Michael O'Kelly

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
(Added old mit.edu webpage)
Current revision (05:29, 11 January 2006) (view source)
 
Line 6: Line 6:
= Avo group web resource =
= Avo group web resource =
-
 
-
<div style="text-align: left;">
 
-
----
 
-
<br /> Reagents list<br />[http://www.mit.edu/~mokelly/avo/enzymes.html Restriction enzymes] (-20C fridge)<br /> Chores list<br /><br />
 
-
----
 
-
<span style="font-style: italic;"><br /> Online tools:</span><br /><div style="margin-left: 40px;">[http://tools.neb.com/NEBcutter2/index.php <span style="font-weight: bold;"><big><span style="font-weight: bold;"></span></big></span>]<span style="font-family: times new roman,times,serif;">[http://tools.neb.com/NEBcutter2/index.php NebCutter V2.0] Restriction and other DNA analysis, with great GUI.<br />[http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi Primer3] Primer design tool best for creating compatible primer pairs for a given template. <br />[http://www.premierbiosoft.com/netprimer/netprlaunch/netprlaunch.html Netprimer] Primer test tool. Verify melting temperatures, hairpins, dimerization, &c of final primer designs. <br /> </span> <span style="font-family: times new roman,times,serif;"> [http://www.ncbi.nlm.nih.gov/ NCBI] National Center for Biotechnology Information</span><br /><span style="font-family: times new roman,times,serif;"> </span><div style="margin-left: 40px;">[http://www.ncbi.nlm.nih.gov/Entrez/index.html Entrez] Biology search engine, e.g. for looking up protein and DNA sequences by name<br />[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed PubMed] Literature search<br />[http://www.ncbi.nlm.nih.gov/BLAST/ BLAST] Basic Local Alignment Search Tool, for DNA/protein alignment and comparison, primer verification, etc.<br /> </div> </div><div style="margin-left: 40px;">[http://scholar.google.com/ Google Scholar] Most general literature search tool. <br /><br /> </div><span style="font-style: italic;">Freeware:</span><br /><div style="margin-left: 40px;">[http://www.ipw.agrl.ethz.ch/%7Elhennig/wingene.html WinGene] Tool for analyzing nucleotide sequences. Best for reverse complements and primer checks.<br />[http://www.umass.edu/microbio/mfi/ MFI] For converting flow cytometer output files to ASCII. Simple free registration. <br />[http://www.openoffice.org/ OpenOffice.org] Open source office environment, fully compatible (well, almost) with MS Office, including Powerpoint.<br />[http://open-perl-ide.sourceforge.net/ Open Perl IDE] Open source Integrated Development environment for Perl. Easy to set up and use.<br />[http://www.activestate.com/Products/ActivePerl/?_x=1 ActivePerl] Easy installation for running Perl scripts in Windows; necessary for Open Perl IDE. <br /><br /> </div><span style="font-style: italic;">Perl scripts:<br /> </span><div style="margin-left: 40px;">[http://www.mit.edu/~mokelly/avo/deannotate_dna.pl deannotate_dna.pl] A useful script for annotating and editing DNA sequences. [http://www.mit.edu/~mokelly/avo/annotation%20documentation.txt This file] provides documentation and an example.<br />[http://www.mit.edu/~mokelly/avo/cytometry.zip cytometry.zip] Package of scripts and executables for quickly processing raw flow cytometer files into a table of histograms. Consult Michael on its use. <br /> </div><div style="margin-left: 40px;"> </div>
 
-
----
 
-
<div style="margin-left: 40px;"> </div><br /><span style="font-style: italic;">Protocols:<br /> </span><div style="margin-left: 40px;"><span style="font-style: italic;"><span style="font-style: italic;"></span></span>General<br /> E. Coli<br /> Yeast<br /> Cyanobacteria<br /> </span><br />
 
-
----
 
-
<div style="text-align: right;">additions, corrections, &c: [mailto:mokelly@mit.edu <mokelly@mit.edu>]<br /> </div> </div> </div>
 

Current revision

I am a graduate student in Prof. van Oudenaarden's lab.

Email me to get an OpenWetWare account.

= Avo group web resource =
Personal tools