diff --git a/index.json b/index.json index ea4cd6d..b38491d 100644 --- a/index.json +++ b/index.json @@ -57,25 +57,12 @@ } ] }, - "allele-engineering-templates": { - "kit": { - "title": "Allele engineering", - "description": "Templates to engineer alleles." - }, - "assemblies": [ - { - "title": "PCR-based targeting", - "description": "Amplify a plasmid fragment adding homology arms to replace a region in the genome.", - "template_file": "pcr_based_targeting.json" - } - ] - }, - "kits-young-moclo-ysd": { + "browse-article-28244182": { "kit": { - "pmid": "PMID:38483353", - "addgene_url": "https://www.addgene.org/kits/young-moclo-ysd", - "title": "MoClo Yeast Secretion and Display (YSD) ", - "description": "Extension to the MoClo YTK kit to optimize secretion and cell surface display of proteins of interest" + "pmid": "PMID:37991801", + "addgene_url": "https://www.addgene.org/kits/pluskal-pombox/#kit-contents", + "title": "POMBOX", + "description": "YTK-based Fission Yeast Cloning Toolkit for Molecular and Synthetic Biology" }, "assemblies": [ { @@ -99,8 +86,8 @@ "fragment_order": [ "1", "2", - "3a'", - "3b'", + "3a", + "3b", "4", "5", "6", @@ -115,8 +102,8 @@ "fragment_order": [ "1", "2", - "3a'", - "3b'", + "3a", + "3b", "4a", "4b", "5", @@ -148,8 +135,8 @@ "fragment_order": [ "1", "2", - "3a'", - "3b'", + "3a", + "3b", "4", "5", "6", @@ -165,8 +152,8 @@ "fragment_order": [ "1", "2", - "3a'", - "3b'", + "3a", + "3b", "4a", "4b", "5", @@ -179,12 +166,59 @@ } ] }, - "kits-moclo-ytk": { + "kits-murray-cidar-moclo-v1": { "kit": { - "pmid": "PMID:25871405", - "addgene_url": "https://www.addgene.org/kits/moclo-ytk/", - "title": "MoClo YTK", - "description": "Golden-gate based modular cloning kit for yeast." + "pmid": null, + "addgene_url": "https://www.addgene.org/kits/murray-cidar-moclo-v1/", + "title": "CIDAR MoClo Extension ", + "description": "110 extra parts for CIDAR + the compatible original CIDAR parts" + }, + "assemblies": [ + { + "title": "Transcriptional Unit", + "description": "5'UTR (with RBS) + promoter + CDS + terminator flanked by Golden Gate adapters", + "fragment_order": [ + "upstream_adapter", + "promoter", + "five_utr", + "cds", + "terminator", + "downstream_adapter" + ], + "template_file": "assembly_template_001.json" + }, + { + "title": "Pre-composed 5'UTR + promoter + CDS", + "description": "Transcriptional Unit that uses a level 0 plasmid containing joined 5'UTR + promoter + CDS", + "fragment_order": [ + "upstream_adapter", + "five_utr_gRna", + "terminator", + "downstream_adapter" + ], + "template_file": "assembly_template_002.json" + } + ] + }, + "allele-engineering-templates": { + "kit": { + "title": "Allele engineering", + "description": "Templates to engineer alleles." + }, + "assemblies": [ + { + "title": "PCR-based targeting", + "description": "Amplify a plasmid fragment adding homology arms to replace a region in the genome.", + "template_file": "pcr_based_targeting.json" + } + ] + }, + "kits-young-moclo-ysd": { + "kit": { + "pmid": "PMID:38483353", + "addgene_url": "https://www.addgene.org/kits/young-moclo-ysd", + "title": "MoClo Yeast Secretion and Display (YSD) ", + "description": "Extension to the MoClo YTK kit to optimize secretion and cell surface display of proteins of interest" }, "assemblies": [ { @@ -208,8 +242,8 @@ "fragment_order": [ "1", "2", - "3a", - "3b", + "3a'", + "3b'", "4", "5", "6", @@ -224,8 +258,8 @@ "fragment_order": [ "1", "2", - "3a", - "3b", + "3a'", + "3b'", "4a", "4b", "5", @@ -257,8 +291,8 @@ "fragment_order": [ "1", "2", - "3a", - "3b", + "3a'", + "3b'", "4", "5", "6", @@ -274,8 +308,8 @@ "fragment_order": [ "1", "2", - "3a", - "3b", + "3a'", + "3b'", "4a", "4b", "5", @@ -288,12 +322,52 @@ } ] }, - "browse-article-28244182": { + "kits-gasser-goldenpics": { "kit": { - "pmid": "PMID:37991801", - "addgene_url": "https://www.addgene.org/browse/article/28244182/", - "title": "POMBOX", - "description": "YTK-based Fission Yeast Cloning Toolkit for Molecular and Synthetic Biology" + "pmid": "PMID:29221460", + "addgene_url": "https://www.addgene.org/kits/gasser-goldenpics", + "title": "GoldenPiCS", + "description": "Flexible modular system for advanced strain engineering in P. pastoris / K. phaffii" + }, + "assemblies": [ + { + "title": "Single TU BB3 plasmid", + "description": "Overexpression of a single TU, direct cloning from BB1 into a special BB3", + "fragment_order": [ + "promoter", + "coding sequence", + "terminator", + "recipient BB3 - single" + ], + "template_file": "assembly_template_001.json" + }, + { + "title": "TU cloning into BB2", + "description": "Cloning of a TU into a BB2 plasmid, for eventual multi-TU assembly into a BB3 plasmid", + "fragment_order": [ + "promoter", + "coding sequence", + "terminator", + "recipient BB2" + ], + "template_file": "assembly_template_002.json" + }, + { + "title": "Multiple BB2 into BB3", + "description": "Cloning of several TUs from BB2 plasmids into a BB3", + "fragment_order": [ + "recipient BB3" + ], + "template_file": "assembly_template_003.json" + } + ] + }, + "kits-moclo-ytk": { + "kit": { + "pmid": "PMID:25871405", + "addgene_url": "https://www.addgene.org/kits/moclo-ytk/", + "title": "MoClo YTK", + "description": "Golden-gate based modular cloning kit for yeast." }, "assemblies": [ { @@ -396,39 +470,5 @@ "template_file": "assembly_template_006.json" } ] - }, - "kits-murray-cidar-moclo-v1": { - "kit": { - "pmid": null, - "addgene_url": "https://www.addgene.org/kits/murray-cidar-moclo-v1/", - "title": "CIDAR MoClo Extension ", - "description": "110 extra parts for CIDAR + the compatible original CIDAR parts" - }, - "assemblies": [ - { - "title": "Transcriptional Unit", - "description": "5'UTR (with RBS) + promoter + CDS + terminator flanked by Golden Gate adapters", - "fragment_order": [ - "upstream_adapter", - "promoter", - "five_utr", - "cds", - "terminator", - "downstream_adapter" - ], - "template_file": "assembly_template_001.json" - }, - { - "title": "Pre-composed 5'UTR + promoter + CDS", - "description": "Transcriptional Unit that uses a level 0 plasmid containing joined 5'UTR + promoter + CDS", - "fragment_order": [ - "upstream_adapter", - "five_utr_gRna", - "terminator", - "downstream_adapter" - ], - "template_file": "assembly_template_002.json" - } - ] } } \ No newline at end of file