# HG changeset patch
# User tduigou
# Date 1634052240 0
# Node ID 37185c8a8f469dfb934d03f9be1bd6e4d0342c45
upload rpbasicdesign v0.3.1
diff -r 000000000000 -r 37185c8a8f46 rpbasicdesign/rpbasicdesign.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rpbasicdesign/rpbasicdesign.xml Tue Oct 12 15:24:00 2021 +0000
@@ -0,0 +1,124 @@
+
+ Build DNA-BOT input files from rpSBML
+
+ rpbasicdesign
+
+
+
+
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+
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+
+ @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 37185c8a8f46 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 Tue Oct 12 15:24:00 2021 +0000
@@ -0,0 +1,339 @@
+
+
+
+
+
+ 1
+ LMS
+
+
+
+
+ BASIC_SEVA_37_CmR_p15A_1
+
+ 1
+
+
+
+
+
+ 1
+
+
+
+ LMP
+
+
+
+
+
+
+ 1
+ PJ23119_BASIC
+
+
+
+
+
+ 1
+
+ U3_RBS3
+
+
+
+
+ P31019
+ 1
+
+
+
+
+
+ U2_RBS3
+
+ 1
+
+
+
+
+
+
+
+ Q84BZ3
+ 1
+
+
+
+
+ 1
+ U1_RBS2
+
+
+
+
+
+
+ Q8FB35
+
+
+ 1
+
+
+
+
+
+
+
+ constraint_7
+
+
+ 1
+
+
+
+
+
+
+ constraint_1
+
+
+
+ 1
+
+
+
+
+ 1
+
+ Q8FB35_0
+
+
+
+
+
+
+
+ constraint_6
+
+
+
+ 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_3
+
+ 1
+
+
+
+
+
+
+
+ constraint_2
+
+ 1
+
+
+
+
+
+
+ LMS_0
+
+ 1
+
+
+
+
+
+
+ constraint_5
+
+
+ 1
+
+
+
+
+
+ LMP_0
+
+
+ 1
+
+
+ BASIC_construct_A1
+ 1
+
+
+
+ U1_RBS2_0
+ 1
+
+
+
+
+
+
+
+
+
+ BASIC_SEVA_37_CmR_p15A_1_0
+ 1
+
+
+
+
+
+ 1
+ P31019_0
+
+
+
+
+
+
+ LMS
+ 1
+
+
+
+
+
+ BASIC_SEVA_37_CmR_p15A_1
+
+
+ 1
+
+
+
+
+ 1
+
+ LMP
+
+
+
+
+
+ 1
+ PJ23119_BASIC
+
+
+
+ U3_RBS3
+
+
+ 1
+
+
+
+ 1
+
+ atgc
+
+ P31019
+
+
+ U2_RBS3
+ 1
+
+
+
+
+
+ atgc
+ Q84BZ3
+ 1
+
+
+
+
+
+ 1
+
+
+ U1_RBS2
+
+
+ 1
+
+
+ atgc
+ Q8FB35
+
+
diff -r 000000000000 -r 37185c8a8f46 rpbasicdesign/test-data/BASIC_construct_A2.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rpbasicdesign/test-data/BASIC_construct_A2.xml Tue Oct 12 15:24:00 2021 +0000
@@ -0,0 +1,339 @@
+
+
+
+
+
+ 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 000000000000 -r 37185c8a8f46 rpbasicdesign/test-data/BASIC_construct_A3.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rpbasicdesign/test-data/BASIC_construct_A3.xml Tue Oct 12 15:24:00 2021 +0000
@@ -0,0 +1,339 @@
+
+
+
+
+
+ 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 000000000000 -r 37185c8a8f46 rpbasicdesign/test-data/biolegio_plate.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rpbasicdesign/test-data/biolegio_plate.csv Tue Oct 12 15:24:00 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 37185c8a8f46 rpbasicdesign/test-data/constructs.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rpbasicdesign/test-data/constructs.csv Tue Oct 12 15:24:00 2021 +0000
@@ -0,0 +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,,,,,,,,,,
diff -r 000000000000 -r 37185c8a8f46 rpbasicdesign/test-data/muconate_example.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rpbasicdesign/test-data/muconate_example.xml Tue Oct 12 15:24:00 2021 +0000
@@ -0,0 +1,762 @@
+
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+ CC(=O)C(=O)O
+ InChI=1S/C3H4O3/c1-2(4)3(5)6/h1H3,(H,5,6)
+ LCTONWCANYUPML-UHFFFAOYSA-N
+
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+ [H+]
+ InChI=1S/p+1
+ GPRLSGONYQIRFK-UHFFFAOYSA-N
+
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+ N=C(O)c1ccc[n+](C2OC(COP(=O)(O)OP(=O)(O)OCC3OC(n4cnc5c(N)ncnc54)C(O)C3O)C(O)C2O)c1
+ InChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/p+1
+ BAWFJGJZGIEFAR-UHFFFAOYSA-O
+
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+ O=C=O
+ InChI=1S/CO2/c2-1-3
+ CURLTUGMZLYLDI-UHFFFAOYSA-N
+
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+ O
+ InChI=1S/H2O/h1H2
+ XLYOFNOQVPJJNP-UHFFFAOYSA-N
+
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+ RR-02-a0cc0be463ff412f-16-F
+ MNXR96458
+
+
+ [H]OC(=O)C([H])=C([H])C([H])=C([H])C(=O)O[H].[H+].[H+]>>O=O.[H]Oc1c([H])c([H])c([H])c([H])c1O[H]
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+ RR-02-36106ef8d9461f98-16-F
+ MNXR106704
+
+
+ [H]Oc1c([H])c([H])c([H])c([H])c1O[H].N=C(O)c1ccc[n+](C2OC(COP(=O)(O)OP(=O)(O)OCC3OC(n4cnc5c(N)ncnc54)C(O)C3O)C(O)C2O)c1.O=C=O.O>>O=O.[H]N=C(O[H])C1=C([H])N(C2([H])OC([H])(C([H])([H])OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C3([H])OC([H])(n4c([H])nc5c(N([H])[H])nc([H])nc54)C([H])(O[H])C3([H])O[H])C([H])(O[H])C2([H])O[H])C([H])=C([H])C1([H])[H].[H]OC(=O)c1c([H])c([H])c([H])c([H])c1O[H].[H+].[H+]
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+ RR-02-6a903acc13abce0f-16-F
+ MNXR104265
+
+
+ [H]OC(=O)c1c([H])c([H])c([H])c([H])c1O[H].CC(=O)C(=O)O>>[H]OC(=O)C(OC1([H])C([H])=C(C(=O)O[H])C([H])=C([H])C1([H])O[H])=C([H])[H]
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diff -r 000000000000 -r 37185c8a8f46 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 Tue Oct 12 15:24:00 2021 +0000
@@ -0,0 +1,13 @@
+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,