User:ShawnDouglas

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*I am a biophysics graduate student in the labs of [http://arep.med.harvard.edu/ George Church] and [http://research2.dfci.harvard.edu/shih/ William Shih].
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==Projects==
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*I am also a teaching assistant for Harvard's 2006 [[IGEM:Harvard/2006| iGEM team]].
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*[http://biomod.net/ BIOMOD] ([[Biomod|Team Wikis]])
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*Find out more at my personal [http://www.shawndouglas.com/ website].
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*[http://cadnano.org/ cadnano]
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==About Me==
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*I'm currently a fellow at the [http://wyss.harvard.edu/ Wyss Institute].
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*I have a [http://www.shawndouglas.com/ personal website].
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*I have worked in the labs of [http://arep.med.harvard.edu/ George Church], [http://research2.dfci.harvard.edu/shih/ William Shih], and [http://bioinfo.mbb.yale.edu/ Mark Gerstein].
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*email: <nowiki>python -c "print ''.join([chr(ord(c)-3) for c in 'vgrxjodvCidv1kduydug1hgx'])"</nowiki>
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==OWW Contributions==
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*Protocol: [[Recombineering/Lambda_red-mediated_gene_replacement|λ red-mediated gene replacement]]
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*[[/scripts|Scripts]] I've written for DNA-related tasks.
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*[http://excel2wiki.net/ Excel spreadsheet to Mediawiki table converter].  Uses my [[Template:Table|table template]].  Or you can try a [http://area23.brightbyte.de/csv2wp.php fancier converter].
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*Read about my experience with [[Contract M13 phage ssDNA Production]].
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*I was a teaching assistant for Harvard's 2006 [[IGEM:Harvard/2006| iGEM team]] and [[Harvard:Biophysics_101/2007 | Biophysics 101]] in 2007.
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==Example Table==
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==Contract ssDNA Production==
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*The following outlines my recent experience with contract research companies.  We attempted to outsource the production of single-stranded DNA produced by M13 phage.  Hopefully someone will find this useful.
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===Companies Contacted===
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'''No response'''
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*[http://www.lamdabiotech.com/displaycategory.asp?Categoryid=36 Lambda biotech] (emailed 3/2/06)
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*[http://www.wisbio.com/ Wisconsin Bioproducts] (voicemail left 3/3/06)
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*[http://www.geneblitz.com/dna_preparation.htm Geneblitz] (emailed 3/8/06)
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*[http://www.fitbiotech.com/products/t_prod8.htm FIT biotech] (emailed 3/8/06)
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*[http://www.cbi-biotech.com/cbi Commonwealth Biotech] (emailed 4/12/06)
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*[http://www.maxim-asia.com/xyen/Index.asp Maxim Biotech] (emailed 4/12/06)
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*[http://www.atglabsinc.com/ ATG Labs] - info@atglabsinc.com (emailed 4/12/06)
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*[http://seracare.com/ Seracare] (emailed 4/12/06)
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*[http://www.retrogen.com/ Retrogen] (emailed 4/12/06)
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*[http://www.usbio.net/Home.aspx US Biological] - service@usbio.net (emailed 4/12/06)
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'''Initial response promising a quote, followed by zero communication'''
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*[http://www.marinbio.com/molecularbio2.html Marinbio] (emailed 3/8/06, 3/26/06, several other times)
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*[http://www.natx.com/PlasmidLargeScale.html Nature Technology Corporation (natx)] - (emailed 3/2, 3/8, 3/23, 3/27, 4/3, 4/12) Shipped them a sample to begin pre-production on 3/27.  Was informed that my sample was "quarantined" on 4/3, and then no further responses were received.
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'''Response received, but not offering M13 ssDNA production'''
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*[http://www.genscript.com/clone_exp.html Genscript] (emailed 3/9, response 3/9)
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*[http://www.lark.com/services%5ccustom_services.html Lark] (emailed 3/9, responses 3/9, 3/13, 3/14)
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*[http://www.agencourt.com/ Agencourt] (emailed 3/6, response 3/7, 3/13)
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*[http://www.invitrogen.com/content.cfm?pageid=11035 Invitrogen] (emailed 3/8, response 3/15)
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*[http://www.puresyn.com/ Puresyn] (emailed 4/4, response 4/5, including phone call followup)
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*[http://www.mwgbiotech.com/html/all/index.php MWG Biotech] (emailed 4/12, response 4/12)
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*[http://paragonbioservices.com/ Paragon] (emailed 4/12, response 4/12)
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*[http://altheatech.com/ Althea Technologies] (emailed 4/4, response 4/6)
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*[http://plasmidfactory.com/ Plasmid Factory] (emailed 4/4, response 4/11)
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===Quotes Received===
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{| {{table}}
{| {{table}}
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| align="center" style="background:#f0f0f0;"|'''Company'''
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| align="center" style="background:#f0f0f0;"|'''name'''
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| align="center" style="background:#f0f0f0;"|'''10 mg'''
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| align="center" style="background:#f0f0f0;"|'''value'''
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| align="center" style="background:#f0f0f0;"|'''20 mg'''
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| align="center" style="background:#f0f0f0;"|'''50 mg'''
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| align="center" style="background:#f0f0f0;"|'''100 mg'''
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| align="center" style="background:#f0f0f0;"|'''500 mg'''
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| align="center" style="background:#f0f0f0;"|'''1000 mg'''
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|-
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| [http://www.ocimumbio.com/web/research_services/research_con.asp Ocimum Bio]|| ||$1,250 ||$3,900 ||$5,900 ||$18,500 ||$25,000
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| pi||3.1415
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|-
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| [http://fermentas.com/ Fermentas]||$6,300|| ||$10,200 ||$14,400 ||$25,700 ||$42,100
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| e||2.7182
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| [http://www.seqwright.com/ Seqwright] || || || ||  ||$28,000 ||
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| golden ratio||1.618
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|-
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| [http://www.lofstrand.com/ Lofstrand] || ||$4,000 ||$7,000 ||$12,000 ||$50,000 ||$90,000
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|-
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| [http://aldevron.com/ Aldevron] || || || || $16,000 || || $90,000
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|-
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| [http://cmt-inc.net/ CMT] || || || || $82,240+ || ||
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|}
|}
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*Table template can be seen here: [[Template:Table]]
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===Orders placed===
 
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*We placed an order with Ocimum Biosolutions for 1000 mg of ssDNA.  The contract they proposed was to deliver 100-200 mg within 14 days, 300 mg within 21 days, and the remaining 500-600 mg within 28 days.  After 21 days, Ocimum was able to deliver 10 mg of highly-contaminated ssDNA.
 
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[[Image:p7308-comparison.png|thumb|2% agarose 10 mM {{mgcl2}}]]
 
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{| {{table}}
 
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| align="center" style="background:#f0f0f0;"|'''Lane'''
 
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| align="center" style="background:#f0f0f0;"|'''Contents'''
 
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| align="center" style="background:#f0f0f0;"|'''Loading Buffer'''
 
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|-
 
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| 0||[[:Image:1kb.png|1kb DNA ladder]] (4 {{ul}})||
 
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|-
 
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| 1||Shih Lab ssDNA (1 {{ul}})||AGLB (2 {{ul}}) + d{{h2o}} (to 12 {{ul}})
 
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|-
 
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| 2||Shih Lab ssDNA (5 {{ul}})||AGLB (2 {{ul}}) + d{{h2o}} (to 12 {{ul}})
 
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|-
 
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| 3||Ocimum ssDNA (1 {{ul}})||AGLB (2 {{ul}}) + d{{h2o}} (to 12 {{ul}})
 
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|-
 
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| 4||Ocimum ssDNA (5 {{ul}})||AGLB (2 {{ul}}) + d{{h2o}} (to 12 {{ul}})
 
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|}
 
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===Outcome===
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__NOTOC__
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In the subsequent two weeks of extremely tedious negotiations, Ocimum refused to offer any discount or compensation, and failed to guarantee any future delivery schedule, and we ultimately canceled our order.
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Revision as of 13:34, 27 May 2012

Projects

About Me

OWW Contributions

Example Table

name value
pi3.1415
e2.7182
golden ratio1.618


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