BU06:resources

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{{BU06}}
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back to the [[:Category: Boston University 2006|BU iGEM main page]] [[Category: Boston University 2006]]
back to the [[:Category: Boston University 2006|BU iGEM main page]] [[Category: Boston University 2006]]
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; Why didn't the Registry include empty resistance plasmids in the DNA shipment?
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====books====
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: Check the [[Registry FAQ]].
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These books are online at ncbi (searchable, but not directly browseable):
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; BioBrick restriction sites : XbaI and SpeI, the [[restriction enzymes]] that form the basis of BioBrick assembly.
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* [http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=mboc4.TOC&depth=10 The Cell]
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;RBS-CDS design issues : how the ribosomal binding site is [http://partsregistry.org/cgi/htdocs/Assembly/rbs_cds.cgi reconciled] with the location of the BioBrick ends.
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* [http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=cooper.TOC&depth=10 The Cell - A Molecular Approach]
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; Key to our Design
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* [http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=cooper.TOC&depth=10 Molecular Cell Biology]
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: [[Help:Glossary:L#Lux_operon|Lux operon]] in the iGEM Glossary
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* [http://en.wikibooks.org/wiki/Biochemistry Biochemistry Wikibook]
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: An overview of the UT Austin's [[Featured_Parts:Light_Sensor|Light Sensor]] system.
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;Vectors
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====protocols====
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* Tons of protocols at [http://openwetware.org/wiki/Protocols OpenWetWare]
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* [https://catalog.invitrogen.com/index.cfm?fuseaction=iProtocol.home Invitrogen iProtocols]
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* [http://www1.qiagen.com/literature/ Quigen's Handbooks & protocols] - be sure to check out the Bench Guide under "General Molecular biology protocols"
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* [http://www.mrw.interscience.wiley.com/cp/cpmb/cpmb_contents_fs.html Current Protocols in Molecular Biology] from Wiley InterScience
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* [http://www.promega.com/guides/ Promega Guides]
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====links====
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* Misc. links at the main iGEM [[Resources]] page (used to be "teaching resources" page
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* [http://partsregistry.org/cgi/htdocs/Assembly/index.cgi standard assembly]
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* [[Abstraction hierarchy and PoPS]]
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* [http://openwetware.org/wiki/Standard_E._coli_Strain_for_BioBricks Standard E. coli Strain for BioBricks]
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* Synthetic Biology articles in [https://dspace.mit.edu/handle/1721.1/18185/browse-title DSpace]:
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** [https://dspace.mit.edu/handle/1721.1/31335 Definitions and Measures of Performance for Standard Biological Parts]
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** [https://dspace.mit.edu/handle/1721.1/19813 Engineering the Interface Between Cellular Chassis and Integrated Biological Systems]
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** [https://dspace.mit.edu/handle/1721.1/32981 GeneJax: A Prototype CAD tool in support of Genome Refactoring]
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* [http://openwetware.org/wiki/BE.109:Systems_engineering/RT-PCR_data_analysis BE.109: RT-PCR data analysis]
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====vectors====
: [http://www.ncbi.nlm.nih.gov/VecScreen/replist.html VecScreen] has a list of all the vector nucleotide sequences in ncbi.
: [http://www.ncbi.nlm.nih.gov/VecScreen/replist.html VecScreen] has a list of all the vector nucleotide sequences in ncbi.
: [http://seq.yeastgenome.org/vectordb/ VectorDB] contains annotations and sequence information for many vectors (2600+) commonly used in molecular biology.
: [http://seq.yeastgenome.org/vectordb/ VectorDB] contains annotations and sequence information for many vectors (2600+) commonly used in molecular biology.
: [http://wishart.biology.ualberta.ca/PlasMapper/ PlasMapper] generates sweet annotated vector-based plasmid maps from a web interface.
: [http://wishart.biology.ualberta.ca/PlasMapper/ PlasMapper] generates sweet annotated vector-based plasmid maps from a web interface.
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* Tons of protocols at [http://openwetware.org/wiki/Protocols OpenWetWare]
+
====miscellaneous====
 +
; Why didn't the Registry include empty resistance plasmids in the DNA shipment?
 +
: Check the [http://partsregistry.org/Registry_FAQ Registry FAQ].
 +
; [http://partsregistry.org/cgi/htdocs/Assembly/index.cgi Standard Assembly] : the basics of building and manipulating Parts, including details about XbaI and SpeI, the restriction enzymes that are the basis of these operations.
 +
;RBS-CDS design issues : how the ribosomal binding site is [http://partsregistry.org/cgi/htdocs/Assembly/rbs_cds.cgi reconciled] with the location of the BioBrick ends.
 +
; Key to our design:
 +
: [http://partsregistry.org/Lux Lux operon] in the Registry Glossary
 +
: [http://prodoric.tu-bs.de/gbpro.php?spos=2462292&epos=2468907&replicon=Photorhabdus%20luminescens%20(subsp.%20laumondii,%20strain%20TT01)|complete%20chromosome&gene_name=&chk_ln=1&chk_block=1&feature=1&bases=80 LuxCDABE] listing in ''prodoric''.
 +
: [http://prodoric.tu-bs.de/vfp/ Virtual Footprint] at prodoric searches for prokaryote promoters in a given sequence.
 +
: An overview of UT Austin's [http://partsregistry.org/Featured_Parts:Light_Sensor Light Sensor] system.
 +
 
 +
[[BU iGEM Training]] <br>
 +
[[Using the wiki]]<br>
 +
[[iGEM 101]]
 +
 
 +
 
 +
----
 +
Team members can store and reference PDFs of scientific papers at http://www.citeulike.org/user/BUiGEM/ (Get the password from Richard) Take a look at tagging feature and the bookmarklet used for posting. (I'll put in more details soon). Here's a list of tags I have so far:
 +
*''part2b'' for papers describing DNA sequences that we could turn into a part
 +
*''part_XYZ'' for papers describing a specific part we might make
 +
*''gene_XYZ'' for papers describing a particular gene in any detail
 +
 
 +
Remember you can apply any number of relevant tags you like to a given paper.
 +
 
 +
Tom Knight's earlier plasmid construction technique: http://web.mit.edu/synbio/release/docs/biobricks.pdf
 +
 
 +
Randy Rettberg sez [http://partsregistry.org/Part:BBa_B0015 B0015] is a pretty reliable terminator.

Latest revision as of 20:13, 20 July 2006

BU06.jpg
Schedule Research Fundraising Resources Members Contact

back to the BU iGEM main page

Contents

books

These books are online at ncbi (searchable, but not directly browseable):

  • [http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=mboc4.TOC&depth=10 The Cell]
  • [http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=cooper.TOC&depth=10 The Cell - A Molecular Approach]
  • [http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=cooper.TOC&depth=10 Molecular Cell Biology]
  • [http://en.wikibooks.org/wiki/Biochemistry Biochemistry Wikibook]

protocols

  • Tons of protocols at [http://openwetware.org/wiki/Protocols OpenWetWare]
  • Invitrogen iProtocols
  • [http://www1.qiagen.com/literature/ Quigen's Handbooks & protocols] - be sure to check out the Bench Guide under "General Molecular biology protocols"
  • [http://www.mrw.interscience.wiley.com/cp/cpmb/cpmb_contents_fs.html Current Protocols in Molecular Biology] from Wiley InterScience
  • [http://www.promega.com/guides/ Promega Guides]

links

vectors

[http://www.ncbi.nlm.nih.gov/VecScreen/replist.html VecScreen] has a list of all the vector nucleotide sequences in ncbi.
[http://seq.yeastgenome.org/vectordb/ VectorDB] contains annotations and sequence information for many vectors (2600+) commonly used in molecular biology.
[http://wishart.biology.ualberta.ca/PlasMapper/ PlasMapper] generates sweet annotated vector-based plasmid maps from a web interface.

miscellaneous

Why didn't the Registry include empty resistance plasmids in the DNA shipment?
Check the [http://partsregistry.org/Registry_FAQ Registry FAQ].
[http
//partsregistry.org/cgi/htdocs/Assembly/index.cgi Standard Assembly] : the basics of building and manipulating Parts, including details about XbaI and SpeI, the restriction enzymes that are the basis of these operations.
RBS-CDS design issues 
how the ribosomal binding site is [http://partsregistry.org/cgi/htdocs/Assembly/rbs_cds.cgi reconciled] with the location of the BioBrick ends.
Key to our design
[http://partsregistry.org/Lux Lux operon] in the Registry Glossary
[http://prodoric.tu-bs.de/gbpro.php?spos=2462292&epos=2468907&replicon=Photorhabdus%20luminescens%20(subsp.%20laumondii,%20strain%20TT01)|complete%20chromosome&gene_name=&chk_ln=1&chk_block=1&feature=1&bases=80 LuxCDABE] listing in prodoric.
[http://prodoric.tu-bs.de/vfp/ Virtual Footprint] at prodoric searches for prokaryote promoters in a given sequence.
An overview of UT Austin's [http://partsregistry.org/Featured_Parts:Light_Sensor Light Sensor] system.

BU iGEM Training
Using the wiki
iGEM 101


Team members can store and reference PDFs of scientific papers at http://www.citeulike.org/user/BUiGEM/ (Get the password from Richard) Take a look at tagging feature and the bookmarklet used for posting. (I'll put in more details soon). Here's a list of tags I have so far:

  • part2b for papers describing DNA sequences that we could turn into a part
  • part_XYZ for papers describing a specific part we might make
  • gene_XYZ for papers describing a particular gene in any detail

Remember you can apply any number of relevant tags you like to a given paper.

Tom Knight's earlier plasmid construction technique: http://web.mit.edu/synbio/release/docs/biobricks.pdf

Randy Rettberg sez [http://partsregistry.org/Part:BBa_B0015 B0015] is a pretty reliable terminator.

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