ U3_RBS2_0
+
+
+ 1
+
+
+
+
+
+ 1
+
+ constraint_5
+
+
+
+
+
+
+
+
+ constraint_7
+
+ 1
+
+
+
+
+ 1
+
+
+ 1
+
+
+
+ U1_RBS1_0
+
+
+
+
+
+
+ BASIC_SEVA_37_CmR_p15A_1_0
+ 1
+
+
+
+
+
+ 1
+
+ P21684_0
+
+
+
+
+
+
+
+
+ LMS_0
+ 1
+
+
+
+
+
+
+ 1
+ LMP_0
+
+
+
+
+
+
+ 1
+
+
+ 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
+
+
+
+ BASIC_SEVA_37_CmR_p15A_1
+
+
+
+ 1
+
+
+
+ 1
+ LMP
+
+
+
+
+
+ 1
+
+
+ PJ23119_BASIC
+
+
+
+
+ U1_RBS1
+ 1
+
+
+
+
+ atgc
+ 1
+
+ P21684
+
+
+ U2_RBS1
+
+
+
+ 1
+
+
+
+
+ P21683
+ atgc
+ 1
+
+
+
+ 1
+
+ U3_RBS2
+
+
+
+
+ atgc
+ 1
+ P21685
+
+
+
diff -r 000000000000 -r e8e8050e9997 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 Thu Nov 18 13:17:02 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 000000000000 -r e8e8050e9997 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 Thu Nov 18 13:17:02 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 000000000000 -r e8e8050e9997 rpbasicdesign/test-data/biolegio_plate.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rpbasicdesign/test-data/biolegio_plate.csv Thu Nov 18 13:17:02 2021 +0000
@@ -0,0 +1,83 @@
+Part/linker,Well,Part concentration (ng/uL)
+L1-S,A1,
+L1-P,B1,
+L2-S,A2,
+L2-P,B2,
+L3-S,A3,
+L3-P,B3,
+L4-S,A4,
+L4-P,B4,
+L5-S,A5,
+L5-P,B5,
+L6-S,A6,
+L6-P,B6,
+LMP-S,A7,
+LMP-P,B7,
+LMS-S,A8,
+LMS-P,B8,
+U1-S,C1,
+U2-S,C2,
+U3-S,C3,
+U1-RBS1-P,C4,
+U1-RBS2-P,C5,
+U1-RBS3-P,C6,
+U1-A01-P,D1,
+U1-A02-P,D2,
+U1-A03-P,D3,
+U1-A04-P,D4,
+U1-A05-P,D5,
+U1-A06-P,D6,
+U1-A07-P,D7,
+U1-A08-P,D8,
+U1-A09-P,D9,
+U1-A10-P,D10,
+U1-A11-P,D11
+U1-A12-P,D12,
+U2-RBS1-P,C7,
+U2-RBS2-P,C8,
+U2-RBS3-P,C9,
+U2-A01-P,E1,
+U2-A02-P,E2,
+U2-A03-P,E3,
+U2-A04-P,E4,
+U2-A05-P,E5,
+U2-A06-P,E6,
+U2-A07-P,E7,
+U2-A08-P,E8,
+U2-A09-P,E9,
+U2-A10-P,E10,
+U2-A11-P,E11
+U2-A12-P,E12,
+U3-RBS1-P,C10,
+U3-RBS2-P,C11,
+U3-RBS3-P,C12,
+U3-A01-P,F1,
+U3-A02-P,F2,
+U3-A03-P,F3,
+U3-A04-P,F4,
+U3-A05-P,F5,
+U3-A06-P,F6,
+U3-A07-P,F7,
+U3-A08-P,F8,
+U3-A09-P,F9,
+U3-A10-P,F10,
+U3-A11-P,F11
+U3-A12-P,F12,
+U1-AM12-P,A10,
+U1-AM24-P,B10,
+U2-AM12-P,A11,
+U2-AM24-P,B11,
+U3-AM12-P,A12,
+U3-AM24-P,B12,
+LF1-S,A9,
+LF1-P,B9,
+LF2-S,G1,
+LF2-P,H1,
+LF3-S,G2,
+LF3-P,H2,
+LF4-S,G3,
+LF4-P,H3,
+LF5-S,G4,
+LF5-P,H4,
+LF6-S,G5,
+LF6-P,H5,
\ No newline at end of file
diff -r 000000000000 -r e8e8050e9997 rpbasicdesign/test-data/constructs.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rpbasicdesign/test-data/constructs.csv Thu Nov 18 13:17:02 2021 +0000
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+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,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 000000000000 -r e8e8050e9997 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 Thu Nov 18 13:17:02 2021 +0000
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diff -r 000000000000 -r e8e8050e9997 rpbasicdesign/test-data/user_parts_plate.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rpbasicdesign/test-data/user_parts_plate.csv Thu Nov 18 13:17:02 2021 +0000
@@ -0,0 +1,7 @@
+Part/linker,Well,Part concentration (ng/uL)
+BASIC_SEVA_37_CmR-p15A.1,A1,
+P21683,B1,
+P21684,C1,
+P21685,D1,
+PJ23101_BASIC,E1,
+PJ23119_BASIC,F1,