Talk:Plasmid backbones

New tables

• B subtillus and/or chromosomal integration - BBa_K090403
• Lim lab plasmids
• T7 expression vector, where promoter is part of the plasmid - BBa_K133041

Plasmids to be split into part and plasmid

BioBrick plasmids

• BBa_K165060 - BioBrick friendly?
• BBa_K165061 - BioBrick friendly?
• BBa_K165063 - BioBrick friendly?

Plasmids to remap

• BBa_K157041

To be updated

• BBa_I732958 -> BBa_I732950-I732835 (by picture)
• BBa_I732958 -> BBa_I732952-I732815<noscar>I732807 (by sequence) -> BBa_I732952-I732962

Physicals locations have been updated

• BBa_J61002 -> BBa_J61002-R0040
• BBa_J61003 -> BBa_J61003-E0040
• BBa_I732950 -> BBa_I732950-I732019
• BBa_I732951 -> BBa_I732950-I732020
• BBa_I732952 -> BBa_I732952-I732807
• BBa_I732953 -> BBa_I732952-I732812
• BBa_I732954 -> BBa_I732952-I732815
• BBa_I732955 -> BBa_I732950-I732827
• BBa_I732956 -> BBa_I732950-I732830
• BBa_I732957 -> BBa_I732950-I732832
• BBa I718019 -> BBa_J61002-I0500
• BBa_J61035 -> BBa_J61035-B0034
• BBa_I732959 -> BBa_I732952-I732962
• BBa_I732960 -> BBa_I732952-I732963
• BBa_I732961 -> BBa_I732952-I732964

Only ever indicated in plasmid field, not part

No remapping needed?

• BBa_J23006 -> BBa_J23006-J23025
• BBa_J23018 -> BBa_J23018-E1010
• BBa_J23019 -> BBa_J23019-E1010
• BBa_I750017 -> BBa_I750017-B0034
• BBa_J70003-I712016 -> BBa_J70022-I712016
• BBa_J52017 -> BBa_J52017-BBa_P1010
• BBa_K125000 -> BBa_K125000-BBa_J33210
• BBa_K157040 -> BBa_K157040-BBa_K157042
• BBa_K106006 -> BBa_K106006-BBa_K106400
• BBa_K106014 -> BBa_K106014-BBa_K106400
• BBa_K106670 -> BBa_K106670-BBa_K106400
• BBa_K106672 -> BBa_K106672-BBa_K106400
• BBa_K106693 -> BBa_K106693-BBa_K106400
• BBa_K106697 -> BBa_K106697-BBa_K106400
• BBa_K106698 -> BBa_K106698-BBa_K106400

Tables

Plasmid location tables

Plasmid backbone	BBa_P1010 (ccdB)	BBa_I52002 (ccdB.pUC19)	BBa_I52001 (ccdB)	BBa_J23025 (OnRFP)	BBa_I739400 (spacer)
pSB1A3	iGEM 2008 dist. Well 1A	iGEM 2008 dist. Well 4B			-
pSB4A5	-	iGEM 2008 dist. Well 2C	iGEM 2008 dist. Well 4C
pSB4K5	-	iGEM 2008 dist. Well 2C	-

Assembly

• high_copy_biobrick_assembly_plasmids
  • //plasmid/assembly
  • //plasmid/copynumber/high
  • //standard/biobrick
• low_or_medium_copy_version5_biobrick_assembly_plasmid
  • //plasmid/assembly
  • //plasmid/copynumber/low or //plasmid/copynumber/medium
  • //plasmid/version/5
  • //standard/biobrick
• inducible_copy_number_biobrick_assembly_plasmid
  • //plasmid/assembly
  • //plasmid/copynumber/inducible
  • //standard/biobrick
• silver_proteinfusion_plasmid
  • //plasmid/proteinfusion
  • //standard/silver

Operation

• low_and_medium_copy_version5_biobrick_operation_plasmid
  • //plasmid/operation
  • //plasmid/copynumber/low or //plasmid/copynumber/medium
  • //plasmid/version/5
  • //standard/biobrick
• low_and_medium_copy_biobrick_operation_plasmid
  • //plasmid/operation
  • //plasmid/copynumber/low or //plasmid/copynumber/medium
  • //standard/biobrick
  • NOT //plasmid/version/5
• multihost_biobrick_operation_plasmids
  • //plasmid/operation
  • //chassis/multihost
  • //standard/biobrick
• eukaryotic biobrick_operation_plasmid
  • //plasmid/operation
  • //chassis/eukaryote
  • //standard/biobrick
• inducible_copy_operation_plasmid
  • //plasmid/operation
  • //plasmid/copynumber/inducible
  • //standard/biobrick

Library screening

• promoter_library_screening_plasmid
  • //plasmid/libraryscreening/promoter
  • //standard/biobrickfriendly

• coding_sequence_library_screening_plasmid
  • //plasmid/libraryscreening/codingsequence
  • //standard/biobrickfriendly

• ribosome_binding_site_coding_sequence_library_screening_plasmid
  • //plasmid/libraryscreening/RBScodingsequence
  • //standard/biobrickfriendly

Construction

• plasmid_replication_origin
  • //plasmid/component/origin
• plasmid_resistance_marker
  • //plasmid/component/resistancemarker
• plasmid_default_inserts
  • //plasmid/component/defaultinsert
• plasmid_insulation
  • //plasmid/component/insulation
• plasmid_primer_binding_sites
  • //plasmid/component/primerbindingsite
• plasmid_cloning_site
  • //plasmid/component/cloningsite
• plasmid_components
  • //plasmid/component/other

Expression

• constitutive_expression_plasmid
  • //plasmid/expression/constitutive
  • //standard/biobrick

• inducible_expression_plasmid
  • //plasmid/expression/inducible
  • //standard/biobrick

Non-BioBrick plasmids

• berkeley_plasmid
  • //plasmid (ideally anything that has //plasmid ... either //plasmid/assembly or //plasmid/operation etc.)
  • //standard/berkeley

• biobrick_friendly_plasmid
  • //plasmid
  • //standard/biobrickfriendly
  • NOT //plasmid/libraryscreening

• synthesis_plasmid
  • //plasmid/synthesis

• tumor_killing_bacteria_plasmid
  • //plasmid
  • //project/tumorkillingbacteria

Categories

• //plasmid/operation vs assembly vs measurement vs construction vs proteinfusion vs archive vs expression vs libraryscreening vs synthesis vs chromosomalintegration
• //plasmid/libraryscreening/promoter vs codingsequence vs RBScodingsequence
• //plasmid/version/1 vs 2 vs 3 vs 4 vs 5
• //chassis/prokaryote/ecoli vs /multihost vs /eukaryote/yeast vs /eukaryote vs /prokaryote/bsubtilis
• //standards/biobrick vs silver vs berkeley vs freiburg vs biobrickfriendly vs lim vs none
  • what did I mean by the difference between biobrick friendly and biobrickcompatible?
• //plasmid/component/origin vs resistancemarker vs insulation vs defaultinsert vs cloningsite vs other
• //plasmid/copynumber/high vs low vs medium vs inducible
• //project/tumorkillingbacteria

Plasmid table types and columns

• Plasmid (all assembly, archive, operation and protein fusion tables)
  • Available/Working
  • Part number
  • Description
  • Resistance
  • Origin (replicon)
  • Copy number
  • Default Insert
  • Chassis
  • Location

• Origin (table "plasmid_replication_origin")
  • Available/Working
  • Part number
  • Description
  • Replicon
  • Copy number
  • Chassis

• Default inserts (table "plasmid_default_inserts")
  • Available/Working
  • Part number
  • Description
  • Chassis

• Antibiotic resistance markers (table "plasmid_resistance_marker")
  • Available/Working
  • Part number
  • Description
  • Resistance

• Insulation (table "plasmid_insulation")
  • Available/Working
  • Part number
  • Description
  • Direction (forward or reverse)
  • Efficiency

• Primer binding sites (table "plasmid_primer_binding_sites")
  • Available/Working
  • Part number
  • Description
  • Primer name
  • Primer sequence
  • Melting temperature

• Cloning sites (table "plasmid_cloning_site")
  • Available/Working
  • Part number
  • Description
  • Standard

• Miscellaneous plasmid component (table "plasmid_components")
  • Available/Working
  • Part number
  • Description

Plasmid parameters

• Plasmid - general
  • Resistance(s)
  • Origin
  • Copy number
  • Default Insert
  • Chassis
  • Location
  • Incompatibility group
  • Recommended concentration of antibiotic
  • Version number
  • Parent plasmid

• Plasmid - archive
  • All general plasmid parameters plus
  • Plasmid which has replaced it

• Origin (table "plasmid_replication_origin")
  • Replicon
  • Copy number
  • Chassis
• Incompatibility group

• Default inserts (table "plasmid_default_inserts")
  • Chassis

• Antibiotic resistance markers (table "plasmid_resistance_marker")
  • Antibiotic
  • Inherit coding sequence parameters - gene name, protein name, swissprot, EC, kegg, PDB
  • Mechanism of action

• Insulation (table "plasmid_insulation")
  • Direction (forward or reverse)
  • Efficiency

• Primer binding sites (table "plasmid_primer_binding_sites")
  • Primer name
  • Primer sequence
  • Melting temperature

• Cloning sites (table "plasmid_cloning_site")
  • Standard

• Miscellaneous plasmid component (table "plasmid_components")

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Part assembly

Assembly of protein fusions

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Building new BioBrick vectors

Non-BioBrick plasmids

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Help!	Part assembly	Assembly of protein fusions	Part measurement	System operation	Building new BioBrick vectors	Non-BioBrick plasmids	Archive