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Merged
manulera merged 1 commit into from
Jul 28, 2025
Merged

update index #81

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196 changes: 118 additions & 78 deletions index.json
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Original file line number Diff line number Diff line change
Expand Up @@ -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": [
{
Expand All @@ -99,8 +86,8 @@
"fragment_order": [
"1",
"2",
"3a'",
"3b'",
"3a",
"3b",
"4",
"5",
"6",
Expand All @@ -115,8 +102,8 @@
"fragment_order": [
"1",
"2",
"3a'",
"3b'",
"3a",
"3b",
"4a",
"4b",
"5",
Expand Down Expand Up @@ -148,8 +135,8 @@
"fragment_order": [
"1",
"2",
"3a'",
"3b'",
"3a",
"3b",
"4",
"5",
"6",
Expand All @@ -165,8 +152,8 @@
"fragment_order": [
"1",
"2",
"3a'",
"3b'",
"3a",
"3b",
"4a",
"4b",
"5",
Expand All @@ -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": [
{
Expand All @@ -208,8 +242,8 @@
"fragment_order": [
"1",
"2",
"3a",
"3b",
"3a'",
"3b'",
"4",
"5",
"6",
Expand All @@ -224,8 +258,8 @@
"fragment_order": [
"1",
"2",
"3a",
"3b",
"3a'",
"3b'",
"4a",
"4b",
"5",
Expand Down Expand Up @@ -257,8 +291,8 @@
"fragment_order": [
"1",
"2",
"3a",
"3b",
"3a'",
"3b'",
"4",
"5",
"6",
Expand All @@ -274,8 +308,8 @@
"fragment_order": [
"1",
"2",
"3a",
"3b",
"3a'",
"3b'",
"4a",
"4b",
"5",
Expand All @@ -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": [
{
Expand Down Expand Up @@ -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"
}
]
}
}
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