Team:Heidelberg/js/notebook/protocols
From 2014.igem.org
var protocols = {
"3cuNZHSvzbmc5wGLz" : { "name" : "Make a liquid culture without any plasmid", "params" : [ { "type" : { "_id" : "nQbZRzR4ZeKkYMr8X", "name" : "Bacteria without any plasmid", "v" : 0 }, "name" : "Bacteria", "multi" : false }, { "type" : { "_id" : "HS9a6rQbkgvXHqtqP", "name" : "Medium", "v" : 1 }, "name" : "Medium", "multi" : false } ], "products" : [ { "allTypes" : [ { "_id" : "8p9DTRXiSoymBbC3T", "name" : "Bacterial culture without any plasmid", "v" : 1 }, { "_id" : "nQbZRzR4ZeKkYMr8X", "name" : "Bacteria without any plasmid", "v" : 0 }, { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } ], "name" : "Culture", "propertyBindings" : { "YW7epnToTmqmHEEwx" : { "1ed8ac857097c4fbbbc15cd373ef96bc" : { "property" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Bacteria", "paramProperty" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" }, "e1520b5997a532c7889f6e8883920ab8" : { "property" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Bacteria", "paramProperty" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" } } }, "types" : [ { "_id" : "8p9DTRXiSoymBbC3T", "name" : "Bacterial culture without any plasmid", "v" : 1 } ] } ], "steps" : [ { "desc" : "Inoculate medium", "inputs" : [ { "desc" : "Volume (ml)", "type" : "ufloat", "required" : true, "multiParam" : null } ] }, { "desc" : "Grow at the preferred temperature of the organism.", "inputs" : [ { "desc" : "Temperature (°C)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Duration (h)", "type" : "ufloat", "required" : true, "multiParam" : null } ] } ] }, "3wt4jvadcLzkvFn9X" : { "name" : "Make a liquid culture carrying three plasmids", "params" : [ { "type" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 }, "name" : "Bacteria carrying three plasmids", "multi" : false }, { "type" : { "_id" : "HS9a6rQbkgvXHqtqP", "name" : "Medium", "v" : 1 }, "name" : "Medium", "multi" : false } ], "products" : [ { "allTypes" : [ { "_id" : "oeN5Sukt5toY6taDR", "name" : "Bacterial culture carrying three plasmids", "v" : 1 }, { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 }, { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } ], "name" : "Culture", "propertyBindings" : { "TnHge69a2HdoogyYG" : { "1558d87b3c90b6b6f071e0956b41972a" : { "property" : { "name" : "Plasmid 2 name", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } }, "source" : { "param" : "Bacteria carrying three plasmids", "paramProperty" : { "name" : "Plasmid 2 name", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } } }, "sourceType" : "paramProperty" }, "22f17faf09867bb581e2c6776c2e9186" : { "property" : { "name" : "Resistance(s) encoded on plasmid 1", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } }, "source" : { "param" : "Bacteria carrying three plasmids", "paramProperty" : { "name" : "Resistance(s) encoded on plasmid 1", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } } }, "sourceType" : "paramProperty" }, "2ab23d19da35facf9f19887a4e325d28" : { "property" : { "name" : "Resistance(s) encoded on plasmid 2", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } }, "source" : { "param" : "Bacteria carrying three plasmids", "paramProperty" : { "name" : "Resistance(s) encoded on plasmid 2", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } } }, "sourceType" : "paramProperty" }, "2b3de1e4d39cf71091ae27f0bbf41cb6" : { "property" : { "name" : "Resistance(s) encoded on plasmid 3", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } }, "source" : { "param" : "Bacteria carrying three plasmids", "paramProperty" : { "name" : "Resistance(s) encoded on plasmid 3", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } } }, "sourceType" : "paramProperty" }, "f922bf1c87974ac79330856f49dc41b7" : { "property" : { "name" : "Plasmid 1 name", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } }, "source" : { "param" : "Bacteria carrying three plasmids", "paramProperty" : { "name" : "Plasmid 1 name", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } } }, "sourceType" : "paramProperty" }, "f941ce021dd20e581e58121991cbb4dd" : { "property" : { "name" : "Plasmid 3 name", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } }, "source" : { "param" : "Bacteria carrying three plasmids", "paramProperty" : { "name" : "Plasmid 3 name", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } } }, "sourceType" : "paramProperty" } }, "YW7epnToTmqmHEEwx" : { "1ed8ac857097c4fbbbc15cd373ef96bc" : { "property" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Bacteria carrying three plasmids", "paramProperty" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" }, "e1520b5997a532c7889f6e8883920ab8" : { "property" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Bacteria carrying three plasmids", "paramProperty" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" } } }, "types" : [ { "_id" : "oeN5Sukt5toY6taDR", "name" : "Bacterial culture carrying three plasmids", "v" : 1 } ] } ], "steps" : [ { "desc" : "Inoculate medium", "inputs" : [ { "desc" : "Volume (ml)", "type" : "ufloat", "required" : true, "multiParam" : null } ] }, { "desc" : "Grow at the preferred temperature of the organism.", "inputs" : [ { "desc" : "Temperature (°C)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Duration (h)", "type" : "ufloat", "required" : true, "multiParam" : null } ] } ] }, "4jCgLAziJ2DSmmcvR" : { "name" : "Streak bacteria without any plasmid onto an agar plate", "params" : [ { "type" : { "_id" : "nQbZRzR4ZeKkYMr8X", "name" : "Bacteria without any plasmid", "v" : 0 }, "name" : "Bacteria without any plasmid", "multi" : false } ], "products" : [ { "allTypes" : [ { "_id" : "s8gikcCG8ZHcj2xPf", "name" : "Agar plate with bacteria without any plasmid", "v" : 1 } ], "name" : "Bacteria", "propertyBindings" : { "s8gikcCG8ZHcj2xPf" : { "1ed8ac857097c4fbbbc15cd373ef96bc" : { "property" : { "name" : "Strain", "from" : { "_id" : "s8gikcCG8ZHcj2xPf", "name" : "Agar plate with bacteria without any plasmid", "v" : 1 } }, "source" : { "param" : "Bacteria without any plasmid", "paramProperty" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" }, "e1520b5997a532c7889f6e8883920ab8" : { "property" : { "name" : "Species", "from" : { "_id" : "s8gikcCG8ZHcj2xPf", "name" : "Agar plate with bacteria without any plasmid", "v" : 1 } }, "source" : { "param" : "Bacteria without any plasmid", "paramProperty" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" } } }, "types" : [ { "_id" : "s8gikcCG8ZHcj2xPf", "name" : "Agar plate with bacteria without any plasmid", "v" : 1 } ] } ], "steps" : [ { "desc" : "Streak the bacteria onto the agar plate", "inputs" : [ { "desc" : "Volume (µl)", "type" : "ufloat", "required" : false, "multiParam" : null } ] } ] }, "53yEPDJz7oRihLz3M" : { "name" : "Dilute non-plasmid dsDNA", "params" : [ { "type" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 }, "name" : "dsDNA", "multi" : false } ], "products" : [ { "allTypes" : [ { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } ], "name" : "DNA", "propertyBindings" : { "k9LEWTcbmQn53Gzo7" : { "49ee3087348e8d44e1feda1917443987" : { "property" : { "name" : "Name", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "param" : "dsDNA", "paramProperty" : { "name" : "Name", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } } }, "sourceType" : "paramProperty" }, "4da843835f15245d46602c3d57b579b6" : { "property" : { "name" : "Concentration (ng/µl)", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 0, "input" : 2 }, "sourceType" : "input" }, "6f8ac39f837ee4598b7358ce18aec601" : { "property" : { "name" : "Tube identifier", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 0, "input" : 1 }, "sourceType" : "input" } } }, "types" : [ { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } ] } ], "steps" : [ { "desc" : "Dilute the DNA.", "inputs" : [ { "desc" : "Diluent (H2O, EB, ...)", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "New tube identifier", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "New concentration (ng/µl)", "type" : "ufloat", "required" : true, "multiParam" : null } ] } ] }, "5K8vL8t4egnG8SRtc" : { "name" : "PCA", "params" : [ { "type" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 }, "name" : "DNA fragment", "multi" : true }, { "type" : { "_id" : "xDrcNcGzZ3JnfqCMo", "name" : "Primer", "v" : 0 }, "name" : "Primer", "multi" : true } ], "products" : [ { "allTypes" : [ { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } ], "name" : "Assembled DNA", "propertyBindings" : { "k9LEWTcbmQn53Gzo7" : { "49ee3087348e8d44e1feda1917443987" : { "property" : { "name" : "Name", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 0, "input" : 2 }, "sourceType" : "input" }, "4da843835f15245d46602c3d57b579b6" : { "property" : { "name" : "Concentration (ng/µl)", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 4, "input" : 2 }, "sourceType" : "input" }, "6f8ac39f837ee4598b7358ce18aec601" : { "property" : { "name" : "Tube identifier", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 4, "input" : 3 }, "sourceType" : "input" } } }, "types" : [ { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } ] }, { "allTypes" : [ { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } ], "name" : "Assembled DNA before amplification", "propertyBindings" : { "k9LEWTcbmQn53Gzo7" : { "49ee3087348e8d44e1feda1917443987" : { "property" : { "name" : "Name", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 0, "input" : 2 }, "sourceType" : "input" }, "4da843835f15245d46602c3d57b579b6" : { "property" : { "name" : "Concentration (ng/µl)", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 4, "input" : 2 }, "sourceType" : "input" }, "6f8ac39f837ee4598b7358ce18aec601" : { "property" : { "name" : "Tube identifier", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 4, "input" : 3 }, "sourceType" : "input" } } }, "types" : [ { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } ] } ], "steps" : [ { "desc" : "For a 20 µl reaction, mix equimolar amounts of the DNA fragments (10 ng to 15 ng in total) and add water to a volume of 10 µl.", "inputs" : [ { "desc" : "Volume of the DNA fragments (µl)", "type" : "ufloat", "required" : true, "multiParam" : "DNA fragment" }, { "desc" : "Volume of water (µl)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Name of the product", "type" : "text", "required" : true, "multiParam" : null } ] }, { "desc" : "Add 10 µl 2X Phusion Flash Master Mix.", "inputs" : [] }, { "desc" : "Place the reaction in a thermocycler and run the following program: Initial denaturation at 98 °C for 10 s; 10 cycles of 1 s denaturation at 98 °C, 5 s annealing at 55 °C, extension at 72 °C for 15 to 30 s/kb of the product; final extension at 72 °C for 5 min.", "inputs" : [ { "desc" : "Extension time (s)", "type" : "ufloat", "required" : true, "multiParam" : null } ] }, { "desc" : "Add 5 µl of the reaction to 25 µl Phusion Flash Master mix. Add primers to a final concentration of 0.5 µM and water to a final volume of 50 µl.", "inputs" : [ { "desc" : "Volume of the primers (µl)", "type" : "ufloat", "required" : true, "multiParam" : "Primer" }, { "desc" : "Volume of water (µl)", "type" : "ufloat", "required" : true, "multiParam" : null } ] }, { "desc" : "Place the reaction in a thermocycler and run the following program: Initial denaturation at 98 °C for 10 s; 20 to 30 cycles of 1 s denaturation at 98 °C, 5 s annealing, extension at 72 °C for 15 to 30 s/kb of the product; final extension at 72 °C for 5 min.", "inputs" : [ { "desc" : "Annealing temperature (°C)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Extension time (s)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Concentration (ng/µl; leave this blank)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Tube identifier (optional)", "type" : "text", "required" : true, "multiParam" : null } ] } ] }, "9S64Hy4vyzPvM4aiC" : { "name" : "DNA purification (Qiagen PCR Purification Kit)", "params" : [ { "type" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 }, "name" : "dsDNA", "multi" : false } ], "products" : [ { "allTypes" : [ { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } ], "name" : "DNA", "propertyBindings" : { "k9LEWTcbmQn53Gzo7" : { "49ee3087348e8d44e1feda1917443987" : { "property" : { "name" : "Name", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "param" : "dsDNA", "paramProperty" : { "name" : "Name", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } } }, "sourceType" : "paramProperty" }, "4da843835f15245d46602c3d57b579b6" : { "property" : { "name" : "Concentration (ng/µl)", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 1, "input" : 0 }, "sourceType" : "input" }, "6f8ac39f837ee4598b7358ce18aec601" : { "property" : { "name" : "Tube identifier", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 0, "input" : 0 }, "sourceType" : "input" } } }, "types" : [ { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } ] } ], "steps" : [ { "desc" : "Follow the Qiagen protocol.", "inputs" : [ { "desc" : "Identifier of the new purified DNA tube", "type" : "text", "required" : true, "multiParam" : null } ] }, { "desc" : "Measure the concentration with a NanoDrop.", "inputs" : [ { "desc" : "Measured concentration (ng/µl)", "type" : "ufloat", "required" : true, "multiParam" : null } ] } ] }, "9TiKPrpdykEiSHFcy" : { "name" : "Make a liquid culture carrying a plasmid", "params" : [ { "type" : { "_id" : "PpBkfrLAqTw2CwNZX", "name" : "Bacteria carrying a plasmid", "v" : 2 }, "name" : "Bacteria", "multi" : false }, { "type" : { "_id" : "HS9a6rQbkgvXHqtqP", "name" : "Medium", "v" : 1 }, "name" : "Medium", "multi" : false } ], "products" : [ { "allTypes" : [ { "_id" : "EZz9pqmLYbZXhdQuZ", "name" : "Bacterial culture carrying a plasmid", "v" : 3 }, { "_id" : "PpBkfrLAqTw2CwNZX", "name" : "Bacteria carrying a plasmid", "v" : 2 }, { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } ], "name" : "Culture", "propertyBindings" : { "PpBkfrLAqTw2CwNZX" : { "0ac71517d2d368cdbabf8b9914716902" : { "property" : { "name" : "Plasmid name", "from" : { "_id" : "PpBkfrLAqTw2CwNZX", "name" : "Bacteria carrying a plasmid", "v" : 2 } }, "source" : { "param" : "Bacteria", "paramProperty" : { "name" : "Plasmid name", "from" : { "_id" : "PpBkfrLAqTw2CwNZX", "name" : "Bacteria carrying a plasmid", "v" : 2 } } }, "sourceType" : "paramProperty" }, "10990dcf66373fff11ef907bc2b1ef97" : { "property" : { "name" : "Resistance(s) encoded by the plasmid", "from" : { "_id" : "PpBkfrLAqTw2CwNZX", "name" : "Bacteria carrying a plasmid", "v" : 2 } }, "source" : { "param" : "Bacteria", "paramProperty" : { "name" : "Resistance(s) encoded by the plasmid", "from" : { "_id" : "PpBkfrLAqTw2CwNZX", "name" : "Bacteria carrying a plasmid", "v" : 2 } } }, "sourceType" : "paramProperty" } }, "YW7epnToTmqmHEEwx" : { "1ed8ac857097c4fbbbc15cd373ef96bc" : { "property" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Bacteria", "paramProperty" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" }, "e1520b5997a532c7889f6e8883920ab8" : { "property" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Bacteria", "paramProperty" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" } } }, "types" : [ { "_id" : "EZz9pqmLYbZXhdQuZ", "name" : "Bacterial culture carrying a plasmid", "v" : 3 } ] } ], "steps" : [ { "desc" : "Inoculate medium", "inputs" : [ { "desc" : "Volume (ml)", "type" : "ufloat", "required" : false, "multiParam" : null }, { "desc" : "Antibiotic(s)", "type" : "text", "required" : false, "multiParam" : null } ] }, { "desc" : "Grow at the preferred temperature of the organism.", "inputs" : [ { "desc" : "Temperature (°C)", "type" : "float", "required" : false, "multiParam" : null }, { "desc" : "Duration (h)", "type" : "ufloat", "required" : false, "multiParam" : null } ] } ] }, "ATv6a4HMeQZMa9WYX" : { "name" : "Dilute plasmid DNA", "params" : [ { "type" : { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 }, "name" : "Plasmid", "multi" : false } ], "products" : [ { "allTypes" : [ { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 }, { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } ], "name" : "Plasmid DNA", "propertyBindings" : { "cvt43tybpDTWdk2xR" : { "c29e15397d29fc94dad70016db7ab2e9" : { "property" : { "name" : "Resistance marker(s)", "from" : { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 } }, "source" : { "param" : "Plasmid", "paramProperty" : { "name" : "Resistance marker(s)", "from" : { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 } } }, "sourceType" : "paramProperty" } }, "k9LEWTcbmQn53Gzo7" : { "49ee3087348e8d44e1feda1917443987" : { "property" : { "name" : "Name", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "param" : "Plasmid", "paramProperty" : { "name" : "Name", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } } }, "sourceType" : "paramProperty" }, "4da843835f15245d46602c3d57b579b6" : { "property" : { "name" : "Concentration (ng/µl)", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 0, "input" : 2 }, "sourceType" : "input" }, "6f8ac39f837ee4598b7358ce18aec601" : { "property" : { "name" : "Tube identifier", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 0, "input" : 1 }, "sourceType" : "input" } } }, "types" : [ { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 } ] } ], "steps" : [ { "desc" : "Dilute the plasmid DNA.", "inputs" : [ { "desc" : "Diluent (H2O, EB, ...)", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "New tube identifier", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "New concentration (ng/µl)", "type" : "ufloat", "required" : true, "multiParam" : null } ] } ] }, "Ae7BXywPx8nNApvPK" : { "name" : "Golden Gate Assembly (isothermal)", "params" : [ { "type" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 }, "name" : "DNA fragment", "multi" : true }, { "type" : { "_id" : "SbkCFMHjvszXAwJNf", "name" : "Restriction enzyme (NEB)", "v" : 2 }, "name" : "Restriction enzyme (NEB)", "multi" : true } ], "products" : [ { "name" : "Assembled plasmid", "types" : [ { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 } ], "allTypes" : [ { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 }, { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } ], "propertyBindings" : { "cvt43tybpDTWdk2xR" : { "c29e15397d29fc94dad70016db7ab2e9" : { "property" : { "name" : "Resistance marker(s)", "from" : { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 } }, "sourceType" : "input", "source" : { "step" : 0, "input" : 3 } } }, "k9LEWTcbmQn53Gzo7" : { "49ee3087348e8d44e1feda1917443987" : { "property" : { "name" : "Name", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "sourceType" : "input", "source" : { "step" : 0, "input" : 2 } }, "6f8ac39f837ee4598b7358ce18aec601" : { "property" : { "name" : "Tube identifier", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "sourceType" : "input", "source" : { "step" : 0, "input" : 4 } }, "4da843835f15245d46602c3d57b579b6" : { "property" : { "name" : "Concentration (ng/µl)", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "sourceType" : "input", "source" : { "step" : 0, "input" : 5 } } } } } ], "steps" : [ { "desc" : "Mix 100 ng of the backbone and equimolar amounts of the insert(s) in water for a total volume of 15 µl.", "inputs" : [ { "desc" : "Volume of the DNA fragments", "type" : "ufloat", "required" : true, "multiParam" : "DNA fragment" }, { "desc" : "Volume of water (µl)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Name of the resulting plasmid", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "Resistance(s) of the resulting plasmid", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "Tube identifier (optional)", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "Total concentration (ng/µl; optional)", "type" : "ufloat", "required" : true, "multiParam" : null } ] }, { "desc" : "Add 1.5 µl of 10X T4 Ligase Buffer and, when using BsaI or another restriction enzyme that requires it, BSA (Bovine Serum Albumin) at a final concentration of 1X.", "inputs" : [ { "desc" : "BSA stock concentration (X)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Volume of BSA (µl)", "type" : "ufloat", "required" : true, "multiParam" : null } ] }, { "desc" : "Add 1 µl of each restriction enzyme and 1 µl of T4 DNA Ligase (2,000,000 cohesive end ligation units/ml).", "inputs" : [] }, { "desc" : "Incubate at 37 °C for 1 h, then heat inactivate at 50 °C and 80 °C for 5 min each.", "inputs" : [] } ] }, "CdKqzhX6FqmmHYKdE" : { "name" : "Maxens neues Protokoll", "params" : [], "products" : [], "steps" : [] }, "D9hHrT2Ere5rrcuXK" : { "name" : "Make competent cells already carrying a plasmid", "params" : [ { "type" : { "_id" : "EZz9pqmLYbZXhdQuZ", "name" : "Bacterial culture carrying a plasmid", "v" : 3 }, "name" : "Bacterial culture", "multi" : false } ], "products" : [ { "allTypes" : [ { "_id" : "ynpgBQKNqRETb9wZF", "name" : "Chemically competent bacteria already carrying a plasmid", "v" : 3 }, { "_id" : "PpBkfrLAqTw2CwNZX", "name" : "Bacteria carrying a plasmid", "v" : 2 }, { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } ], "name" : "Competent cells", "propertyBindings" : { "PpBkfrLAqTw2CwNZX" : { "0ac71517d2d368cdbabf8b9914716902" : { "property" : { "name" : "Plasmid name", "from" : { "_id" : "PpBkfrLAqTw2CwNZX", "name" : "Bacteria carrying a plasmid", "v" : 2 } }, "source" : { "param" : "Bacterial culture", "paramProperty" : { "name" : "Plasmid name", "from" : { "_id" : "PpBkfrLAqTw2CwNZX", "name" : "Bacteria carrying a plasmid", "v" : 2 } } }, "sourceType" : "paramProperty" }, "10990dcf66373fff11ef907bc2b1ef97" : { "property" : { "name" : "Resistance(s) encoded by the plasmid", "from" : { "_id" : "PpBkfrLAqTw2CwNZX", "name" : "Bacteria carrying a plasmid", "v" : 2 } }, "source" : { "param" : "Bacterial culture", "paramProperty" : { "name" : "Resistance(s) encoded by the plasmid", "from" : { "_id" : "PpBkfrLAqTw2CwNZX", "name" : "Bacteria carrying a plasmid", "v" : 2 } } }, "sourceType" : "paramProperty" } }, "YW7epnToTmqmHEEwx" : { "1ed8ac857097c4fbbbc15cd373ef96bc" : { "property" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Bacterial culture", "paramProperty" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" }, "e1520b5997a532c7889f6e8883920ab8" : { "property" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Bacterial culture", "paramProperty" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" } } }, "types" : [ { "_id" : "ynpgBQKNqRETb9wZF", "name" : "Chemically competent bacteria already carrying a plasmid", "v" : 3 } ] } ], "steps" : [ { "desc" : "Follow the protocol outlined in RFC 99.", "inputs" : [] } ] }, "E8wraGbztRq8EsET7" : { "name" : "Make a glycerol stock of bacteria carrying a plasmid", "params" : [ { "type" : { "_id" : "EZz9pqmLYbZXhdQuZ", "name" : "Bacterial culture carrying a plasmid", "v" : 2 }, "name" : "Culture", "multi" : false } ], "products" : [ { "allTypes" : [ { "_id" : "aGtyYHkAAF7Qcrhic", "name" : "Glycerol stock of bacteria carrying a plasmid", "v" : 2 } ], "name" : "Glycerol stock", "propertyBindings" : { "PpBkfrLAqTw2CwNZX" : { "0ac71517d2d368cdbabf8b9914716902" : { "property" : { "name" : "Plasmid name", "from" : { "_id" : "PpBkfrLAqTw2CwNZX", "name" : "Bacteria carrying a plasmid", "v" : 1 } }, "source" : { "param" : "Culture", "paramProperty" : { "name" : "Plasmid name", "from" : { "_id" : "PpBkfrLAqTw2CwNZX", "name" : "Bacteria carrying a plasmid", "v" : 1 } } }, "sourceType" : "paramProperty" }, "10990dcf66373fff11ef907bc2b1ef97" : { "property" : { "name" : "Resistance(s) encoded by the plasmid", "from" : { "_id" : "PpBkfrLAqTw2CwNZX", "name" : "Bacteria carrying a plasmid", "v" : 1 } }, "source" : { "param" : "Culture", "paramProperty" : { "name" : "Resistance(s) encoded by the plasmid", "from" : { "_id" : "PpBkfrLAqTw2CwNZX", "name" : "Bacteria carrying a plasmid", "v" : 1 } } }, "sourceType" : "paramProperty" } }, "YW7epnToTmqmHEEwx" : { "1ed8ac857097c4fbbbc15cd373ef96bc" : { "property" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Culture", "paramProperty" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" }, "e1520b5997a532c7889f6e8883920ab8" : { "property" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Culture", "paramProperty" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" } } }, "types" : [ { "_id" : "aGtyYHkAAF7Qcrhic", "name" : "Glycerol stock of bacteria carrying a plasmid", "v" : 2 } ] } ], "steps" : [ { "desc" : "Mix an aliquot of a LB culture with the same volume of storage buffer", "inputs" : [] }, { "desc" : "Freeze at -80 °C", "inputs" : [] } ] }, "ENCvtL4jWZQW72hE5" : { "name" : "Restriction digest (NEB)", "params" : [ { "type" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 }, "name" : "dsDNA", "multi" : true }, { "type" : { "_id" : "SbkCFMHjvszXAwJNf", "name" : "Restriction enzyme (NEB)", "v" : 2 }, "name" : "Restriction enzyme (NEB)", "multi" : true } ], "products" : [ { "name" : "DNA", "types" : [ { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } ], "allTypes" : [ { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } ], "propertyBindings" : { "k9LEWTcbmQn53Gzo7" : { "49ee3087348e8d44e1feda1917443987" : { "property" : { "name" : "Name", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "sourceType" : "input", "source" : { "step" : 3, "input" : 2 } }, "6f8ac39f837ee4598b7358ce18aec601" : { "property" : { "name" : "Tube identifier", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "sourceType" : "ask", "source" : null }, "4da843835f15245d46602c3d57b579b6" : { "property" : { "name" : "Concentration (ng/µl)", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "sourceType" : "ask", "source" : null } } } } ], "steps" : [ { "desc" : "Mix purified DNA with water", "inputs" : [ { "desc" : "Volume of water (µl)", "type" : "ufloat", "required" : false, "multiParam" : null }, { "desc" : "Volume of DNA (µl)", "type" : "ufloat", "required" : false, "multiParam" : "dsDNA" } ] }, { "desc" : "Add buffer", "inputs" : [ { "desc" : "Which buffer?", "type" : "text", "required" : false, "multiParam" : null }, { "desc" : "Volume (µl)", "type" : "float", "required" : false, "multiParam" : null } ] }, { "desc" : "Add restriction enzyme(s)", "inputs" : [ { "desc" : "Volume (µl)", "type" : "ufloat", "required" : false, "multiParam" : "Restriction enzyme (NEB)" } ] }, { "desc" : "Incubate", "inputs" : [ { "desc" : "Temperature (°C)", "type" : "float", "required" : false, "multiParam" : null }, { "desc" : "Duration (min)", "type" : "ufloat", "required" : false, "multiParam" : null }, { "desc" : "Name of the resulting DNA fragment(s)", "type" : "text", "required" : true, "multiParam" : null } ] }, { "desc" : "Optional heat inactivation", "inputs" : [ { "desc" : "Temperature (°C)", "type" : "float", "required" : false, "multiParam" : null }, { "desc" : "Duration (min)", "type" : "ufloat", "required" : false, "multiParam" : null } ] } ] }, "F2oNT7tGTyGFCjAB9" : { "name" : "Make competent cells not yet carrying any plasmid", "params" : [ { "type" : { "_id" : "8p9DTRXiSoymBbC3T", "name" : "Bacterial culture without any plasmid", "v" : 1 }, "name" : "Bacterial culture without any plasmid", "multi" : false } ], "products" : [ { "allTypes" : [ { "_id" : "Xwooe4QfsLfskZNvG", "name" : "Chemically competent bacteria without any plasmid", "v" : 0 }, { "_id" : "nQbZRzR4ZeKkYMr8X", "name" : "Bacteria without any plasmid", "v" : 0 }, { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } ], "name" : "Competent cells", "propertyBindings" : { "YW7epnToTmqmHEEwx" : { "1ed8ac857097c4fbbbc15cd373ef96bc" : { "property" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Bacterial culture without any plasmid", "paramProperty" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" }, "e1520b5997a532c7889f6e8883920ab8" : { "property" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Bacterial culture without any plasmid", "paramProperty" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" } } }, "types" : [ { "_id" : "Xwooe4QfsLfskZNvG", "name" : "Chemically competent bacteria without any plasmid", "v" : 0 } ] } ], "steps" : [ { "desc" : "Follow the protocol outlined in RFC 99.", "inputs" : [] } ] }, "FY69K4x7xdaJT6Lzk" : { "name" : "Pick a colony carrying three plasmids from an agar plate", "params" : [ { "type" : { "_id" : "MzS2Gbq22sfG4j8BW", "name" : "Agar plate with bacteria carrying three plasmids", "v" : 0 }, "name" : "Agar plate with bacteria carrying three plasmids", "multi" : false } ], "products" : [ { "allTypes" : [ { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 }, { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } ], "name" : "Colony", "propertyBindings" : { "TnHge69a2HdoogyYG" : { "1558d87b3c90b6b6f071e0956b41972a" : { "property" : { "name" : "Plasmid 2 name", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } }, "source" : { "param" : "Agar plate with bacteria carrying three plasmids", "paramProperty" : { "name" : "Plasmid 2 name", "from" : { "_id" : "MzS2Gbq22sfG4j8BW", "name" : "Agar plate with bacteria carrying three plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" }, "22f17faf09867bb581e2c6776c2e9186" : { "property" : { "name" : "Resistance(s) encoded on plasmid 1", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } }, "source" : { "param" : "Agar plate with bacteria carrying three plasmids", "paramProperty" : { "name" : "Resistance(s) encoded on plasmid 1", "from" : { "_id" : "MzS2Gbq22sfG4j8BW", "name" : "Agar plate with bacteria carrying three plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" }, "2ab23d19da35facf9f19887a4e325d28" : { "property" : { "name" : "Resistance(s) encoded on plasmid 2", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } }, "source" : { "param" : "Agar plate with bacteria carrying three plasmids", "paramProperty" : { "name" : "Resistance(s) encoded on plasmid 2", "from" : { "_id" : "MzS2Gbq22sfG4j8BW", "name" : "Agar plate with bacteria carrying three plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" }, "2b3de1e4d39cf71091ae27f0bbf41cb6" : { "property" : { "name" : "Resistance(s) encoded on plasmid 3", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } }, "source" : { "param" : "Agar plate with bacteria carrying three plasmids", "paramProperty" : { "name" : "Resistance(s) encoded on plasmid 3", "from" : { "_id" : "MzS2Gbq22sfG4j8BW", "name" : "Agar plate with bacteria carrying three plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" }, "f922bf1c87974ac79330856f49dc41b7" : { "property" : { "name" : "Plasmid 1 name", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } }, "source" : { "param" : "Agar plate with bacteria carrying three plasmids", "paramProperty" : { "name" : "Plasmid 1 name", "from" : { "_id" : "MzS2Gbq22sfG4j8BW", "name" : "Agar plate with bacteria carrying three plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" }, "f941ce021dd20e581e58121991cbb4dd" : { "property" : { "name" : "Plasmid 3 name", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } }, "source" : { "param" : "Agar plate with bacteria carrying three plasmids", "paramProperty" : { "name" : "Plasmid 3 name", "from" : { "_id" : "MzS2Gbq22sfG4j8BW", "name" : "Agar plate with bacteria carrying three plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" } }, "YW7epnToTmqmHEEwx" : { "1ed8ac857097c4fbbbc15cd373ef96bc" : { "property" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Agar plate with bacteria carrying three plasmids", "paramProperty" : { "name" : "Strain", "from" : { "_id" : "MzS2Gbq22sfG4j8BW", "name" : "Agar plate with bacteria carrying three plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" }, "e1520b5997a532c7889f6e8883920ab8" : { "property" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Agar plate with bacteria carrying three plasmids", "paramProperty" : { "name" : "Species", "from" : { "_id" : "MzS2Gbq22sfG4j8BW", "name" : "Agar plate with bacteria carrying three plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" } } }, "types" : [ { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } ] } ], "steps" : [ { "desc" : "Pick up a sterile tip with a pipette. Dip it into a single colony so it attaches to the tip without applying suction.", "inputs" : [ { "desc" : "Colony number (arbitrary)", "type" : "text", "required" : true, "multiParam" : null } ] } ] }, "HA9CLF2Z4kgY3J5rE" : { "name" : "Make a liquid culture carrying two plasmids", "params" : [ { "type" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 }, "name" : "Bacteria carrying two plasmids", "multi" : false }, { "type" : { "_id" : "HS9a6rQbkgvXHqtqP", "name" : "Medium", "v" : 1 }, "name" : "Medium", "multi" : false } ], "products" : [ { "allTypes" : [ { "_id" : "REPr8yPYRdPN6gKRB", "name" : "Bacterial culture carrying two plasmids", "v" : 0 }, { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 }, { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } ], "name" : "Culture", "propertyBindings" : { "YW7epnToTmqmHEEwx" : { "1ed8ac857097c4fbbbc15cd373ef96bc" : { "property" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Bacteria carrying two plasmids", "paramProperty" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" }, "e1520b5997a532c7889f6e8883920ab8" : { "property" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Bacteria carrying two plasmids", "paramProperty" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" } }, "xJHpdoBri9Ay3g5bP" : { "1558d87b3c90b6b6f071e0956b41972a" : { "property" : { "name" : "Plasmid 2 name", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } }, "source" : { "param" : "Bacteria carrying two plasmids", "paramProperty" : { "name" : "Plasmid 2 name", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" }, "22f17faf09867bb581e2c6776c2e9186" : { "property" : { "name" : "Resistance(s) encoded on plasmid 1", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } }, "source" : { "param" : "Bacteria carrying two plasmids", "paramProperty" : { "name" : "Resistance(s) encoded on plasmid 1", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" }, "2ab23d19da35facf9f19887a4e325d28" : { "property" : { "name" : "Resistance(s) encoded on plasmid 2", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } }, "source" : { "param" : "Bacteria carrying two plasmids", "paramProperty" : { "name" : "Resistance(s) encoded on plasmid 2", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" }, "f922bf1c87974ac79330856f49dc41b7" : { "property" : { "name" : "Plasmid 1 name", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } }, "source" : { "param" : "Bacteria carrying two plasmids", "paramProperty" : { "name" : "Plasmid 1 name", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" } } }, "types" : [ { "_id" : "REPr8yPYRdPN6gKRB", "name" : "Bacterial culture carrying two plasmids", "v" : 0 } ] } ], "steps" : [ { "desc" : "Inoculate medium", "inputs" : [ { "desc" : "Volume (ml)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Antibiotics", "type" : "text", "required" : true, "multiParam" : null } ] }, { "desc" : "Grow at the preferred temperature of the organism.", "inputs" : [ { "desc" : "Temperature (°C)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Duration (h)", "type" : "ufloat", "required" : true, "multiParam" : null } ] } ] }, "JPmjNykwWASQiD9PX" : { "name" : "Gel Electrophoresis", "params" : [ { "type" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 1 }, "name" : "dsDNA", "multi" : "1" } ], "products" : [ { "name" : "Gel", "types" : [ { "_id" : "QCyBocmukGKrzbkYb", "name" : "Agarose Gel", "v" : 0 } ], "allTypes" : [ { "_id" : "QCyBocmukGKrzbkYb", "name" : "Agarose Gel", "v" : 0 } ], "propertyBindings" : {} } ], "steps" : [ { "desc" : "Measure out 7.5 g of agarose.", "inputs" : [] }, { "desc" : "Pour agarose powder into microwavable flask along with 500mL of 1xTAE.", "inputs" : [] }, { "desc" : "Microwave for 1-3min (until the agarose is completely dissolved and there is a nice rolling boil).", "inputs" : [] }, { "desc" : "Let agarose solution cool down for 5min.", "inputs" : [] }, { "desc" : "Add 10 µl of 10 mg/l ethidium bromide (EtBr) stock solution (final concentration 0.2 mg/l). EtBr binds to the DNA and allows you to visualize the DNA under ultraviolet (UV) light.", "inputs" : [] }, { "desc" : "Pour the agarose into a gel tray with the well comb in place.", "inputs" : [] }, { "desc" : "Place newly poured gel at 4°C for 10-15 minutes OR let sit at room temperature for 20-30 minutes, until it has completely solidified.", "inputs" : [] }, { "desc" : "Add loading buffer to each of your digest samples.", "inputs" : [] }, { "desc" : "Once solidified, place the agarose gel into the gel box (electrophoresis unit).", "inputs" : [] }, { "desc" : "Fill gel box with 1xTAE until the gel is covered.", "inputs" : [] }, { "desc" : "Carefully load your samples into the additional wells of the gel (recommended: 15 µl).", "inputs" : [ { "desc" : "Volume (µl)", "type" : "ufloat", "required" : false, "multiParam" : "dsDNA" } ] }, { "desc" : "Run the gel at 80-150 V until the dye line is approximately 75-80 % of the way down the gel.", "inputs" : [ { "desc" : "Voltage (V)", "type" : "ufloat", "required" : false, "multiParam" : null }, { "desc" : "Duration (min)", "type" : "ufloat", "required" : false, "multiParam" : null } ] }, { "desc" : "Turn OFF power, disconnect the electrodes from the power source, and then carefully remove the gel from the gel box.", "inputs" : [] }, { "desc" : "Using any device that has UV light, visualize your DNA fragments.", "inputs" : [] } ] }, "NgpLzurL2RKFojWWA" : { "name" : "PCR from Bacteria (colony PCR or genomic amplification)", "params" : [ { "type" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 }, "name" : "Bacteria", "multi" : false }, { "type" : { "_id" : "xDrcNcGzZ3JnfqCMo", "name" : "Primer", "v" : 0 }, "name" : "Primer", "multi" : true } ], "products" : [ { "allTypes" : [ { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } ], "name" : "Amplificate", "propertyBindings" : { "k9LEWTcbmQn53Gzo7" : { "49ee3087348e8d44e1feda1917443987" : { "property" : { "name" : "Name", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 4, "input" : 11 }, "sourceType" : "input" }, "4da843835f15245d46602c3d57b579b6" : { "property" : { "name" : "Concentration (ng/µl)", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 3, "input" : 0 }, "sourceType" : "input" }, "6f8ac39f837ee4598b7358ce18aec601" : { "property" : { "name" : "Tube identifier", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 4, "input" : 12 }, "sourceType" : "input" } } }, "types" : [ { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } ] } ], "steps" : [ { "desc" : "Suspend the picked colony in 10 µl to 20 µl of sterile H2O (or use inoculated medium).", "inputs" : [] }, { "desc" : "Mix 12.5 µl OneTaq 2X Master Mix (NEB) with 1 µl of the bacterial suspension.", "inputs" : [] }, { "desc" : "Add primers to a final concentration of 0.5 µM.", "inputs" : [ { "desc" : "Volume (µl)", "type" : "ufloat", "required" : true, "multiParam" : "Primer" } ] }, { "desc" : "Add H2O to a final volume of 25 µl.", "inputs" : [ { "desc" : "Volume (µl)", "type" : "ufloat", "required" : true, "multiParam" : null } ] }, { "desc" : "Run your thermocycler.", "inputs" : [ { "desc" : "Initial denaturation temperature (°C)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Initial denaturation time (s)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Denaturation temperature (°C)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Denaturation time (s)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : " Annealing temperature (°C)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Annealing time (s)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Extension temperature (°C)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Extension time (s)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Number of cycles", "type" : "uint", "required" : true, "multiParam" : null }, { "desc" : "Final extension temperature (°C)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Final extension time (s)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Name of the amplificate", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "Tube identifier", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "Concentration (ng/µl; leave this blank)", "type" : "ufloat", "required" : false, "multiParam" : null } ] } ] }, "Nm75fDvHCr38nXJBo" : { "name" : "Miniprep", "params" : [ { "type" : { "_id" : "EZz9pqmLYbZXhdQuZ", "name" : "Bacterial culture carrying a plasmid", "v" : 2 }, "name" : "Bacterial culture", "multi" : false } ], "products" : [ { "allTypes" : [ { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 } ], "name" : "Purified plasmid", "propertyBindings" : { "cvt43tybpDTWdk2xR" : { "c29e15397d29fc94dad70016db7ab2e9" : { "property" : { "name" : "Resistance marker(s)", "from" : { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 } }, "source" : { "param" : "Bacterial culture", "paramProperty" : { "name" : "Resistance(s) encoded by the plasmid", "from" : { "_id" : "PpBkfrLAqTw2CwNZX", "name" : "Bacteria carrying a plasmid", "v" : 1 } } }, "sourceType" : "paramProperty" } }, "k9LEWTcbmQn53Gzo7" : { "49ee3087348e8d44e1feda1917443987" : { "property" : { "name" : "Name", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "param" : "Bacterial culture", "paramProperty" : { "name" : "Plasmid name", "from" : { "_id" : "PpBkfrLAqTw2CwNZX", "name" : "Bacteria carrying a plasmid", "v" : 1 } } }, "sourceType" : "paramProperty" }, "4da843835f15245d46602c3d57b579b6" : { "property" : { "name" : "Concentration (ng/µl)", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 1, "input" : 0 }, "sourceType" : "input" }, "6f8ac39f837ee4598b7358ce18aec601" : { "property" : { "name" : "Tube identifier", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 0, "input" : 0 }, "sourceType" : "input" } } }, "types" : [ { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 } ] } ], "steps" : [ { "desc" : "Follow the Qiagen protocol", "inputs" : [ { "desc" : "Plasmid tube identifier", "type" : "text", "required" : true, "multiParam" : null } ] }, { "desc" : "Measure the concentration on a NanoDrop", "inputs" : [ { "desc" : "Measured concentration (ng/µl)", "type" : "ufloat", "required" : true, "multiParam" : null } ] } ] }, "P6LsqW4xkJYaXHFJN" : { "name" : "Heat shock plasmid transformation (1 -> 2 plasmid)", "params" : [ { "type" : { "_id" : "ynpgBQKNqRETb9wZF", "name" : "Chemically competent bacteria already carrying a plasmid", "v" : 3 }, "name" : "Chemically competent bacteria already carrying a plasmid", "multi" : false }, { "type" : { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 }, "name" : "Plasmid", "multi" : false } ], "products" : [ { "allTypes" : [ { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 }, { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } ], "name" : "Transformed bacteria", "propertyBindings" : { "YW7epnToTmqmHEEwx" : { "1ed8ac857097c4fbbbc15cd373ef96bc" : { "property" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Chemically competent bacteria already carrying a plasmid", "paramProperty" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" }, "e1520b5997a532c7889f6e8883920ab8" : { "property" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Chemically competent bacteria already carrying a plasmid", "paramProperty" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" } }, "xJHpdoBri9Ay3g5bP" : { "1558d87b3c90b6b6f071e0956b41972a" : { "property" : { "name" : "Plasmid 2 name", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } }, "source" : { "param" : "Plasmid", "paramProperty" : { "name" : "Name", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } } }, "sourceType" : "paramProperty" }, "22f17faf09867bb581e2c6776c2e9186" : { "property" : { "name" : "Resistance(s) encoded on plasmid 1", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } }, "source" : { "param" : "Chemically competent bacteria already carrying a plasmid", "paramProperty" : { "name" : "Resistance(s) encoded by the plasmid", "from" : { "_id" : "PpBkfrLAqTw2CwNZX", "name" : "Bacteria carrying a plasmid", "v" : 2 } } }, "sourceType" : "paramProperty" }, "2ab23d19da35facf9f19887a4e325d28" : { "property" : { "name" : "Resistance(s) encoded on plasmid 2", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } }, "source" : { "param" : "Plasmid", "paramProperty" : { "name" : "Resistance marker(s)", "from" : { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 } } }, "sourceType" : "paramProperty" }, "f922bf1c87974ac79330856f49dc41b7" : { "property" : { "name" : "Plasmid 1 name", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } }, "source" : { "param" : "Chemically competent bacteria already carrying a plasmid", "paramProperty" : { "name" : "Plasmid name", "from" : { "_id" : "PpBkfrLAqTw2CwNZX", "name" : "Bacteria carrying a plasmid", "v" : 2 } } }, "sourceType" : "paramProperty" } } }, "types" : [ { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } ] } ], "steps" : [ { "desc" : "Set a heat block to 42 °C.", "inputs" : [] }, { "desc" : "Thaw an aliquot chemically competent bacteria on ice.", "inputs" : [] }, { "desc" : "Add plasmid DNA to the aliquot and mix gently by flicking the tube.", "inputs" : [ { "desc" : "Volume of DNA (µl)", "type" : "ufloat", "required" : true, "multiParam" : null } ] }, { "desc" : "Incubate the bacteria on ice for 10 min to 30 min.", "inputs" : [ { "desc" : "Duration (min)", "type" : "ufloat", "required" : true, "multiParam" : null } ] }, { "desc" : "Heat shock the bacteria for exactly 30 s (20 s for E. coli BL21(DE3)).", "inputs" : [ { "desc" : "Duration (s)", "type" : "ufloat", "required" : true, "multiParam" : null } ] }, { "desc" : "Incubate the bacteria on ice for approx. 5 min.", "inputs" : [ { "desc" : "Duration (min)", "type" : "ufloat", "required" : true, "multiParam" : null } ] }, { "desc" : "Add 1 ml of SOC or LB medium and recover the plasmids for 1 h at 37 °C while shaking (optional if the new plasmid only adds an Ampicillin resistance).", "inputs" : [ { "desc" : "Volume (µl)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Duration (min)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Temperature (°C)", "type" : "ufloat", "required" : true, "multiParam" : null } ] }, { "desc" : "Optionally spin down the recovered suspension and resuspend it in a minimal volume of medium.", "inputs" : [] }, { "desc" : "Plate the suspension on agar supplemented with the appropriate antibiotics (fill in the appropriate protocol here!).", "inputs" : [] } ] }, "PxYonEdgff39dmkhq" : { "name" : "Plasmid purification (Qiagen PCR Purification Kit)", "params" : [ { "type" : { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 }, "name" : "Plasmid", "multi" : false } ], "products" : [ { "allTypes" : [ { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 }, { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } ], "name" : "Purified plasmid", "propertyBindings" : { "cvt43tybpDTWdk2xR" : { "c29e15397d29fc94dad70016db7ab2e9" : { "property" : { "name" : "Resistance marker(s)", "from" : { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 } }, "source" : { "param" : "Plasmid", "paramProperty" : { "name" : "Resistance marker(s)", "from" : { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 } } }, "sourceType" : "paramProperty" } }, "k9LEWTcbmQn53Gzo7" : { "49ee3087348e8d44e1feda1917443987" : { "property" : { "name" : "Name", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "param" : "Plasmid", "paramProperty" : { "name" : "Name", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } } }, "sourceType" : "paramProperty" }, "4da843835f15245d46602c3d57b579b6" : { "property" : { "name" : "Concentration (ng/µl)", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 1, "input" : 0 }, "sourceType" : "input" }, "6f8ac39f837ee4598b7358ce18aec601" : { "property" : { "name" : "Tube identifier", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 0, "input" : 0 }, "sourceType" : "input" } } }, "types" : [ { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 } ] } ], "steps" : [ { "desc" : "Follow the Qiagen protocol.", "inputs" : [ { "desc" : "Identifier of the new purified plasmid tube", "type" : "text", "required" : true, "multiParam" : null } ] }, { "desc" : "Measure the concentration with a NanoDrop.", "inputs" : [ { "desc" : "Measured concentration (ng/µl)", "type" : "ufloat", "required" : true, "multiParam" : null } ] } ] }, "TD9txcymCuToDta7x" : { "name" : "Anneal complementary oligonucleotides", "params" : [ { "type" : { "_id" : "xDrcNcGzZ3JnfqCMo", "name" : "Primer", "v" : 0 }, "name" : "Oligo", "multi" : true } ], "products" : [ { "allTypes" : [ { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } ], "name" : "dsDNA", "propertyBindings" : { "k9LEWTcbmQn53Gzo7" : { "49ee3087348e8d44e1feda1917443987" : { "property" : { "name" : "Name", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 0, "input" : 1 }, "sourceType" : "input" }, "4da843835f15245d46602c3d57b579b6" : { "property" : { "name" : "Concentration (ng/µl)", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 0, "input" : 3 }, "sourceType" : "input" }, "6f8ac39f837ee4598b7358ce18aec601" : { "property" : { "name" : "Tube identifier", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 0, "input" : 2 }, "sourceType" : "input" } } }, "types" : [ { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } ] } ], "steps" : [ { "desc" : "Mix equal amounts of the oligonucleotides in an appropriate buffer.", "inputs" : [ { "desc" : "Buffer used", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "Name of the resulting dsDNA", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "Tube identifier", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "Concentration (ng/µl)", "type" : "ufloat", "required" : true, "multiParam" : null } ] }, { "desc" : "Heat the mixture to 95 °C, then slowly cool it down to room temperature over approx. 45 min (by switching of the heat block or using a ramp-cool method in a thermocycler).", "inputs" : [] } ] }, "WSMMH3bg6CcrcAJ3x" : { "name" : "Phusion Flash PCR ", "params" : [ { "type" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 1 }, "name" : "dsDNA", "multi" : true }, { "type" : { "_id" : "xDrcNcGzZ3JnfqCMo", "name" : "Primer", "v" : 0 }, "name" : "Primer", "multi" : true } ], "products" : [ { "allTypes" : [ { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 1 } ], "name" : "Amplificate", "propertyBindings" : { "k9LEWTcbmQn53Gzo7" : { "49ee3087348e8d44e1feda1917443987" : { "property" : { "name" : "Name", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 1 } }, "source" : { "step" : 4, "input" : 11 }, "sourceType" : "input" } } }, "types" : [ { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 1 } ] } ], "steps" : [ { "desc" : "Add H2O to a final volume of 50 µl.", "inputs" : [ { "desc" : "Volume (µl)", "type" : "ufloat", "required" : true, "multiParam" : null } ] }, { "desc" : "Add 25 µl 2X Phusion Flash Master Mix.", "inputs" : [] }, { "desc" : "Add primers to a final concentration of 0.5 µM.", "inputs" : [ { "desc" : "Volume (µl)", "type" : "ufloat", "required" : true, "multiParam" : "Primer" } ] }, { "desc" : "Add 2.5 pg to 25 ng template DNA.", "inputs" : [ { "desc" : "Volume (µl)", "type" : "ufloat", "required" : true, "multiParam" : "dsDNA" } ] }, { "desc" : "Run your thermocycler.", "inputs" : [ { "desc" : "Initial denaturation temperature (°C)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Initial denaturation time (s)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Denaturation temperature (°C)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Denaturation time (s)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Annealing temperature (°C)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Annealing time (s)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Extension temperature (°C)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Extension time (s)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Number of cycles", "type" : "uint", "required" : true, "multiParam" : null }, { "desc" : "Final Extension temperature (°C)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Final Extension time (s)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Name of the amplificate", "type" : "text", "required" : true, "multiParam" : null } ] } ] }, "ZuE3NijkBg4WwpzKc" : { "name" : "Recovery of plasmid DNA from filter paper", "params" : [], "products" : [ { "allTypes" : [ { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 } ], "name" : "Plasmid", "propertyBindings" : { "cvt43tybpDTWdk2xR" : { "c29e15397d29fc94dad70016db7ab2e9" : { "property" : { "name" : "Resistance marker(s)", "from" : { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 } }, "source" : { "step" : 0, "input" : 1 }, "sourceType" : "input" } }, "k9LEWTcbmQn53Gzo7" : { "49ee3087348e8d44e1feda1917443987" : { "property" : { "name" : "Name", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 0, "input" : 0 }, "sourceType" : "input" }, "4da843835f15245d46602c3d57b579b6" : { "property" : { "name" : "Concentration (ng/µl)", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 0, "input" : 3 }, "sourceType" : "input" }, "6f8ac39f837ee4598b7358ce18aec601" : { "property" : { "name" : "Tube identifier", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 0, "input" : 2 }, "sourceType" : "input" } } }, "types" : [ { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 } ] } ], "steps" : [ { "desc" : "Use clean gloves and cut the marked circle area that contains the dried plasmid DNA.", "inputs" : [ { "desc" : "Plasmid name", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "Resistance marker(s)", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "Tube identifier", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "Concentration (ng/µl; leave this blank)", "type" : "ufloat", "required" : false, "multiParam" : null } ] }, { "desc" : "Using clean forceps, insert the filter paper into a 1.5 ml micro centrifuge tube. Add 50 µl of pure water (or until the paper is completely soaked), vortex briefly and incubate at room temperature for 5 minutes. Vortex again and centrifuge the tube for a few seconds.", "inputs" : [] }, { "desc" : "Remove about 5 µl of supernatant for use in transfecting E. coli by electroporation or chemical means. Please do not try to use the DNA directly for any application other than to transform bacteria and prepare a plasmid stock.", "inputs" : [] }, { "desc" : "Store the remainder of the filter paper/water mix at -20 or -80 °C as a permanent archive in case that your plasmid stock ever gets lost or if something turns out to be wrong with it.", "inputs" : [] } ] }, "bSEHCZgLpXJ6nb9ze" : { "name" : "Streak bacteria carrying three plasmid onto an agar plate", "params" : [ { "type" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 }, "name" : "Bacteria carrying three plasmids", "multi" : false } ], "products" : [ { "allTypes" : [ { "_id" : "MzS2Gbq22sfG4j8BW", "name" : "Agar plate with bacteria carrying three plasmids", "v" : 0 } ], "name" : "Agar plate", "propertyBindings" : { "MzS2Gbq22sfG4j8BW" : { "1558d87b3c90b6b6f071e0956b41972a" : { "property" : { "name" : "Plasmid 2 name", "from" : { "_id" : "MzS2Gbq22sfG4j8BW", "name" : "Agar plate with bacteria carrying three plasmids", "v" : 0 } }, "source" : { "param" : "Bacteria carrying three plasmids", "paramProperty" : { "name" : "Plasmid 2 name", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } } }, "sourceType" : "paramProperty" }, "1ed8ac857097c4fbbbc15cd373ef96bc" : { "property" : { "name" : "Strain", "from" : { "_id" : "MzS2Gbq22sfG4j8BW", "name" : "Agar plate with bacteria carrying three plasmids", "v" : 0 } }, "source" : { "param" : "Bacteria carrying three plasmids", "paramProperty" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" }, "22f17faf09867bb581e2c6776c2e9186" : { "property" : { "name" : "Resistance(s) encoded on plasmid 1", "from" : { "_id" : "MzS2Gbq22sfG4j8BW", "name" : "Agar plate with bacteria carrying three plasmids", "v" : 0 } }, "source" : { "param" : "Bacteria carrying three plasmids", "paramProperty" : { "name" : "Resistance(s) encoded on plasmid 1", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } } }, "sourceType" : "paramProperty" }, "2ab23d19da35facf9f19887a4e325d28" : { "property" : { "name" : "Resistance(s) encoded on plasmid 2", "from" : { "_id" : "MzS2Gbq22sfG4j8BW", "name" : "Agar plate with bacteria carrying three plasmids", "v" : 0 } }, "source" : { "param" : "Bacteria carrying three plasmids", "paramProperty" : { "name" : "Resistance(s) encoded on plasmid 2", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } } }, "sourceType" : "paramProperty" }, "2b3de1e4d39cf71091ae27f0bbf41cb6" : { "property" : { "name" : "Resistance(s) encoded on plasmid 3", "from" : { "_id" : "MzS2Gbq22sfG4j8BW", "name" : "Agar plate with bacteria carrying three plasmids", "v" : 0 } }, "source" : { "param" : "Bacteria carrying three plasmids", "paramProperty" : { "name" : "Resistance(s) encoded on plasmid 3", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } } }, "sourceType" : "paramProperty" }, "e1520b5997a532c7889f6e8883920ab8" : { "property" : { "name" : "Species", "from" : { "_id" : "MzS2Gbq22sfG4j8BW", "name" : "Agar plate with bacteria carrying three plasmids", "v" : 0 } }, "source" : { "param" : "Bacteria carrying three plasmids", "paramProperty" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" }, "f922bf1c87974ac79330856f49dc41b7" : { "property" : { "name" : "Plasmid 1 name", "from" : { "_id" : "MzS2Gbq22sfG4j8BW", "name" : "Agar plate with bacteria carrying three plasmids", "v" : 0 } }, "source" : { "param" : "Bacteria carrying three plasmids", "paramProperty" : { "name" : "Plasmid 1 name", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } } }, "sourceType" : "paramProperty" }, "f941ce021dd20e581e58121991cbb4dd" : { "property" : { "name" : "Plasmid 3 name", "from" : { "_id" : "MzS2Gbq22sfG4j8BW", "name" : "Agar plate with bacteria carrying three plasmids", "v" : 0 } }, "source" : { "param" : "Bacteria carrying three plasmids", "paramProperty" : { "name" : "Plasmid 3 name", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } } }, "sourceType" : "paramProperty" } } }, "types" : [ { "_id" : "MzS2Gbq22sfG4j8BW", "name" : "Agar plate with bacteria carrying three plasmids", "v" : 0 } ] } ], "steps" : [ { "desc" : "Streak the bacteria onto the agar plate or use sterile glass beads.", "inputs" : [ { "desc" : "Volume (µl)", "type" : "ufloat", "required" : true, "multiParam" : null } ] } ] }, "ejzAEWvtdZ7g9ju6j" : { "name" : "Gel extraction of a plasmid", "params" : [ { "type" : { "_id" : "QCyBocmukGKrzbkYb", "name" : "Agarose Gel", "v" : 0 }, "name" : "Agarose Gel", "multi" : true } ], "products" : [ { "allTypes" : [ { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 }, { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } ], "name" : "Excised plasmid", "propertyBindings" : { "cvt43tybpDTWdk2xR" : { "c29e15397d29fc94dad70016db7ab2e9" : { "property" : { "name" : "Resistance marker(s)", "from" : { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 } }, "source" : { "step" : 0, "input" : 2 }, "sourceType" : "input" } }, "k9LEWTcbmQn53Gzo7" : { "49ee3087348e8d44e1feda1917443987" : { "property" : { "name" : "Name", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 0, "input" : 1 }, "sourceType" : "input" }, "4da843835f15245d46602c3d57b579b6" : { "property" : { "name" : "Concentration (ng/µl)", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 2, "input" : 0 }, "sourceType" : "input" }, "6f8ac39f837ee4598b7358ce18aec601" : { "property" : { "name" : "Tube identifier", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 1, "input" : 0 }, "sourceType" : "input" } } }, "types" : [ { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 } ] } ], "steps" : [ { "desc" : "Using a clean scalpel, excise the desired band(s) from the agarose gel.", "inputs" : [ { "desc" : "Lanes/bands", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "Name of the excised plasmid", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "Resistance marker(s) of the excised plasmid", "type" : "text", "required" : true, "multiParam" : null } ] }, { "desc" : "Follow the Qiagen protocol.", "inputs" : [ { "desc" : "Identifier of the resulting tube", "type" : "text", "required" : true, "multiParam" : null } ] }, { "desc" : "Mesaure the concentration on a NanoDrop.", "inputs" : [ { "desc" : "Measured concentration (ng/µl)", "type" : "ufloat", "required" : true, "multiParam" : null } ] } ] }, "gM7FyZeyNrM4hwxZk" : { "name" : "Dissolve plasmid DNA from the registry distribution", "params" : [], "products" : [ { "allTypes" : [ { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 } ], "name" : "Plasmid", "propertyBindings" : { "cvt43tybpDTWdk2xR" : { "c29e15397d29fc94dad70016db7ab2e9" : { "property" : { "name" : "Resistance marker(s)", "from" : { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 } }, "source" : { "step" : 0, "input" : 4 }, "sourceType" : "input" } }, "k9LEWTcbmQn53Gzo7" : { "49ee3087348e8d44e1feda1917443987" : { "property" : { "name" : "Name", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 0, "input" : 3 }, "sourceType" : "input" }, "4da843835f15245d46602c3d57b579b6" : { "property" : { "name" : "Concentration (ng/µl)", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 0, "input" : 6 }, "sourceType" : "input" }, "6f8ac39f837ee4598b7358ce18aec601" : { "property" : { "name" : "Tube identifier", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 0, "input" : 5 }, "sourceType" : "input" } } }, "types" : [ { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 } ] } ], "steps" : [ { "desc" : "Add 10 µl H2O to the well of the registry distribution if it was not previously used.", "inputs" : [ { "desc" : "Distribution (year)", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "Plate", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "Well", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "Plasmid name", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "Resistance marker(s)", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "Tube identifier (leave this field blank)", "type" : "text", "required" : false, "multiParam" : null }, { "desc" : "Concentration (ng/µl; leave this field blank)", "type" : "ufloat", "required" : false, "multiParam" : null } ] }, { "desc" : "Use 1-2 µl for transformation.", "inputs" : [] } ] }, "hmhE7AHgjXE8Khw6M" : { "name" : "Gel extraction", "params" : [ { "type" : { "_id" : "QCyBocmukGKrzbkYb", "name" : "Agarose Gel", "v" : 0 }, "name" : "Agarose Gel", "multi" : true } ], "products" : [ { "allTypes" : [ { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } ], "name" : "Excised DNA fragment", "propertyBindings" : { "k9LEWTcbmQn53Gzo7" : { "49ee3087348e8d44e1feda1917443987" : { "property" : { "name" : "Name", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 0, "input" : 1 }, "sourceType" : "input" }, "4da843835f15245d46602c3d57b579b6" : { "property" : { "name" : "Concentration (ng/µl)", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 2, "input" : 0 }, "sourceType" : "input" }, "6f8ac39f837ee4598b7358ce18aec601" : { "property" : { "name" : "Tube identifier", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 1, "input" : 0 }, "sourceType" : "input" } } }, "types" : [ { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } ] } ], "steps" : [ { "desc" : "Using a clean scalpel, excise the desired band(s) from the agarose gel.", "inputs" : [ { "desc" : "Lanes/bands", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "Name of the excised DNA fragment", "type" : "text", "required" : true, "multiParam" : null } ] }, { "desc" : "Follow the Qiagen protocol.", "inputs" : [ { "desc" : "Identifier of the resulting tube", "type" : "text", "required" : true, "multiParam" : null } ] }, { "desc" : "Mesaure the concentration on a NanoDrop.", "inputs" : [ { "desc" : "Measured concentration (ng/µl)", "type" : "ufloat", "required" : true, "multiParam" : null } ] } ] }, "jT9cdZ9T5JgFDEJXe" : { "name" : "Heat shock plasmid transformation (2 -> 3 plasmids)", "params" : [ { "type" : { "_id" : "GRdscXrjMDhW6E8FF", "name" : "Chemically competent bacteria already carrying two plasmid", "v" : 0 }, "name" : "Chemically competent bacteria already carrying two plasmid", "multi" : false }, { "type" : { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 }, "name" : "Plasmid", "multi" : false } ], "products" : [ { "allTypes" : [ { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 }, { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } ], "name" : "Transformed bacteria", "propertyBindings" : { "TnHge69a2HdoogyYG" : { "1558d87b3c90b6b6f071e0956b41972a" : { "property" : { "name" : "Plasmid 2 name", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } }, "source" : { "param" : "Chemically competent bacteria already carrying two plasmid", "paramProperty" : { "name" : "Plasmid 2 name", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" }, "22f17faf09867bb581e2c6776c2e9186" : { "property" : { "name" : "Resistance(s) encoded on plasmid 1", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } }, "source" : { "param" : "Chemically competent bacteria already carrying two plasmid", "paramProperty" : { "name" : "Resistance(s) encoded on plasmid 1", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" }, "2ab23d19da35facf9f19887a4e325d28" : { "property" : { "name" : "Resistance(s) encoded on plasmid 2", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } }, "source" : { "param" : "Chemically competent bacteria already carrying two plasmid", "paramProperty" : { "name" : "Resistance(s) encoded on plasmid 2", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" }, "2b3de1e4d39cf71091ae27f0bbf41cb6" : { "property" : { "name" : "Resistance(s) encoded on plasmid 3", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } }, "source" : { "param" : "Plasmid", "paramProperty" : { "name" : "Resistance marker(s)", "from" : { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 } } }, "sourceType" : "paramProperty" }, "f922bf1c87974ac79330856f49dc41b7" : { "property" : { "name" : "Plasmid 1 name", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } }, "source" : { "param" : "Chemically competent bacteria already carrying two plasmid", "paramProperty" : { "name" : "Plasmid 1 name", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" }, "f941ce021dd20e581e58121991cbb4dd" : { "property" : { "name" : "Plasmid 3 name", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } }, "source" : { "param" : "Plasmid", "paramProperty" : { "name" : "Name", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } } }, "sourceType" : "paramProperty" } }, "YW7epnToTmqmHEEwx" : { "1ed8ac857097c4fbbbc15cd373ef96bc" : { "property" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Chemically competent bacteria already carrying two plasmid", "paramProperty" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" }, "e1520b5997a532c7889f6e8883920ab8" : { "property" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Chemically competent bacteria already carrying two plasmid", "paramProperty" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" } } }, "types" : [ { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } ] } ], "steps" : [ { "desc" : "Set a heat block to 42 °C.", "inputs" : [] }, { "desc" : "Thaw an aliquot chemically competent bacteria on ice.", "inputs" : [] }, { "desc" : "Add plasmid DNA to the aliquot and mix gently by flicking the tube.", "inputs" : [ { "desc" : "Volume of DNA (µl)", "type" : "ufloat", "required" : true, "multiParam" : null } ] }, { "desc" : "Incubate the bacteria on ice for 10 min to 30 min.", "inputs" : [ { "desc" : "Duration (min)", "type" : "ufloat", "required" : true, "multiParam" : null } ] }, { "desc" : "Heat shock the bacteria for exactly 30 s (20 s for E. coli BL21(DE3)).", "inputs" : [ { "desc" : "Duration (s)", "type" : "ufloat", "required" : true, "multiParam" : null } ] }, { "desc" : "Incubate the bacteria on ice for approx. 5 min.", "inputs" : [ { "desc" : "Duration (min)", "type" : "ufloat", "required" : true, "multiParam" : null } ] }, { "desc" : "Add 1 ml of SOC or LB medium and recover the plasmids for 1 h at 37 °C while shaking (optional if the new plasmid only adds an Ampicillin resistance).", "inputs" : [ { "desc" : "Volume (µl)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Duration (min)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Temperature (°C)", "type" : "ufloat", "required" : true, "multiParam" : null } ] }, { "desc" : "Optionally spin down the recovered suspension and resuspend it in a minimal volume of medium.", "inputs" : [] }, { "desc" : "Plate the suspension on agar supplemented with the appropriate antibiotics (fill in the appropriate protocol here!).", "inputs" : [] } ] }, "kKiCHxutJLzPKayCC" : { "name" : "Streak bacteria carrying two plasmids onto an agar plate", "params" : [ { "type" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 }, "name" : "Bacteria carrying two plasmids", "multi" : false } ], "products" : [ { "allTypes" : [ { "_id" : "BcetWv5RJeQcBmfee", "name" : "Agar plate with bacteria carrying two plasmids", "v" : 0 } ], "name" : "Agar plate", "propertyBindings" : { "BcetWv5RJeQcBmfee" : { "1558d87b3c90b6b6f071e0956b41972a" : { "property" : { "name" : "Plasmid 2 name", "from" : { "_id" : "BcetWv5RJeQcBmfee", "name" : "Agar plate with bacteria carrying two plasmids", "v" : 0 } }, "source" : { "param" : "Bacteria carrying two plasmids", "paramProperty" : { "name" : "Plasmid 2 name", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" }, "1ed8ac857097c4fbbbc15cd373ef96bc" : { "property" : { "name" : "Strain", "from" : { "_id" : "BcetWv5RJeQcBmfee", "name" : "Agar plate with bacteria carrying two plasmids", "v" : 0 } }, "source" : { "param" : "Bacteria carrying two plasmids", "paramProperty" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" }, "22f17faf09867bb581e2c6776c2e9186" : { "property" : { "name" : "Resistance(s) encoded on plasmid 1", "from" : { "_id" : "BcetWv5RJeQcBmfee", "name" : "Agar plate with bacteria carrying two plasmids", "v" : 0 } }, "source" : { "param" : "Bacteria carrying two plasmids", "paramProperty" : { "name" : "Resistance(s) encoded on plasmid 1", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" }, "2ab23d19da35facf9f19887a4e325d28" : { "property" : { "name" : "Resistance(s) encoded on plasmid 2", "from" : { "_id" : "BcetWv5RJeQcBmfee", "name" : "Agar plate with bacteria carrying two plasmids", "v" : 0 } }, "source" : { "param" : "Bacteria carrying two plasmids", "paramProperty" : { "name" : "Resistance(s) encoded on plasmid 2", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" }, "e1520b5997a532c7889f6e8883920ab8" : { "property" : { "name" : "Species", "from" : { "_id" : "BcetWv5RJeQcBmfee", "name" : "Agar plate with bacteria carrying two plasmids", "v" : 0 } }, "source" : { "param" : "Bacteria carrying two plasmids", "paramProperty" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" }, "f922bf1c87974ac79330856f49dc41b7" : { "property" : { "name" : "Plasmid 1 name", "from" : { "_id" : "BcetWv5RJeQcBmfee", "name" : "Agar plate with bacteria carrying two plasmids", "v" : 0 } }, "source" : { "param" : "Bacteria carrying two plasmids", "paramProperty" : { "name" : "Plasmid 1 name", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" } } }, "types" : [ { "_id" : "BcetWv5RJeQcBmfee", "name" : "Agar plate with bacteria carrying two plasmids", "v" : 0 } ] } ], "steps" : [ { "desc" : "Streak the bacteria onto the agar plate or use sterile glass beads.", "inputs" : [ { "desc" : "Volume (µl)", "type" : "ufloat", "required" : true, "multiParam" : null } ] } ] }, "kxBySpW3SnbWuYMRw" : { "name" : "Streak bacteria carrying a plasmid onto an agar plate", "params" : [ { "type" : { "_id" : "PpBkfrLAqTw2CwNZX", "name" : "Bacteria carrying a plasmid", "v" : 2 }, "name" : "Bacteria carrying a plasmid", "multi" : false } ], "products" : [ { "allTypes" : [ { "_id" : "D2DD2v2FYpYQLFwji", "name" : "Agar plate with bacteria carrying a plasmid", "v" : 0 } ], "name" : "Agar plate", "propertyBindings" : { "D2DD2v2FYpYQLFwji" : { "0ac71517d2d368cdbabf8b9914716902" : { "property" : { "name" : "Plasmid name", "from" : { "_id" : "D2DD2v2FYpYQLFwji", "name" : "Agar plate with bacteria carrying a plasmid", "v" : 0 } }, "source" : { "param" : "Bacteria carrying a plasmid", "paramProperty" : { "name" : "Plasmid name", "from" : { "_id" : "PpBkfrLAqTw2CwNZX", "name" : "Bacteria carrying a plasmid", "v" : 2 } } }, "sourceType" : "paramProperty" }, "1ed8ac857097c4fbbbc15cd373ef96bc" : { "property" : { "name" : "Strain", "from" : { "_id" : "D2DD2v2FYpYQLFwji", "name" : "Agar plate with bacteria carrying a plasmid", "v" : 0 } }, "source" : { "param" : "Bacteria carrying a plasmid", "paramProperty" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" }, "e1520b5997a532c7889f6e8883920ab8" : { "property" : { "name" : "Species", "from" : { "_id" : "D2DD2v2FYpYQLFwji", "name" : "Agar plate with bacteria carrying a plasmid", "v" : 0 } }, "source" : { "param" : "Bacteria carrying a plasmid", "paramProperty" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" }, "e4963ca4d4576f5cb6f8af52e3d038b6" : { "property" : { "name" : "Resistances(s) encoded on the plasmid", "from" : { "_id" : "D2DD2v2FYpYQLFwji", "name" : "Agar plate with bacteria carrying a plasmid", "v" : 0 } }, "source" : { "param" : "Bacteria carrying a plasmid", "paramProperty" : { "name" : "Resistance(s) encoded by the plasmid", "from" : { "_id" : "PpBkfrLAqTw2CwNZX", "name" : "Bacteria carrying a plasmid", "v" : 2 } } }, "sourceType" : "paramProperty" } } }, "types" : [ { "_id" : "D2DD2v2FYpYQLFwji", "name" : "Agar plate with bacteria carrying a plasmid", "v" : 0 } ] } ], "steps" : [ { "desc" : "Streak the bacteria onto the agar plate or use sterile glass beads.", "inputs" : [ { "desc" : "Volume (µl)", "type" : "ufloat", "required" : true, "multiParam" : null } ] } ] }, "mJNyMCoEko3JKRv5x" : { "name" : "Heat shock plasmid transformation (0 -> 1 plasmid)", "params" : [ { "type" : { "_id" : "Xwooe4QfsLfskZNvG", "name" : "Chemically competent bacteria without any plasmid", "v" : 0 }, "name" : "Chemically competent bacteria", "multi" : false }, { "type" : { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 }, "name" : "Plasmid", "multi" : false } ], "products" : [ { "allTypes" : [ { "_id" : "PpBkfrLAqTw2CwNZX", "name" : "Bacteria carrying a plasmid", "v" : 2 }, { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } ], "name" : "Bacteria carrying the plasmid", "propertyBindings" : { "PpBkfrLAqTw2CwNZX" : { "0ac71517d2d368cdbabf8b9914716902" : { "property" : { "name" : "Plasmid name", "from" : { "_id" : "PpBkfrLAqTw2CwNZX", "name" : "Bacteria carrying a plasmid", "v" : 2 } }, "source" : { "param" : "Plasmid", "paramProperty" : { "name" : "Name", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } } }, "sourceType" : "paramProperty" }, "10990dcf66373fff11ef907bc2b1ef97" : { "property" : { "name" : "Resistance(s) encoded by the plasmid", "from" : { "_id" : "PpBkfrLAqTw2CwNZX", "name" : "Bacteria carrying a plasmid", "v" : 2 } }, "source" : { "param" : "Plasmid", "paramProperty" : { "name" : "Resistance marker(s)", "from" : { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 } } }, "sourceType" : "paramProperty" } }, "YW7epnToTmqmHEEwx" : { "1ed8ac857097c4fbbbc15cd373ef96bc" : { "property" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Chemically competent bacteria", "paramProperty" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" }, "e1520b5997a532c7889f6e8883920ab8" : { "property" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Chemically competent bacteria", "paramProperty" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" } } }, "types" : [ { "_id" : "PpBkfrLAqTw2CwNZX", "name" : "Bacteria carrying a plasmid", "v" : 2 } ] } ], "steps" : [ { "desc" : "Set a heat block to 42 °C.", "inputs" : [] }, { "desc" : "Thaw an aliquot chemically competent bacteria on ice.", "inputs" : [] }, { "desc" : "Add plasmid DNA to the aliquot and mix gently by flicking the tube.", "inputs" : [ { "desc" : "Volume of DNA (µl)", "type" : "ufloat", "required" : true, "multiParam" : null } ] }, { "desc" : "Incubate the bacteria on ice for 10 min to 30 min.", "inputs" : [ { "desc" : "Duration (min)", "type" : "ufloat", "required" : true, "multiParam" : null } ] }, { "desc" : "Heat shock the bacteria for exactly 30 s (20 s for E. coli BL21(DE3)).", "inputs" : [ { "desc" : "Duration (s)", "type" : "ufloat", "required" : true, "multiParam" : null } ] }, { "desc" : "Incubate the bacteria on ice for approx. 5 min.", "inputs" : [ { "desc" : "Duration (min)", "type" : "ufloat", "required" : true, "multiParam" : null } ] }, { "desc" : "Add 1 ml of SOC or LB medium and recover the plasmids for 1 h at 37 °C while shaking (optional if the new plasmid only adds an Ampicillin resistance).", "inputs" : [ { "desc" : "Volume (µl)", "type" : "ufloat", "required" : false, "multiParam" : null }, { "desc" : "Duration (min)", "type" : "ufloat", "required" : false, "multiParam" : null }, { "desc" : "Temperature (°C)", "type" : "float", "required" : false, "multiParam" : null } ] }, { "desc" : "Optionally spin down the recovered suspension and resuspend it in a minimal volume of medium.", "inputs" : [] }, { "desc" : "Plate the suspension on agar supplemented with the appropriate antibiotics (fill in the appropriate protocol here!).", "inputs" : [] } ] }, "maDx7F6ry8Mw5JmKf" : { "name" : "Pick a colony carrying a plasmid from an agar plate", "params" : [ { "type" : { "_id" : "D2DD2v2FYpYQLFwji", "name" : "Agar plate with bacteria carrying a plasmid", "v" : 0 }, "name" : "Agar plate with bacteria carrying a plasmid", "multi" : false } ], "products" : [ { "allTypes" : [ { "_id" : "PpBkfrLAqTw2CwNZX", "name" : "Bacteria carrying a plasmid", "v" : 2 }, { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } ], "name" : "Colony", "propertyBindings" : { "PpBkfrLAqTw2CwNZX" : { "0ac71517d2d368cdbabf8b9914716902" : { "property" : { "name" : "Plasmid name", "from" : { "_id" : "PpBkfrLAqTw2CwNZX", "name" : "Bacteria carrying a plasmid", "v" : 2 } }, "source" : { "param" : "Agar plate with bacteria carrying a plasmid", "paramProperty" : { "name" : "Plasmid name", "from" : { "_id" : "D2DD2v2FYpYQLFwji", "name" : "Agar plate with bacteria carrying a plasmid", "v" : 0 } } }, "sourceType" : "paramProperty" }, "10990dcf66373fff11ef907bc2b1ef97" : { "property" : { "name" : "Resistance(s) encoded by the plasmid", "from" : { "_id" : "PpBkfrLAqTw2CwNZX", "name" : "Bacteria carrying a plasmid", "v" : 2 } }, "source" : { "param" : "Agar plate with bacteria carrying a plasmid", "paramProperty" : { "name" : "Resistances(s) encoded on the plasmid", "from" : { "_id" : "D2DD2v2FYpYQLFwji", "name" : "Agar plate with bacteria carrying a plasmid", "v" : 0 } } }, "sourceType" : "paramProperty" } }, "YW7epnToTmqmHEEwx" : { "1ed8ac857097c4fbbbc15cd373ef96bc" : { "property" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Agar plate with bacteria carrying a plasmid", "paramProperty" : { "name" : "Strain", "from" : { "_id" : "D2DD2v2FYpYQLFwji", "name" : "Agar plate with bacteria carrying a plasmid", "v" : 0 } } }, "sourceType" : "paramProperty" }, "e1520b5997a532c7889f6e8883920ab8" : { "property" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Agar plate with bacteria carrying a plasmid", "paramProperty" : { "name" : "Species", "from" : { "_id" : "D2DD2v2FYpYQLFwji", "name" : "Agar plate with bacteria carrying a plasmid", "v" : 0 } } }, "sourceType" : "paramProperty" } } }, "types" : [ { "_id" : "PpBkfrLAqTw2CwNZX", "name" : "Bacteria carrying a plasmid", "v" : 2 } ] } ], "steps" : [ { "desc" : "Pick up a sterile tip with a pipette. Dip it into a single colony so it attaches to the tip without applying suction.", "inputs" : [ { "desc" : "Colony number (arbitrary)", "type" : "text", "required" : true, "multiParam" : null } ] }, { "desc" : "Resuspend the colony in sterile medium or water.", "inputs" : [] } ] }, "ms6uHrB9Fv23Tge2J" : { "name" : "Make a glycerol stock of bacteria carrying two plasmid", "params" : [ { "type" : { "_id" : "REPr8yPYRdPN6gKRB", "name" : "Bacterial culture carrying two plasmids", "v" : 0 }, "name" : "Bacterial culture carrying two plasmids", "multi" : false } ], "products" : [ { "allTypes" : [ { "_id" : "rStb6rLuoj5YiEcYc", "name" : "Glycerol stock of bacteria carrying two plasmids", "v" : 0 }, { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 }, { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } ], "name" : "Glycerol stock", "propertyBindings" : { "YW7epnToTmqmHEEwx" : { "1ed8ac857097c4fbbbc15cd373ef96bc" : { "property" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Bacterial culture carrying two plasmids", "paramProperty" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" }, "e1520b5997a532c7889f6e8883920ab8" : { "property" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Bacterial culture carrying two plasmids", "paramProperty" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" } }, "xJHpdoBri9Ay3g5bP" : { "1558d87b3c90b6b6f071e0956b41972a" : { "property" : { "name" : "Plasmid 2 name", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } }, "source" : { "param" : "Bacterial culture carrying two plasmids", "paramProperty" : { "name" : "Plasmid 2 name", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" }, "22f17faf09867bb581e2c6776c2e9186" : { "property" : { "name" : "Resistance(s) encoded on plasmid 1", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } }, "source" : { "param" : "Bacterial culture carrying two plasmids", "paramProperty" : { "name" : "Resistance(s) encoded on plasmid 1", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" }, "2ab23d19da35facf9f19887a4e325d28" : { "property" : { "name" : "Resistance(s) encoded on plasmid 2", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } }, "source" : { "param" : "Bacterial culture carrying two plasmids", "paramProperty" : { "name" : "Resistance(s) encoded on plasmid 2", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" }, "f922bf1c87974ac79330856f49dc41b7" : { "property" : { "name" : "Plasmid 1 name", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } }, "source" : { "param" : "Bacterial culture carrying two plasmids", "paramProperty" : { "name" : "Plasmid 1 name", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" } } }, "types" : [ { "_id" : "rStb6rLuoj5YiEcYc", "name" : "Glycerol stock of bacteria carrying two plasmids", "v" : 0 } ] } ], "steps" : [ { "desc" : "Mix an aliquot of a LB culture with the same volume of storage buffer.", "inputs" : [] }, { "desc" : "Freeze at -80 °C.", "inputs" : [] } ] }, "mzGLz4CZBhmDHNivi" : { "name" : "Make Medium", "params" : [], "products" : [ { "allTypes" : [ { "_id" : "HS9a6rQbkgvXHqtqP", "name" : "Medium", "v" : 0 } ], "name" : "Medium", "propertyBindings" : { "HS9a6rQbkgvXHqtqP" : { "445236f3cc0cda3bb87208a67be7d3f4" : { "property" : { "name" : "Antibiotics", "from" : { "_id" : "HS9a6rQbkgvXHqtqP", "name" : "Medium", "v" : 1 } }, "source" : { "step" : 0, "input" : 2 }, "sourceType" : "input" }, "49ee3087348e8d44e1feda1917443987" : { "property" : { "name" : "Name", "from" : { "_id" : "HS9a6rQbkgvXHqtqP", "name" : "Medium", "v" : 1 } }, "source" : { "step" : 0, "input" : 0 }, "sourceType" : "input" }, "98fc9226c3fe878e39cd048fbd1c3692" : { "property" : { "name" : "Short name", "from" : { "_id" : "HS9a6rQbkgvXHqtqP", "name" : "Medium", "v" : 1 } }, "source" : { "step" : 0, "input" : 3 }, "sourceType" : "input" }, "f15c1cae7882448b3fb0404682e17e61" : { "property" : { "name" : "Content", "from" : { "_id" : "HS9a6rQbkgvXHqtqP", "name" : "Medium", "v" : 1 } }, "source" : { "step" : 0, "input" : 1 }, "sourceType" : "input" } } }, "types" : [ { "_id" : "HS9a6rQbkgvXHqtqP", "name" : "Medium", "v" : 0 } ] } ], "steps" : [ { "desc" : "Put appropriate amount of Mediums powder, put it into correct bottle, label it correctly and put in the correct box for autoclavation", "inputs" : [ { "desc" : "Name of the Medium", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "Content of the Medium", "type" : "text", "required" : false, "multiParam" : null }, { "desc" : "Antibiotics of the Medium", "type" : "text", "required" : false, "multiParam" : null }, { "desc" : "Short Name of the Medium", "type" : "text", "required" : false, "multiParam" : null } ] } ] }, "n4Sg8s8AfhMEtQtFH" : { "name" : "Plasmid ligation with T4 DNA Ligase (NEB)", "params" : [ { "type" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 }, "name" : "dsDNA", "multi" : true } ], "products" : [ { "allTypes" : [ { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 } ], "name" : "Plasmid", "propertyBindings" : { "cvt43tybpDTWdk2xR" : { "c29e15397d29fc94dad70016db7ab2e9" : { "property" : { "name" : "Resistance marker(s)", "from" : { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 } }, "source" : { "step" : 1, "input" : 3 }, "sourceType" : "input" } }, "k9LEWTcbmQn53Gzo7" : { "49ee3087348e8d44e1feda1917443987" : { "property" : { "name" : "Name", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 1, "input" : 1 }, "sourceType" : "input" }, "4da843835f15245d46602c3d57b579b6" : { "property" : { "name" : "Concentration (ng/µl)", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 1, "input" : 4 }, "sourceType" : "input" }, "6f8ac39f837ee4598b7358ce18aec601" : { "property" : { "name" : "Tube identifier", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 1, "input" : 2 }, "sourceType" : "input" } } }, "types" : [ { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 } ] } ], "steps" : [ { "desc" : "Mix water and T4 DNA Ligase Buffer (NEB).", "inputs" : [ { "desc" : "Volume of water (µl)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Volume of buffer(µl)", "type" : "ufloat", "required" : true, "multiParam" : null } ] }, { "desc" : "Add DNA.", "inputs" : [ { "desc" : "Volume of DNA (µl)", "type" : "ufloat", "required" : true, "multiParam" : "dsDNA" }, { "desc" : "Name of the resulting plasmid", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "Identifier of the resulting plasmid tube", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "Resistance marker(s) on the resulting plasmid", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "Total DNA concentration (ng/µl)", "type" : "ufloat", "required" : false, "multiParam" : null } ] }, { "desc" : "Incubate at room temperature.", "inputs" : [ { "desc" : "Duration (min)", "type" : "ufloat", "required" : true, "multiParam" : null } ] } ] }, "oFoQguhSKQKC2Hfms" : { "name" : "Gather bacteria carrying a plasmid from an agar plate", "params" : [ { "type" : { "_id" : "D2DD2v2FYpYQLFwji", "name" : "Agar plate with bacteria carrying a plasmid", "v" : 0 }, "name" : "Agar plate with bacteria carrying a plasmid", "multi" : false } ], "products" : [ { "allTypes" : [ { "_id" : "PpBkfrLAqTw2CwNZX", "name" : "Bacteria carrying a plasmid", "v" : 2 }, { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } ], "name" : "Bacteria", "propertyBindings" : { "PpBkfrLAqTw2CwNZX" : { "0ac71517d2d368cdbabf8b9914716902" : { "property" : { "name" : "Plasmid name", "from" : { "_id" : "PpBkfrLAqTw2CwNZX", "name" : "Bacteria carrying a plasmid", "v" : 2 } }, "source" : { "param" : "Agar plate with bacteria carrying a plasmid", "paramProperty" : { "name" : "Plasmid name", "from" : { "_id" : "D2DD2v2FYpYQLFwji", "name" : "Agar plate with bacteria carrying a plasmid", "v" : 0 } } }, "sourceType" : "paramProperty" }, "10990dcf66373fff11ef907bc2b1ef97" : { "property" : { "name" : "Resistance(s) encoded by the plasmid", "from" : { "_id" : "PpBkfrLAqTw2CwNZX", "name" : "Bacteria carrying a plasmid", "v" : 2 } }, "source" : { "param" : "Agar plate with bacteria carrying a plasmid", "paramProperty" : { "name" : "Resistances(s) encoded on the plasmid", "from" : { "_id" : "D2DD2v2FYpYQLFwji", "name" : "Agar plate with bacteria carrying a plasmid", "v" : 0 } } }, "sourceType" : "paramProperty" } }, "YW7epnToTmqmHEEwx" : { "1ed8ac857097c4fbbbc15cd373ef96bc" : { "property" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Agar plate with bacteria carrying a plasmid", "paramProperty" : { "name" : "Strain", "from" : { "_id" : "D2DD2v2FYpYQLFwji", "name" : "Agar plate with bacteria carrying a plasmid", "v" : 0 } } }, "sourceType" : "paramProperty" }, "e1520b5997a532c7889f6e8883920ab8" : { "property" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Agar plate with bacteria carrying a plasmid", "paramProperty" : { "name" : "Species", "from" : { "_id" : "D2DD2v2FYpYQLFwji", "name" : "Agar plate with bacteria carrying a plasmid", "v" : 0 } } }, "sourceType" : "paramProperty" } } }, "types" : [ { "_id" : "PpBkfrLAqTw2CwNZX", "name" : "Bacteria carrying a plasmid", "v" : 2 } ] } ], "steps" : [ { "desc" : "Using a sterile item, gather some bacteria from the plate.", "inputs" : [] } ] }, "ojKqKzgeLkvNvLDgw" : { "name" : "Heat shock plasmid transformation (0 -> 2 plasmids)", "params" : [ { "type" : { "_id" : "Xwooe4QfsLfskZNvG", "name" : "Chemically competent bacteria without any plasmid", "v" : 0 }, "name" : "Chemically competent bacteria without any plasmid", "multi" : false }, { "type" : { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 }, "name" : "Plasmid 1", "multi" : false }, { "type" : { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 }, "name" : "Plasmid 2", "multi" : false } ], "products" : [ { "allTypes" : [ { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 }, { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } ], "name" : "Transformed bacteria", "propertyBindings" : { "YW7epnToTmqmHEEwx" : { "1ed8ac857097c4fbbbc15cd373ef96bc" : { "property" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Chemically competent bacteria without any plasmid", "paramProperty" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" }, "e1520b5997a532c7889f6e8883920ab8" : { "property" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Chemically competent bacteria without any plasmid", "paramProperty" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" } }, "xJHpdoBri9Ay3g5bP" : { "1558d87b3c90b6b6f071e0956b41972a" : { "property" : { "name" : "Plasmid 2 name", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } }, "source" : { "param" : "Plasmid 2", "paramProperty" : { "name" : "Name", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } } }, "sourceType" : "paramProperty" }, "22f17faf09867bb581e2c6776c2e9186" : { "property" : { "name" : "Resistance(s) encoded on plasmid 1", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } }, "source" : { "param" : "Plasmid 1", "paramProperty" : { "name" : "Resistance marker(s)", "from" : { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 } } }, "sourceType" : "paramProperty" }, "2ab23d19da35facf9f19887a4e325d28" : { "property" : { "name" : "Resistance(s) encoded on plasmid 2", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } }, "source" : { "param" : "Plasmid 2", "paramProperty" : { "name" : "Resistance marker(s)", "from" : { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 } } }, "sourceType" : "paramProperty" }, "f922bf1c87974ac79330856f49dc41b7" : { "property" : { "name" : "Plasmid 1 name", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } }, "source" : { "param" : "Plasmid 1", "paramProperty" : { "name" : "Name", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } } }, "sourceType" : "paramProperty" } } }, "types" : [ { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } ] } ], "steps" : [ { "desc" : "Set a heat block to 42 °C.", "inputs" : [] }, { "desc" : "Thaw an aliquot chemically competent bacteria on ice.", "inputs" : [] }, { "desc" : "Add plasmid DNA to the aliquot and mix gently by flicking the tube.", "inputs" : [ { "desc" : "Volume of plasmid 1 (µl)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Volume of plasmid 2 (µl)", "type" : "ufloat", "required" : true, "multiParam" : null } ] }, { "desc" : "Incubate the bacteria on ice for 10 min to 30 min.", "inputs" : [ { "desc" : "Duration (min)", "type" : "ufloat", "required" : true, "multiParam" : null } ] }, { "desc" : "Heat shock the bacteria for exactly 30 s (20 s for E. coli BL21(DE3)).", "inputs" : [ { "desc" : "Duration (s)", "type" : "ufloat", "required" : true, "multiParam" : null } ] }, { "desc" : "Incubate the bacteria on ice for approx. 5 min.", "inputs" : [ { "desc" : "Duration (min)", "type" : "ufloat", "required" : true, "multiParam" : null } ] }, { "desc" : "Add 1 ml of SOC or LB medium and recover the plasmids for 1 h at 37 °C while shaking.", "inputs" : [ { "desc" : "Volume (µl)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Duration (min)", "type" : "ufloat", "required" : true, "multiParam" : null } ] }, { "desc" : "Optionally spin down the recovered suspension and resuspend it in a minimal volume of medium.", "inputs" : [] }, { "desc" : "Plate the suspension on agar supplemented with the appropriate antibiotics (fill in the appropriate protocol here!).", "inputs" : [] } ] }, "ovMK2ktEeSommgLa2" : { "name" : "Heat shock plasmid transformation (1 -> 3 plasmids)", "params" : [ { "type" : { "_id" : "ynpgBQKNqRETb9wZF", "name" : "Chemically competent bacteria already carrying a plasmid", "v" : 3 }, "name" : "Chemically competent bacteria already carrying a plasmid", "multi" : false }, { "type" : { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 }, "name" : "Plasmid 1", "multi" : false }, { "type" : { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 }, "name" : "Plasmid 2", "multi" : false } ], "products" : [ { "allTypes" : [ { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 }, { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } ], "name" : "Transformed bacteria", "propertyBindings" : { "TnHge69a2HdoogyYG" : { "1558d87b3c90b6b6f071e0956b41972a" : { "property" : { "name" : "Plasmid 2 name", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } }, "source" : { "param" : "Plasmid 1", "paramProperty" : { "name" : "Name", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } } }, "sourceType" : "paramProperty" }, "22f17faf09867bb581e2c6776c2e9186" : { "property" : { "name" : "Resistance(s) encoded on plasmid 1", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } }, "source" : { "param" : "Chemically competent bacteria already carrying a plasmid", "paramProperty" : { "name" : "Resistance(s) encoded by the plasmid", "from" : { "_id" : "PpBkfrLAqTw2CwNZX", "name" : "Bacteria carrying a plasmid", "v" : 2 } } }, "sourceType" : "paramProperty" }, "2ab23d19da35facf9f19887a4e325d28" : { "property" : { "name" : "Resistance(s) encoded on plasmid 2", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } }, "source" : { "param" : "Plasmid 1", "paramProperty" : { "name" : "Resistance marker(s)", "from" : { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 } } }, "sourceType" : "paramProperty" }, "2b3de1e4d39cf71091ae27f0bbf41cb6" : { "property" : { "name" : "Resistance(s) encoded on plasmid 3", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } }, "source" : { "param" : "Plasmid 2", "paramProperty" : { "name" : "Resistance marker(s)", "from" : { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 } } }, "sourceType" : "paramProperty" }, "f922bf1c87974ac79330856f49dc41b7" : { "property" : { "name" : "Plasmid 1 name", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } }, "source" : { "param" : "Chemically competent bacteria already carrying a plasmid", "paramProperty" : { "name" : "Plasmid name", "from" : { "_id" : "PpBkfrLAqTw2CwNZX", "name" : "Bacteria carrying a plasmid", "v" : 2 } } }, "sourceType" : "paramProperty" }, "f941ce021dd20e581e58121991cbb4dd" : { "property" : { "name" : "Plasmid 3 name", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } }, "source" : { "param" : "Plasmid 2", "paramProperty" : { "name" : "Name", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } } }, "sourceType" : "paramProperty" } }, "YW7epnToTmqmHEEwx" : { "1ed8ac857097c4fbbbc15cd373ef96bc" : { "property" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Chemically competent bacteria already carrying a plasmid", "paramProperty" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" }, "e1520b5997a532c7889f6e8883920ab8" : { "property" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Chemically competent bacteria already carrying a plasmid", "paramProperty" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" } } }, "types" : [ { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } ] } ], "steps" : [ { "desc" : "Set a heat block to 42 °C.", "inputs" : [] }, { "desc" : "Thaw an aliquot chemically competent bacteria on ice.", "inputs" : [] }, { "desc" : "Add plasmid DNA to the aliquot and mix gently by flicking the tube.", "inputs" : [ { "desc" : "Volume of plasmid 1 (µl)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Volume of plasmid 2 (µl)", "type" : "ufloat", "required" : true, "multiParam" : null } ] }, { "desc" : "Incubate the bacteria on ice for 10 min to 30 min.", "inputs" : [ { "desc" : "Duration (min)", "type" : "ufloat", "required" : true, "multiParam" : null } ] }, { "desc" : "Heat shock the bacteria for exactly 30 s (20 s for E. coli BL21(DE3)).", "inputs" : [ { "desc" : "Duration (s)", "type" : "ufloat", "required" : true, "multiParam" : null } ] }, { "desc" : "Incubate the bacteria on ice for approx. 5 min.", "inputs" : [ { "desc" : "Duration (min)", "type" : "ufloat", "required" : true, "multiParam" : null } ] }, { "desc" : "Add 1 ml of SOC or LB medium and recover the plasmids for 1 h at 37 °C while shaking.", "inputs" : [ { "desc" : "Volume (µl)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Duration (min)", "type" : "ufloat", "required" : true, "multiParam" : null } ] }, { "desc" : "Optionally spin down the recovered suspension and resuspend it in a minimal volume of medium.", "inputs" : [] }, { "desc" : "Plate the suspension on agar supplemented with the appropriate antibiotics (fill in the appropriate protocol here!).", "inputs" : [] } ] }, "pk9LqRH9ot8JiKx23" : { "name" : "Make a glycerol stock of bacteria without any plasmid", "params" : [ { "type" : { "_id" : "8p9DTRXiSoymBbC3T", "name" : "Bacterial culture without any plasmid", "v" : 1 }, "name" : "Bacterial culture", "multi" : false } ], "products" : [ { "allTypes" : [ { "_id" : "43wT4pL9HtNJZkbXg", "name" : "Glycerol stock of bacteria without any plasmid", "v" : 0 }, { "_id" : "nQbZRzR4ZeKkYMr8X", "name" : "Bacteria without any plasmid", "v" : 0 }, { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } ], "name" : "Glycerol stock", "propertyBindings" : { "YW7epnToTmqmHEEwx" : { "1ed8ac857097c4fbbbc15cd373ef96bc" : { "property" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Bacterial culture", "paramProperty" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" }, "e1520b5997a532c7889f6e8883920ab8" : { "property" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Bacterial culture", "paramProperty" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" } } }, "types" : [ { "_id" : "43wT4pL9HtNJZkbXg", "name" : "Glycerol stock of bacteria without any plasmid", "v" : 0 } ] } ], "steps" : [ { "desc" : "Mix an aliquot of a LB culture with the same volume of storage buffer.", "inputs" : [] }, { "desc" : "Freeze at -80 °C.", "inputs" : [] } ] }, "qGNf5sATkiC4P7RqF" : { "name" : "Gather bacteria carrying two plasmids from an agar plate", "params" : [ { "type" : { "_id" : "BcetWv5RJeQcBmfee", "name" : "Agar plate with bacteria carrying two plasmids", "v" : 0 }, "name" : "Agar plate with bacteria carrying two plasmids", "multi" : false } ], "products" : [ { "allTypes" : [ { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 }, { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } ], "name" : "Bacteria", "propertyBindings" : { "YW7epnToTmqmHEEwx" : { "1ed8ac857097c4fbbbc15cd373ef96bc" : { "property" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Agar plate with bacteria carrying two plasmids", "paramProperty" : { "name" : "Strain", "from" : { "_id" : "BcetWv5RJeQcBmfee", "name" : "Agar plate with bacteria carrying two plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" }, "e1520b5997a532c7889f6e8883920ab8" : { "property" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Agar plate with bacteria carrying two plasmids", "paramProperty" : { "name" : "Species", "from" : { "_id" : "BcetWv5RJeQcBmfee", "name" : "Agar plate with bacteria carrying two plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" } }, "xJHpdoBri9Ay3g5bP" : { "1558d87b3c90b6b6f071e0956b41972a" : { "property" : { "name" : "Plasmid 2 name", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } }, "source" : { "param" : "Agar plate with bacteria carrying two plasmids", "paramProperty" : { "name" : "Plasmid 2 name", "from" : { "_id" : "BcetWv5RJeQcBmfee", "name" : "Agar plate with bacteria carrying two plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" }, "22f17faf09867bb581e2c6776c2e9186" : { "property" : { "name" : "Resistance(s) encoded on plasmid 1", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } }, "source" : { "param" : "Agar plate with bacteria carrying two plasmids", "paramProperty" : { "name" : "Resistance(s) encoded on plasmid 1", "from" : { "_id" : "BcetWv5RJeQcBmfee", "name" : "Agar plate with bacteria carrying two plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" }, "2ab23d19da35facf9f19887a4e325d28" : { "property" : { "name" : "Resistance(s) encoded on plasmid 2", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } }, "source" : { "param" : "Agar plate with bacteria carrying two plasmids", "paramProperty" : { "name" : "Resistance(s) encoded on plasmid 2", "from" : { "_id" : "BcetWv5RJeQcBmfee", "name" : "Agar plate with bacteria carrying two plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" }, "f922bf1c87974ac79330856f49dc41b7" : { "property" : { "name" : "Plasmid 1 name", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } }, "source" : { "param" : "Agar plate with bacteria carrying two plasmids", "paramProperty" : { "name" : "Plasmid 1 name", "from" : { "_id" : "BcetWv5RJeQcBmfee", "name" : "Agar plate with bacteria carrying two plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" } } }, "types" : [ { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } ] } ], "steps" : [ { "desc" : "Using a sterile item, gather some bacteria from the plate.", "inputs" : [] } ] }, "rruYDCjZRHTSEgj9g" : { "name" : "Expression of Dnmt1 (linear)", "params" : [ { "multi" : false, "name" : "Protein", "type" : { "_id" : "EvktbSLNuky83N3ve", "name" : "Protein", "v" : 0 } } ], "products" : [ { "allTypes" : [ { "_id" : "EvktbSLNuky83N3ve", "name" : "Protein", "v" : 0 } ], "name" : "Dnmt1 (linear)", "propertyBindings" : { "EvktbSLNuky83N3ve" : { "cf61794ef8e0f6c9fd2fc60c97816c58" : { "property" : { "name" : "Molecular weight (kDa)", "from" : { "_id" : "EvktbSLNuky83N3ve", "name" : "Protein", "v" : 0 } }, "source" : { "param" : "Protein", "paramProperty" : { "name" : "Molecular weight (kDa)", "from" : { "_id" : "EvktbSLNuky83N3ve", "name" : "Protein", "v" : 0 } } }, "sourceType" : "paramProperty" } } }, "types" : [ { "_id" : "EvktbSLNuky83N3ve", "name" : "Protein", "v" : 0 } ] } ], "steps" : [ { "desc" : "Transform the plasmid harboring DNMT1 (Kanamycin resistant) into Rosetta DE3 competent cells (Chloramphenicol resistant) ( negative control untransformed)", "inputs" : [ { "desc" : "(Transformation protocol)", "type" : "text", "required" : true, "multiParam" : null } ] }, { "desc" : "Inoculate a few colonies to 40 ml LB+Kan+Cm medium to grow the cells overnight at 37 °C (Prepare 4l LB+Kan+Cm medium to autoclave)", "inputs" : [ { "desc" : "Culturing size", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "Incubation time (h)", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "Incubation temperature (°C)", "type" : "text", "required" : true, "multiParam" : null } ] }, { "desc" : "Dispense 10 ml of the growth culture into each 1 l flask and grow the cells at 37 °C. When the cell OD reaches ~0.6, lower the temperature to 15-20 °C", "inputs" : [ { "desc" : "Incubation time (min)", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "Incubation temperature (°C)", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "OD when lowering temperature", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "lowered incubation temperature (°C)", "type" : "text", "required" : true, "multiParam" : null } ] }, { "desc" : "30 min later, add IPTG (0.4 mM final concentration) and ZnCl2 (0.1 mM final concentration) into the media and continue to grow the cells overnight.", "inputs" : [ { "desc" : "added IPTG concentration (mM)", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "added ZnCl2 concentration (mM)", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "incubation time (h)", "type" : "text", "required" : true, "multiParam" : null } ] }, { "desc" : "Spin down the cells at 4000 rpm for 20 min (4 °C, 5th or 6th floor, fill 500 ml buckets for Ja10 rotor to 375 ml), and resuspend the cell paste in HisTrap loading buffer, with approximately 20 ml buffer for each liter of cell paste. (Take sample S1, accordingly C1 from untransformed control)", "inputs" : [ { "desc" : "spin down rpm ", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "spin down time (min)", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "resuspension amount", "type" : "text", "required" : true, "multiParam" : null } ] }, { "desc" : "SONICATION of the cells (Lohmann group, cold room 4th floor) while keeping them on ice, disrupt the cells using sonication. To avoid the protein degradation and aggregation, add PMSF and DTT to 1 μM and 0.5 mM respectively.", "inputs" : [ { "desc" : "added PMSF concentration (µM)", "type" : "uint", "required" : true, "multiParam" : null }, { "desc" : "added DTT concentration (mM)", "type" : "uint", "required" : true, "multiParam" : null } ] }, { "desc" : "Place the sonication tip in the sample, close to the bottom, but not touching the tube. Select the right program: Microtip: yes; Amplitude 60; Working time 2 min; On 0.02; Off 0.05 After 5 minutes, check if the sample did not heat up and repeat the program one more time. Clean the tip with some ethanol after use.", "inputs" : [ { "desc" : "Amplitude", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "Working time (min)", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "On", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "Off", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "Working time (min)", "type" : "text", "required" : true, "multiParam" : null } ] }, { "desc" : "After the cell is lysed, spin down the cell lysate using high speed or ultracentrifuge (17000 rpm x 45 min, Ti70 rotor, thick wall tubes [355631], filled to 15 ml)", "inputs" : [ { "desc" : "rpm", "type" : "uint", "required" : true, "multiParam" : null }, { "desc" : "time (min)", "type" : "uint", "required" : true, "multiParam" : null } ] }, { "desc" : "Collect the supernatant. If any aggregates or particles are visible, filter the supernatant with a 0.2 µm filter using a syringe. (Take sample from supernatant S2 and pellet S3, accordingly C2 and C3 from untransformed control)", "inputs" : [ { "desc" : "filtering due to visible aggregates ", "type" : "bool", "required" : true, "multiParam" : null } ] }, { "desc" : "Load the supernatant to pre-equilibrated HisTrap column, wash the column using 200 ml of chilled His trap loading buffer, and elute the fusion protein using elution buffer.", "inputs" : [ { "desc" : "wash volume (ml)", "type" : "uint", "required" : true, "multiParam" : null }, { "desc" : "elute volume (ml)", "type" : "uint", "required" : true, "multiParam" : null } ] }, { "desc" : "Collect the eluent and dialyze the protein sample against dialysis buffer overnight at 4C. > Optional: adding protease inhibitor cocktail tablets will help DNMT1 from proteolytic degradation.", "inputs" : [ { "desc" : "Dialysis time (h)", "type" : "uint", "required" : true, "multiParam" : null }, { "desc" : "protease inhibitor cocktail tablet", "type" : "bool", "required" : true, "multiParam" : null } ] }, { "desc" : "Take out sample from dialysis tube, spin down the sample and remove any precipitate", "inputs" : [ { "desc" : "rpm", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "time (min)", "type" : "text", "required" : true, "multiParam" : null } ] }, { "desc" : "Load the supernatant to the Heparin column, then apply the salt gradient with Buffer A and B. The target protein is expected to elute at 0.4-0.5 M NaCl.", "inputs" : [] }, { "desc" : "Collect the fractions and run the SDS Page to examine the protein (~100 kD). Pool together the protein fraction with significant purity", "inputs" : [] }, { "desc" : "Concentrate the fractions to about 1 ml using concentration spin columns (25MWCO)", "inputs" : [] }, { "desc" : "The protein is finally purified through a 16/60 Superdex 200 size exclusion column using Gel filtration buffer", "inputs" : [] }, { "desc" : "After the gel filtration, the protein will be examined by SDS page. The fractions with >90% purity will be pooled", "inputs" : [] }, { "desc" : "Concentration of sample and storage at -80C freezer.", "inputs" : [] } ] }, "v97Nktv4idauP3hYh" : { "name" : "Make competent cells already carrying two plasmid", "params" : [ { "type" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 }, "name" : "Bacteria carrying two plasmids", "multi" : false } ], "products" : [ { "allTypes" : [ { "_id" : "GRdscXrjMDhW6E8FF", "name" : "Chemically competent bacteria already carrying two plasmid", "v" : 0 }, { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 }, { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } ], "name" : "Competent cells", "propertyBindings" : { "YW7epnToTmqmHEEwx" : { "1ed8ac857097c4fbbbc15cd373ef96bc" : { "property" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Bacteria carrying two plasmids", "paramProperty" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" }, "e1520b5997a532c7889f6e8883920ab8" : { "property" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Bacteria carrying two plasmids", "paramProperty" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" } }, "xJHpdoBri9Ay3g5bP" : { "1558d87b3c90b6b6f071e0956b41972a" : { "property" : { "name" : "Plasmid 2 name", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } }, "source" : { "param" : "Bacteria carrying two plasmids", "paramProperty" : { "name" : "Plasmid 2 name", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" }, "22f17faf09867bb581e2c6776c2e9186" : { "property" : { "name" : "Resistance(s) encoded on plasmid 1", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } }, "source" : { "param" : "Bacteria carrying two plasmids", "paramProperty" : { "name" : "Resistance(s) encoded on plasmid 1", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" }, "2ab23d19da35facf9f19887a4e325d28" : { "property" : { "name" : "Resistance(s) encoded on plasmid 2", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } }, "source" : { "param" : "Bacteria carrying two plasmids", "paramProperty" : { "name" : "Resistance(s) encoded on plasmid 2", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" }, "f922bf1c87974ac79330856f49dc41b7" : { "property" : { "name" : "Plasmid 1 name", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } }, "source" : { "param" : "Bacteria carrying two plasmids", "paramProperty" : { "name" : "Plasmid 1 name", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" } } }, "types" : [ { "_id" : "GRdscXrjMDhW6E8FF", "name" : "Chemically competent bacteria already carrying two plasmid", "v" : 0 } ] } ], "steps" : [ { "desc" : "Follow the protocol outlined in RFC 99.", "inputs" : [] } ] }, "vB88pigyWbKvmKir6" : { "name" : "Pick a colony without any plasmid from an agar plate", "params" : [ { "type" : { "_id" : "s8gikcCG8ZHcj2xPf", "name" : "Agar plate with bacteria without any plasmid", "v" : 1 }, "name" : "Agar plate with bacteria without any plasmid", "multi" : false } ], "products" : [ { "allTypes" : [ { "_id" : "nQbZRzR4ZeKkYMr8X", "name" : "Bacteria without any plasmid", "v" : 0 }, { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } ], "name" : "Colony", "propertyBindings" : { "YW7epnToTmqmHEEwx" : { "1ed8ac857097c4fbbbc15cd373ef96bc" : { "property" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Agar plate with bacteria without any plasmid", "paramProperty" : { "name" : "Strain", "from" : { "_id" : "s8gikcCG8ZHcj2xPf", "name" : "Agar plate with bacteria without any plasmid", "v" : 1 } } }, "sourceType" : "paramProperty" }, "e1520b5997a532c7889f6e8883920ab8" : { "property" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Agar plate with bacteria without any plasmid", "paramProperty" : { "name" : "Species", "from" : { "_id" : "s8gikcCG8ZHcj2xPf", "name" : "Agar plate with bacteria without any plasmid", "v" : 1 } } }, "sourceType" : "paramProperty" } } }, "types" : [ { "_id" : "nQbZRzR4ZeKkYMr8X", "name" : "Bacteria without any plasmid", "v" : 0 } ] } ], "steps" : [ { "desc" : "Pick a single colony from the agar plate using a sterile pipette tip.", "inputs" : [ { "desc" : "Colony number", "type" : "uint", "required" : true, "multiParam" : null } ] }, { "desc" : "Resuspend the colony in appropriate medium to make a culture or in sterile water.", "inputs" : [] } ] }, "vj752RxeBbHsHi83w" : { "name" : "Pick a colony carrying two plasmids from an agar plate", "params" : [ { "type" : { "_id" : "BcetWv5RJeQcBmfee", "name" : "Agar plate with bacteria carrying two plasmids", "v" : 0 }, "name" : "Agar plate with bacteria carrying two plasmids", "multi" : false } ], "products" : [ { "allTypes" : [ { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 }, { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } ], "name" : "Picked colony", "propertyBindings" : { "YW7epnToTmqmHEEwx" : { "1ed8ac857097c4fbbbc15cd373ef96bc" : { "property" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Agar plate with bacteria carrying two plasmids", "paramProperty" : { "name" : "Strain", "from" : { "_id" : "BcetWv5RJeQcBmfee", "name" : "Agar plate with bacteria carrying two plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" }, "e1520b5997a532c7889f6e8883920ab8" : { "property" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Agar plate with bacteria carrying two plasmids", "paramProperty" : { "name" : "Species", "from" : { "_id" : "BcetWv5RJeQcBmfee", "name" : "Agar plate with bacteria carrying two plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" } }, "xJHpdoBri9Ay3g5bP" : { "1558d87b3c90b6b6f071e0956b41972a" : { "property" : { "name" : "Plasmid 2 name", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } }, "source" : { "param" : "Agar plate with bacteria carrying two plasmids", "paramProperty" : { "name" : "Plasmid 2 name", "from" : { "_id" : "BcetWv5RJeQcBmfee", "name" : "Agar plate with bacteria carrying two plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" }, "22f17faf09867bb581e2c6776c2e9186" : { "property" : { "name" : "Resistance(s) encoded on plasmid 1", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } }, "source" : { "param" : "Agar plate with bacteria carrying two plasmids", "paramProperty" : { "name" : "Resistance(s) encoded on plasmid 1", "from" : { "_id" : "BcetWv5RJeQcBmfee", "name" : "Agar plate with bacteria carrying two plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" }, "2ab23d19da35facf9f19887a4e325d28" : { "property" : { "name" : "Resistance(s) encoded on plasmid 2", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } }, "source" : { "param" : "Agar plate with bacteria carrying two plasmids", "paramProperty" : { "name" : "Resistance(s) encoded on plasmid 2", "from" : { "_id" : "BcetWv5RJeQcBmfee", "name" : "Agar plate with bacteria carrying two plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" }, "f922bf1c87974ac79330856f49dc41b7" : { "property" : { "name" : "Plasmid 1 name", "from" : { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } }, "source" : { "param" : "Agar plate with bacteria carrying two plasmids", "paramProperty" : { "name" : "Plasmid 1 name", "from" : { "_id" : "BcetWv5RJeQcBmfee", "name" : "Agar plate with bacteria carrying two plasmids", "v" : 0 } } }, "sourceType" : "paramProperty" } } }, "types" : [ { "_id" : "xJHpdoBri9Ay3g5bP", "name" : "Bacteria carrying two plasmids", "v" : 0 } ] } ], "steps" : [ { "desc" : "Pick up a sterile tip with a pipette. Dip it into a single colony so it attaches to the tip without applying suction.", "inputs" : [ { "desc" : "Colony number (arbitrary)", "type" : "text", "required" : true, "multiParam" : null } ] }, { "desc" : "Resuspend the colony in sterile medium or water.", "inputs" : [] } ] }, "xBmBAjXPQntkvc8d5" : { "name" : "Make a glycerol stock of bacteria carrying three plasmids", "params" : [ { "type" : { "_id" : "oeN5Sukt5toY6taDR", "name" : "Bacterial culture carrying three plasmids", "v" : 1 }, "name" : "Bacterial culture carrying three plasmids", "multi" : false } ], "products" : [ { "allTypes" : [ { "_id" : "LkWcfF5oC8LrsvrNc", "name" : "Glycerol stock of bacteria carrying three plasmids", "v" : 1 }, { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 }, { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } ], "name" : "Glycerol stock", "propertyBindings" : { "TnHge69a2HdoogyYG" : { "1558d87b3c90b6b6f071e0956b41972a" : { "property" : { "name" : "Plasmid 2 name", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } }, "source" : { "param" : "Bacterial culture carrying three plasmids", "paramProperty" : { "name" : "Plasmid 2 name", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } } }, "sourceType" : "paramProperty" }, "22f17faf09867bb581e2c6776c2e9186" : { "property" : { "name" : "Resistance(s) encoded on plasmid 1", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } }, "source" : { "param" : "Bacterial culture carrying three plasmids", "paramProperty" : { "name" : "Resistance(s) encoded on plasmid 1", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } } }, "sourceType" : "paramProperty" }, "2ab23d19da35facf9f19887a4e325d28" : { "property" : { "name" : "Resistance(s) encoded on plasmid 2", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } }, "source" : { "param" : "Bacterial culture carrying three plasmids", "paramProperty" : { "name" : "Resistance(s) encoded on plasmid 2", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } } }, "sourceType" : "paramProperty" }, "2b3de1e4d39cf71091ae27f0bbf41cb6" : { "property" : { "name" : "Resistance(s) encoded on plasmid 3", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } }, "source" : { "param" : "Bacterial culture carrying three plasmids", "paramProperty" : { "name" : "Resistance(s) encoded on plasmid 3", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } } }, "sourceType" : "paramProperty" }, "f922bf1c87974ac79330856f49dc41b7" : { "property" : { "name" : "Plasmid 1 name", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } }, "source" : { "param" : "Bacterial culture carrying three plasmids", "paramProperty" : { "name" : "Plasmid 1 name", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } } }, "sourceType" : "paramProperty" }, "f941ce021dd20e581e58121991cbb4dd" : { "property" : { "name" : "Plasmid 3 name", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } }, "source" : { "param" : "Bacterial culture carrying three plasmids", "paramProperty" : { "name" : "Plasmid 3 name", "from" : { "_id" : "TnHge69a2HdoogyYG", "name" : "Bacteria carrying three plasmids", "v" : 1 } } }, "sourceType" : "paramProperty" } }, "YW7epnToTmqmHEEwx" : { "1ed8ac857097c4fbbbc15cd373ef96bc" : { "property" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Bacterial culture carrying three plasmids", "paramProperty" : { "name" : "Strain", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" }, "e1520b5997a532c7889f6e8883920ab8" : { "property" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } }, "source" : { "param" : "Bacterial culture carrying three plasmids", "paramProperty" : { "name" : "Species", "from" : { "_id" : "YW7epnToTmqmHEEwx", "name" : "Bacteria", "v" : 0 } } }, "sourceType" : "paramProperty" } } }, "types" : [ { "_id" : "LkWcfF5oC8LrsvrNc", "name" : "Glycerol stock of bacteria carrying three plasmids", "v" : 1 } ] } ], "steps" : [ { "desc" : "Mix an aliquot of a LB culture with the same volume of storage buffer.", "inputs" : [] }, { "desc" : "Freeze at -80 °C.", "inputs" : [] } ] }, "z46dHCjoZpLkNgm4k" : { "name" : "CPEC", "params" : [ { "type" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 }, "name" : "Backbone", "multi" : false }, { "type" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 }, "name" : "Insert", "multi" : true } ], "products" : [ { "allTypes" : [ { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 }, { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } ], "name" : "Assembled plasmid", "propertyBindings" : { "cvt43tybpDTWdk2xR" : { "c29e15397d29fc94dad70016db7ab2e9" : { "property" : { "name" : "Resistance marker(s)", "from" : { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 } }, "source" : { "step" : 2, "input" : 3 }, "sourceType" : "input" } }, "k9LEWTcbmQn53Gzo7" : { "49ee3087348e8d44e1feda1917443987" : { "property" : { "name" : "Name", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 2, "input" : 2 }, "sourceType" : "input" }, "4da843835f15245d46602c3d57b579b6" : { "property" : { "name" : "Concentration (ng/µl)", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 2, "input" : 5 }, "sourceType" : "input" }, "6f8ac39f837ee4598b7358ce18aec601" : { "property" : { "name" : "Tube identifier", "from" : { "_id" : "k9LEWTcbmQn53Gzo7", "name" : "dsDNA", "v" : 3 } }, "source" : { "step" : 2, "input" : 4 }, "sourceType" : "input" } } }, "types" : [ { "_id" : "cvt43tybpDTWdk2xR", "name" : "Plasmid", "v" : 4 } ] } ], "steps" : [ { "desc" : "Mix the DNA fragments at the desired ratio. Optionally add a small amount of DMSO.", "inputs" : [ { "desc" : "Insert-to-vector ratio", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Volume of the backbone fragment (µl)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Volume of the insert fragments (µl)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Volume of DMSO (µl)", "type" : "ufloat", "required" : true, "multiParam" : null } ] }, { "desc" : "Add 2X Phusion Flash Master Mix", "inputs" : [ { "desc" : "Volume (µl)", "type" : "text", "required" : true, "multiParam" : null } ] }, { "desc" : "Place the reaction in a thermocycler and run the following program: Initial denaturation at 98 °C for 10 s; 1 to 30 cycles of 1 s denaturation at 98 °C, 5 s annealing, extension at 72 °C for 15 to 30 s/kb of the longest fragment; final extension at 72 °C for 5 min.", "inputs" : [ { "desc" : "Annealing temperature (°C)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Extension time (s)", "type" : "ufloat", "required" : true, "multiParam" : null }, { "desc" : "Name of the resulting plasmid", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "Resistance marker(s) of the resulting plasmid", "type" : "text", "required" : true, "multiParam" : null }, { "desc" : "Identifier of this reaction (optional)", "type" : "text", "required" : false, "multiParam" : null }, { "desc" : "Concentration (ng/µl; leave this blank)", "type" : "ufloat", "required" : false, "multiParam" : null } ] } ] }
};