User:Nkuldell:SB starter kit

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Use this space as a scratch pad for your ideas and thoughts and experiences as we develop some teaching materials geared for SB starters (e.g. iGEM teams without resident synthetic biology community, or social scientists trying to understand technology that underlies the field).  
Use this space as a scratch pad for your ideas and thoughts and experiences as we develop some teaching materials geared for SB starters (e.g. iGEM teams without resident synthetic biology community, or social scientists trying to understand technology that underlies the field).  
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The slate is still nearly blank, though I've seeded this sight with some organizational ideas....all subject to change and heavy editing.
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The slate is still nearly blank, though I've seeded this site with some organizational ideas....all subject to change and heavy editing.<br>
 +
 
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look at resourced listed on James Brown's "getting started" site: [http://parts2.mit.edu/wiki/index.php/Resources]
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One thought offered by Caroline, "the limits of your language are the limits of your world"-Ludwig Wittgenstein
=="front page"==
=="front page"==
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==Tab: Lab techniques/Registry Starter kit==
==Tab: Lab techniques/Registry Starter kit==
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*mRFP cloning exampls
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*mRFP cloning examples
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*[http://parts.mit.edu/registry/index.php/Part:BBa_J16000 BBa_J16000] and [http://parts.mit.edu/registry/index.php/Part:BBa_J16002 BBa_J16002] are the two parts which I'd like students to start with for the following reasons:
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**Employs the idea of putting both basic parts and component ("inverter device") parts together. 
 +
**Both systems can be controlled using externally added chemicals (IPTG, Tetracycline) with measurable flourescence output
 +
**All parts well-characterized
 +
**mCherry protein has LVA tag for fast degradation
 +
**Non-linear behaviour exhibits complexity beyond electronic parts
 +
**Contains almost all canonical part categories (RBS, regulatory, device, terminator, protein coding, reporter...)
==Social implications==
==Social implications==
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==Notes/comments==
==Notes/comments==
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I think we could exemplify the concept of abstraction and stress its importance by designing the iGEM tutorial / primer in a hierarchical way, such that any step in an initially superficial "high-level" recipe for constructing an archetypal device out of parts from the registry could be deepened and explored for more sophisticated, complicated "low-level" information.  Maybe we could use AJAX to facilitate the expansion and compression of the levels of abstaction.  Or maybe we should just use normal hyperlinks.  In any case, I think it would be really neat if the whole primer initially took up no more than one page when printed out. I think that degree of simplification would necessitate a mature abstraction hierarchy (and hence could be a good goal for us) and its initial brevity would make it less overwhelming for newcomers. --[[User:Macowell|Macowell]] 00:37, 23 June 2006 (EDT)
==Useful teaching resources already freely available==
==Useful teaching resources already freely available==
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===books===
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These books are online at ncbi (searchable, but not directly browseable):
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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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* [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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* [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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* [http://en.wikibooks.org/wiki/Biochemistry Biochemistry Wikibook]
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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 [http://www1.qiagen.com/literature/BenchGuide/pdf/1017778_BenchGuide.pdf Bench Guide pdf] 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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===papers & presentations===
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* SB2.0 [http://webcast.berkeley.edu/events/details.php?webcastid=15766 Webcasts]
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* [http://webcast.berkeley.edu/courses/archive.php?seriesid=1906978261 Synthetic Biology seminars] webcast from Berkeley
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* [http://www.keckfutures.org/site/PageServer?pagename=Past_Life_Eng_Conference_Presentations&JServSessionIdr003=z9jzbic5g1.app13b Life Engineering Symposium] webcasts (19-20 August 2005)
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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://www.nature.com/msb/journal/v2/n1/pdf/msb4100073.pdf Synthetic biology: new engineering rules for an emerging discipline.  (Review Article)]<small>Mol. Syst. Biol. doi:10.1038/msb4100073</small>
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* [http://www.bio.davidson.edu/courses/synthetic/read.html Synthetic Biology readings] listed at Davidson College
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* [http://www.ssbjournal.com/ Synthetic and Systems Biology] - the new open-access journal, not yet launched
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===other websites===
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* [http://www.dnai.org/ DNAi] - excellent interactive explanations of the science of basic molecular biology.  For instance, check out the "Recombining DNA" animation under Manipulation->Techniques->Cutting & Pasting
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* '''[http://parts.mit.edu/registry/index.php/Help:Contents Registry Help page] - start here!'''
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* [http://parts.mit.edu/wiki/index.php/Resources Teaching Resources] at the iGEM wiki
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* Blogs
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===misc===
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* [http://nobelprize.org/nobel_prizes/chemistry/articles/berg/ Asilomar and Recombinant DNA] at Nobelprize.org by Paul Berg, 1980 Nobel Laureate in Chemistry
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* [http://parts.mit.edu/r/parts/htdocs/Assembly/index.cgi standard assembly]
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* [http://parts2.mit.edu/wiki/index.php/Abstraction_hierarchy_and_PoPS 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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* [http://openwetware.org/wiki/BE.109:Systems_engineering/RT-PCR_data_analysis BE.109: RT-PCR data analysis]

Current revision

Use this space as a scratch pad for your ideas and thoughts and experiences as we develop some teaching materials geared for SB starters (e.g. iGEM teams without resident synthetic biology community, or social scientists trying to understand technology that underlies the field).

The slate is still nearly blank, though I've seeded this site with some organizational ideas....all subject to change and heavy editing.

look at resourced listed on James Brown's "getting started" site: [1]

One thought offered by Caroline, "the limits of your language are the limits of your world"-Ludwig Wittgenstein

Contents

"front page"

  • welcomes to synthetic biology
  • two sentence overview of the field
  • two sentence overview of goals of tutorial
  • two sentence overview of how to use tutorial

Tab: Biology for Engineers

  • culture celebrates understanding and description of natural world
  • central dogma
  • start with "this is a cell"
  • unifying example to ground details?

Tab: Engineering for Biologists

  • culture celebrates building things
  • predictable
  • modular, interchangeable components
  • measurement
  • standards

Tab: Lab techniques/Registry Starter kit

  • mRFP cloning examples
  • BBa_J16000 and BBa_J16002 are the two parts which I'd like students to start with for the following reasons:
    • Employs the idea of putting both basic parts and component ("inverter device") parts together.
    • Both systems can be controlled using externally added chemicals (IPTG, Tetracycline) with measurable flourescence output
    • All parts well-characterized
    • mCherry protein has LVA tag for fast degradation
    • Non-linear behaviour exhibits complexity beyond electronic parts
    • Contains almost all canonical part categories (RBS, regulatory, device, terminator, protein coding, reporter...)

Social implications

  • might direct to Q/A from PoET/SB collaboration
  • this may not need a tab or section of its own

Notes/comments

I think we could exemplify the concept of abstraction and stress its importance by designing the iGEM tutorial / primer in a hierarchical way, such that any step in an initially superficial "high-level" recipe for constructing an archetypal device out of parts from the registry could be deepened and explored for more sophisticated, complicated "low-level" information. Maybe we could use AJAX to facilitate the expansion and compression of the levels of abstaction. Or maybe we should just use normal hyperlinks. In any case, I think it would be really neat if the whole primer initially took up no more than one page when printed out. I think that degree of simplification would necessitate a mature abstraction hierarchy (and hence could be a good goal for us) and its initial brevity would make it less overwhelming for newcomers. --Macowell 00:37, 23 June 2006 (EDT)

Useful teaching resources already freely available

books

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

protocols

papers & presentations

other websites

  • DNAi - excellent interactive explanations of the science of basic molecular biology. For instance, check out the "Recombining DNA" animation under Manipulation->Techniques->Cutting & Pasting
  • Registry Help page - start here!
  • Teaching Resources at the iGEM wiki
  • Blogs

misc

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