Merge branch 'master' of https://github.com/leasunhy/SYSU-Software-2015 into design-tool

Author: linjinjin123

manager.py

@@ -8,7 +8,7 @@
 from server.tools.preload import preload_parts, get_file_list
 from server.tools.random_text import random_text
 
-app = create_app('default')
+app = create_app('production')
 
 manager = Manager(app)
 def make_shell_context():

server/models/equation.py

@@ -151,7 +151,7 @@ def preload_from_file(filename):
         with open(filename, 'r') as f:
             for line in f:
                 line = line.strip()
-                if not line: continue
+                if not line or line.startswith('#'): continue
 
                 ele = eval(line, {'__builtins__':None}, {})
                 e = EquationBase()

server/models/preload/devices/Lihui/5Device2.txt

@@ -15,4 +15,4 @@ Ptet_1	amilCP_1	normal
 amilCP_1	AmilCP_1	promotion
 amilCP_1	tetA_1	normal
 tetA_1	TetA_1	promotion
-TetA_1	tetR_1	promotion
+TetA_1	Pqrr4_1	promotion

server/models/preload/equations/Lihui/0802(2).py

@@ -0,0 +1,26 @@
+#   ('a_{cs}', 5)
+#   ('k_{cc}', 1)
+#   ('k_{cd}', 1)
+#   ('d_{CqsS}', 0.5)
+#   ('d_{CqsSp}', 1)
+#   ('alaph_{U}', 5)
+#   ('beta_{cu}', 1)
+#   ('k_{cu}', 2)
+#   ('d_{LuxU}', 0.65)
+#   ('d_{LuxUp}', 0.12)
+#   ('beta_{uo}', 3.2)
+#   ('k_{uo}', 2)
+#   ('d_{LuxOp}', 0.12)
+#   ('atr', 1)
+#   ('d_{TetR}', 0.12)
+#   ('h_{0}', 1.5)
+#   ('n', 3)
+#   ('d_{TetA}', 0.12)
+#   ('beta_{TetR}', 5)
+
+['CqsS', ['CqsSp'], [('a_{cs}', 5),('k_{cc}', 1),('k_{cd}', 1),('d_{CqsS}', 0.5)], '{{a_{cs}}}-{{k_{cc}}}*CqsS+{{k_{cd}}}*CqsSp-{{d_{CqsS}}}*CqsS']
+['CqsS', [], [('d_{CqsS}', 0.5)], '-{{d_{CqsS}}}*CqsS']
+
+
+['CqsSq', ['CAI'], [('k_{cc}', 1),('k_{cd}', 1),('d_{CqsSp}', 1)], '{{k_{cc}}}*CAI - {{k_{cd}}}*CqsSp - {{d_{CqsSp}}}*CqsSp']
+

server/models/preload/equations/Lihui/0802_2.py

@@ -0,0 +1,10 @@
+Band-Pass Filter 2011ETH_Zurich
+High input level result in high cytoplasmic levels of CI and of LacIM1. LacIM1 represses the expression of GFP. Low input level results in low LacIM1 and CI concentrations. GFP is transcriptional repressed by LacI, which is expressed at low CI concentrations. Only intermediate signals results in a moderate level of CI and LacIM1.
+High input level result in high cytoplasmic levels of CI and of LacIM1. LacIM1 represses the expression of GFP. Low input level results in low LacIM1 and CI concentrations. GFP is transcriptional repressed by LacI, which is expressed at low CI concentrations. Only intermediate signals results in a moderate level of CI and LacIM1.
+Filter,tetR,cI,lacI
+http://2011.igem.org/Team:ETH_Zurich
+http://2011.igem.org/Team:ETH_Zurich/Biology/Cloning
+-1
+ALCR_1
+GFP_1
+{"parts":[{"partID":"ALCR_128","partName":"ALCR","partAttr":"ALCR","positionX":521,"positionY":-21},{"partID":"PConst_129","partName":"PConst","partAttr":"PConst","positionX":623,"positionY":-21},{"partID":"tetR_130","partName":"tetR","partAttr":"tetR","positionX":807,"positionY":-21},{"partID":"TetR_131","partName":"TetR","partAttr":"TetR","positionX":743,"positionY":112},{"partID":"cI_133","partName":"cI","partAttr":"cI","positionX":204,"positionY":-12},{"partID":"PtetR_134","partName":"PtetR","partAttr":"PtetR","positionX":591,"positionY":215},{"partID":"lacIm1_135","partName":"lacIm1","partAttr":"lacIm1","positionX":783,"positionY":215},{"partID":"LacIM1_136","partName":"LacIM1","partAttr":"LacIM1","positionX":722,"positionY":349},{"partID":"CI_137","partName":"CI","partAttr":"CI","positionX":300,"positionY":75},{"partID":"GFP_139","partName":"GFP","partAttr":"GFP","positionX":581,"positionY":598},{"partID":"lacI_140","partName":"lacI","partAttr":"lacI","positionX":356,"positionY":195},{"partID":"LacI_141","partName":"LacI","partAttr":"LacI","positionX":503,"positionY":339},{"partID":"gfp_142","partName":"gfp","partAttr":"gfp","positionX":581,"positionY":469},{"partID":"RBS_143","partName":"RBS","partAttr":"RBS","positionX":715,"positionY":-21},{"partID":"Terminator_144","partName":"Terminator","partAttr":"Terminator","positionX":902,"positionY":-21},{"partID":"Terminator_145","partName":"Terminator","partAttr":"Terminator","positionX":882,"positionY":215},{"partID":"RBS_146","partName":"RBS","partAttr":"RBS","positionX":686,"positionY":215},{"partID":"Promoter_147","partName":"Promoter","partAttr":"Promoter","positionX":28,"positionY":-12},{"partID":"RBS_148","partName":"RBS","partAttr":"RBS","positionX":117,"positionY":-12},{"partID":"Promoter_149","partName":"Promoter","partAttr":"Promoter","positionX":172,"positionY":195},{"partID":"RBS_150","partName":"RBS","partAttr":"RBS","positionX":263,"positionY":195},{"partID":"Terminator_151","partName":"Terminator","partAttr":"Terminator","positionX":297,"positionY":-12},{"partID":"Terminator_152","partName":"Terminator","partAttr":"Terminator","positionX":452,"positionY":195},{"partID":"Terminator_153","partName":"Terminator","partAttr":"Terminator","positionX":712,"positionY":469},{"partID":"Promoter_154","partName":"Promoter","partAttr":"Promoter","positionX":353,"positionY":469},{"partID":"RBS_155","partName":"RBS","partAttr":"RBS","positionX":457,"positionY":469}],"name":"Band_Pass Filter 2011ETH_Zurich","relationship":[{"start":"ALCR_128","end":"PConst_129","type":"inhibition"},{"start":"tetR_130","end":"TetR_131","type":"promotion"},{"start":"TetR_131","end":"PtetR_134","type":"inhibition"},{"start":"lacIm1_135","end":"LacIM1_136","type":"promotion"},{"start":"cI_133","end":"CI_137","type":"promotion"},{"start":"CI_137","end":"lacI_140","type":"inhibition"},{"start":"lacI_140","end":"LacI_141","type":"promotion"},{"start":"LacIM1_136","end":"gfp_142","type":"inhibition"},{"start":"gfp_142","end":"GFP_139","type":"promotion"},{"start":"LacI_141","end":"gfp_142","type":"inhibition"},{"start":"PConst_129","end":"RBS_143","type":"normal"},{"start":"RBS_143","end":"tetR_130","type":"normal"},{"start":"tetR_130","end":"Terminator_144","type":"normal"},{"start":"PtetR_134","end":"RBS_146","type":"normal"},{"start":"RBS_146","end":"lacIm1_135","type":"normal"},{"start":"lacIm1_135","end":"Terminator_145","type":"normal"},{"start":"Promoter_147","end":"RBS_148","type":"normal"},{"start":"RBS_148","end":"cI_133","type":"normal"},{"start":"cI_133","end":"Terminator_151","type":"normal"},{"start":"RBS_150","end":"lacI_140","type":"normal"},{"start":"Promoter_149","end":"RBS_150","type":"normal"},{"start":"lacI_140","end":"Terminator_152","type":"normal"},{"start":"Promoter_154","end":"RBS_155","type":"normal"},{"start":"RBS_155","end":"gfp_142","type":"normal"},{"start":"gfp_142","end":"Terminator_153","type":"normal"}],"interfaceA":"interfaceB-partName","interfaceB":"interfaceA-partName","backbone":[{"start":[0,56],"end":[329,56]},{"start":[940,50],"end":[587,50]},{"start":[137,264],"end":[483,265]},{"start":[925,285],"end":[554,285]},{"start":[316,537],"end":[744,538]}]}

server/models/preload/new_devices/ShengKun/Band-Pass Filter 2011ETH_Zurich.txt

@@ -0,0 +1,10 @@
+Bioreactor 2008Ottawa
+This device responds to IP and expresses the Arabidopsis CRE1 cytokinin receptor.
+Upon binding inducer, CRE1 phosphorylates the histidine phosphor-transfer protein YPD1. In yeast, YPD1 is normally affected by the cell surface osmosensor histidine kinase SLN1. Under normal conditions, SLN1 is constitutively phosphorylated and its kinase activity maintains YPD1 in its phosphorylated state. YPD1 in turn regulates two parallel pathways by transferring its phosphate to two proteins: SSK1 and SKN7. SSK1 phosphorylation is key to suppressing the yeast��s HOG1 pathway �C a stress reponse pathway to high osmolarity, whose activity is lethal under normal conditions. YPD1 also shuttles into the nucleus and activates the SKN7 transcription factor by phosphorylation. In the design, SKN7 was preferred over SSK1 because the SLN1-YPD1-SSK1 pathway is known to affect many high-osmolarity response genes. In order to make SKN7 inducible to IP stimulation (i.e. not constitutively phosphorylated), SLN1 had to be deleted; however, SLN1 deletion is lethal due to activation of the HOG1 pathway.
+YPD1,SSK1,SKN7,HOG1,PTP2 
+http://2008.igem.org/Team:University_of_Ottawa
+http://2008.igem.org/Team:University_of_Ottawa/Notebook
+-1
+IP_1
+RFP_1
+{"parts":[{"partID":"AtCRE1_35","partName":"AtCRE1","partAttr":"AtCRE1","positionX":540,"positionY":0},{"partID":"ATCRE1_36","partName":"ATCRE1","partAttr":"ATCRE1","positionX":647,"positionY":86},{"partID":"IP_37","partName":"IP","partAttr":"IP","positionX":520,"positionY":260},{"partID":"YPD1_38","partName":"YPD1","partAttr":"YPD1","positionX":840,"positionY":120},{"partID":"SKN7_39","partName":"SKN7","partAttr":"SKN7","positionX":853,"positionY":293},{"partID":"PSSRE_40","partName":"PSSRE","partAttr":"PSSRE","positionX":760,"positionY":428},{"partID":"PSSRE_42","partName":"PSSRE","partAttr":"PSSRE","positionX":133,"positionY":146},{"partID":"Ckx_44","partName":"Ckx","partAttr":"Ckx","positionX":380,"positionY":300},{"partID":"SSK1_45","partName":"SSK1","partAttr":"SSK1","positionX":670,"positionY":340},{"partID":"HOG1_46","partName":"HOG1","partAttr":"HOG1","positionX":580,"positionY":471},{"partID":"ptp2_48","partName":"ptp2","partAttr":"ptp2","positionX":340,"positionY":380},{"partID":"PTP2_49","partName":"PTP2","partAttr":"PTP2","positionX":433,"positionY":471},{"partID":"PCyc1_51","partName":"PCyc1","partAttr":"PCyc1","positionX":350,"positionY":0},{"partID":"ckx_54","partName":"ckx","partAttr":"ckx","positionX":333,"positionY":146},{"partID":"PPRP22_55","partName":"PPRP22","partAttr":"PPRP22","positionX":140,"positionY":380},{"partID":"RBS_56","partName":"RBS","partAttr":"RBS","positionX":240,"positionY":380},{"partID":"RBS_57","partName":"RBS","partAttr":"RBS","positionX":233,"positionY":146},{"partID":"RBS_58","partName":"RBS","partAttr":"RBS","positionX":440,"positionY":0},{"partID":"Terminator_59","partName":"Terminator","partAttr":"Terminator","positionX":640,"positionY":0},{"partID":"Terminator_60","partName":"Terminator","partAttr":"Terminator","positionX":448,"positionY":380},{"partID":"Terminator_61","partName":"Terminator","partAttr":"Terminator","positionX":428,"positionY":146},{"partID":"RFP_79","partName":"RFP","partAttr":"RFP","positionX":960,"positionY":560},{"partID":"rfp_80","partName":"rfp","partAttr":"rfp","positionX":960,"positionY":428},{"partID":"RBS_81","partName":"RBS","partAttr":"RBS","positionX":860,"positionY":428},{"partID":"Terminator_82","partName":"Terminator","partAttr":"Terminator","positionX":1060,"positionY":428}],"name":"Bioreactor 2008Ottawa","relationship":[{"start":"AtCRE1_35","end":"ATCRE1_36","type":"promotion"},{"start":"IP_37","end":"ATCRE1_36","type":"promotion"},{"start":"ATCRE1_36","end":"YPD1_38","type":"promotion"},{"start":"YPD1_38","end":"SKN7_39","type":"promotion"},{"start":"SKN7_39","end":"PSSRE_40","type":"promotion"},{"start":"Ckx_44","end":"IP_37","type":"inhibition"},{"start":"YPD1_38","end":"SSK1_45","type":"promotion"},{"start":"SSK1_45","end":"HOG1_46","type":"inhibition"},{"start":"ptp2_48","end":"PTP2_49","type":"promotion"},{"start":"PTP2_49","end":"HOG1_46","type":"inhibition"},{"start":"ckx_54","end":"Ckx_44","type":"promotion"},{"start":"PSSRE_42","end":"RBS_57","type":"normal"},{"start":"RBS_57","end":"ckx_54","type":"normal"},{"start":"PPRP22_55","end":"RBS_56","type":"normal"},{"start":"RBS_56","end":"ptp2_48","type":"normal"},{"start":"PCyc1_51","end":"RBS_58","type":"normal"},{"start":"RBS_58","end":"AtCRE1_35","type":"normal"},{"start":"ckx_54","end":"Terminator_61","type":"normal"},{"start":"ptp2_48","end":"Terminator_60","type":"normal"},{"start":"AtCRE1_35","end":"Terminator_59","type":"normal"},{"start":"rfp_80","end":"RFP_79","type":"promotion"},{"start":"rfp_80","end":"Terminator_82","type":"normal"},{"start":"rfp_80","end":"RBS_81","type":"normal"},{"start":"RBS_81","end":"PSSRE_40","type":"normal"}],"interfaceA":"interfaceB-partName","interfaceB":"interfaceA-partName","backbone":[{"start":[315,69],"end":[675,69]},{"start":[94,218],"end":[459,216]},{"start":[107,451],"end":[482,451]},{"start":[728,496],"end":[1090,497]}]}

server/models/preload/new_devices/ShengKun/Band_Pass Filter 2011ETH_Zurich.png

@@ -0,0 +1,10 @@
+Biosensor- Acetaldehyde 2011ETH_Zurich
+This is a senor of acetaldehyde.
+Acetaldehyde associates with constitutively expressed receptor ALCR. ALCR-acetaldehyde complex can bind to its cognate operator, and inhibits the transcription of the genes under the control of the PAlcR promoter.
+Biosensor,Acetaldehyde
+http://2011.igem.org/Team:ETH_Zurich
+http://2011.igem.org/Team:ETH_Zurich/Biology/Cloning
+-1
+Acetaldehyde_1
+ALCR_1
+{"parts":[{"partID":"Acetaldehyde_107","partName":"Acetaldehyde","partAttr":"Acetaldehyde","positionX":139,"positionY":-5},{"partID":"promoter_108","partName":"promoter","partAttr":"promoter","positionX":141,"positionY":133},{"partID":"RBS:BBa_B0034_109","partName":"RBS","partAttr":"RBS:BBa_B0034","positionX":249,"positionY":133},{"partID":"AlcR_110","partName":"AlcR","partAttr":"AlcR","positionX":358,"positionY":133},{"partID":"Terminator:BBa_B0010_111","partName":"Terminator","partAttr":"Terminator:BBa_B0010","positionX":467,"positionY":133},{"partID":"Terminator:BBa_B0010_112","partName":"Terminator","partAttr":"Terminator:BBa_B0010","positionX":577,"positionY":133},{"partID":"ALCR_113","partName":"ALCR","partAttr":"ALCR","positionX":358,"positionY":280}],"name":"Biosensor_ Acetaldehyde 2011ETH_Zurich","relationship":[{"start":"Acetaldehyde_107","end":"promoter_108","type":"inhibition"},{"start":"RBS:BBa_B0034_109","end":"AlcR_110","type":"normal"},{"start":"AlcR_110","end":"Terminator:BBa_B0010_111","type":"normal"},{"start":"Terminator:BBa_B0010_111","end":"Terminator:BBa_B0010_112","type":"normal"},{"start":"AlcR_110","end":"ALCR_113","type":"promotion"},{"start":"promoter_108","end":"RBS:BBa_B0034_109","type":"normal"}],"interfaceA":"interfaceB-partName","interfaceB":"interfaceA-partName","backbone":[{"start":[105,200],"end":[615,201]}]}