User:ShawnDouglas

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
m (Contract ssDNA Production)
Current revision (19:58, 8 October 2013) (view source)
(About Me)
 
(47 intermediate revisions not shown.)
Line 1: Line 1:
-
*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].
+
==Projects==
-
*I am also a teaching assistant for Harvard's 2006 [[IGEM:Harvard/2006| iGEM team]].
+
*[http://biomod.net/ BIOMOD] ([[Biomod|Team Wikis]])
-
*Find out more at my personal [http://www.shawndouglas.com/ website].
+
*[http://cadnano.org/ cadnano]
 +
==About Me==
 +
*I am current an Assistant Professor at [http://bionano.ucsf.edu/ UCSF]
 +
*I was previously a fellow at the [http://wyss.harvard.edu/ Wyss Institute].
 +
*I have a [http://www.shawndouglas.com/ personal website].
 +
*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].
 +
*email: <nowiki>python -c "print ''.join([chr(ord(c)-3) for c in 'vkdzq1grxjodvCxfvi1hgx'])"</nowiki>
 +
==OWW Contributions==
 +
*Protocol: [[Recombineering/Lambda_red-mediated_gene_replacement|λ red-mediated gene replacement]]
 +
*[[/scripts|Scripts]] I've written for DNA-related tasks.
 +
*[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].
 +
*Read about my experience with [[Contract M13 phage ssDNA Production]].
 +
*I was a teaching assistant for Harvard's 2006 [[IGEM:Harvard/2006| iGEM team]] and [[Harvard:Biophysics_101/2007 | Biophysics 101]] in 2007.
-
 
+
==Example Table==
-
==Contract ssDNA Production==
+
-
The following outlines my recent experience with contract research.  We attempted to outsource the production and purification of single-stranded DNA produced by M13 phage.  It wasn't a happy experience, but hopefully someone will find this useful.
+
-
 
+
-
===Companies Contacted===
+
-
'''No response'''
+
-
*[http://www.lamdabiotech.com/displaycategory.asp?Categoryid=36 Lambda biotech] (emailed 3/2/06)
+
-
*[http://www.wisbio.com/ Wisconsin Bioproducts] (voicemail left 3/3/06)
+
-
*[http://www.geneblitz.com/dna_preparation.htm Geneblitz] (emailed 3/8/06)
+
-
*[http://www.fitbiotech.com/products/t_prod8.htm FIT biotech] (emailed 3/8/06)
+
-
*[http://www.cbi-biotech.com/cbi Commonwealth Biotech] (emailed 4/12/06)
+
-
*[http://www.maxim-asia.com/xyen/Index.asp Maxim Biotech] (emailed 4/12/06)
+
-
*[http://www.atglabsinc.com/ ATG Labs] - info@atglabsinc.com (emailed 4/12/06)
+
-
*[http://seracare.com/ Seracare] (emailed 4/12/06)
+
-
*[http://www.retrogen.com/ Retrogen] (emailed 4/12/06)
+
-
*[http://www.usbio.net/Home.aspx US Biological] - service@usbio.net (emailed 4/12/06)
+
-
 
+
-
'''Initial response promising a quote, followed by zero communication'''
+
-
*[http://www.marinbio.com/molecularbio2.html Marinbio] (emailed 3/8/06, 3/26/06, several other times)
+
-
*[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.
+
-
 
+
-
'''Response received, but not offering M13 ssDNA production'''
+
-
*[http://www.genscript.com/clone_exp.html Genscript] (emailed 3/9, response 3/9)
+
-
*[http://www.lark.com/services%5ccustom_services.html Lark] (emailed 3/9, responses 3/9, 3/13, 3/14)
+
-
*[http://www.agencourt.com/ Agencourt] (emailed 3/6, response 3/7, 3/13)
+
-
*[http://www.invitrogen.com/content.cfm?pageid=11035 Invitrogen] (emailed 3/8, response 3/15)
+
-
*[http://www.puresyn.com/ Puresyn] (emailed 4/4, response 4/5, including phone call followup)
+
-
*[http://www.mwgbiotech.com/html/all/index.php MWG Biotech] (emailed 4/12, response 4/12)
+
-
*[http://paragonbioservices.com/ Paragon] (emailed 4/12, response 4/12)
+
-
*[http://altheatech.com/ Althea Technologies] (emailed 4/4, response 4/6)
+
-
*[http://plasmidfactory.com/ Plasmid Factory] (emailed 4/4, response 4/11)
+
-
 
+
-
 
+
-
===Quotes Received===
+
{| {{table}}
{| {{table}}
-
| align="center" style="background:#f0f0f0;"|'''Company'''
+
| align="center" style="background:#f0f0f0;"|'''name'''
-
| align="center" style="background:#f0f0f0;"|'''10 mg'''
+
| align="center" style="background:#f0f0f0;"|'''value'''
-
| align="center" style="background:#f0f0f0;"|'''20 mg'''
+
-
| align="center" style="background:#f0f0f0;"|'''50 mg'''
+
-
| align="center" style="background:#f0f0f0;"|'''100 mg'''
+
-
| align="center" style="background:#f0f0f0;"|'''500 mg'''
+
-
| align="center" style="background:#f0f0f0;"|'''1000 mg'''
+
|-
|-
-
| [http://www.ocimumbio.com/web/research_services/research_con.asp Ocimum Bio]|| ||$1,250 ||$3,900 ||$5,900 ||$18,500 ||$25,000
+
| pi||3.1415
|-
|-
-
| [http://fermentas.com/ Fermentas]||$6,300|| ||$10,200 ||$14,400 ||$25,700 ||$42,100
+
| e||2.7182
|-
|-
-
| [http://www.seqwright.com/ Seqwright] || || || ||  ||$28,000 ||
+
| golden ratio||1.618
-
|-
+
-
| [http://www.lofstrand.com/ Lofstrand] || ||$4,000 ||$7,000 ||$12,000 ||$50,000 ||$90,000
+
-
|-
+
-
| [http://aldevron.com/ Aldevron] || || || || $16,000 || || $90,000
+
-
|-
+
-
| [http://cmt-inc.net/ CMT] || || || || $82,240+ || ||
+
|}
|}
 +
*Table template can be seen here: [[Template:Table]]
-
===Orders placed===
 
-
*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.
 
-
 
-
[[Image:p7308-comparison.png|thumb|2% agarose 10 mM {{mgcl2}}]]
 
-
{| {{table}}
 
-
| align="center" style="background:#f0f0f0;"|'''Lane'''
 
-
| align="center" style="background:#f0f0f0;"|'''Contents'''
 
-
| align="center" style="background:#f0f0f0;"|'''Loading Buffer'''
 
-
|-
 
-
| 0||[[:Image:1kb.png|1kb DNA ladder]] (4 {{ul}})||
 
-
|-
 
-
| 1||Shih Lab ssDNA (1 {{ul}})||AGLB (2 {{ul}}) + d{{h2o}} (to 12 {{ul}})
 
-
|-
 
-
| 2||Shih Lab ssDNA (5 {{ul}})||AGLB (2 {{ul}}) + d{{h2o}} (to 12 {{ul}})
 
-
|-
 
-
| 3||Ocimum ssDNA (1 {{ul}})||AGLB (2 {{ul}}) + d{{h2o}} (to 12 {{ul}})
 
-
|-
 
-
| 4||Ocimum ssDNA (5 {{ul}})||AGLB (2 {{ul}}) + d{{h2o}} (to 12 {{ul}})
 
-
|}
 
-
 
-
===Outcome===
 
-
We went with the deceptively low bid, and after 3 weeks we received what ''would'' have amounted to 1/50th of what we were promised by that time, and 1/100th of our total order -- that is, if it had been clean, usable DNA. 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 were ultimately forced to cancel our order.
 
__NOTOC__
__NOTOC__

Current revision

Projects

About Me

OWW Contributions

Example Table

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


Personal tools