BU06:resources

From 2006.igem.org

Latest revision as of 20:13, 20 July 2006

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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

• Misc. links at the main iGEM Resources page (used to be "teaching resources" page
• [http://partsregistry.org/cgi/htdocs/Assembly/index.cgi standard assembly]
• Abstraction hierarchy and PoPS

• [http://openwetware.org/wiki/Standard_E._coli_Strain_for_BioBricks Standard E. coli Strain for BioBricks]
• Synthetic Biology articles in DSpace:
  • Definitions and Measures of Performance for Standard Biological Parts
  • Engineering the Interface Between Cellular Chassis and Integrated Biological Systems
  • GeneJax: A Prototype CAD tool in support of Genome Refactoring
• [http://openwetware.org/wiki/BE.109:Systems_engineering/RT-PCR_data_analysis BE.109: RT-PCR data analysis]

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.