Van Oudenaarden Lab:Internal

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<br /> Reagents list<br />[[Van_Oudenaarden_Lab:Enzymes | Restriction enzymes]] (-20C fridge)<br /> Chores list<br /><br />
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<br />[[Van_Oudenaarden_Lab:ImProToo | '''Image Processing Tools''' ]]
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<br /> Reagents list<br />[[Van_Oudenaarden_Lab:Enzymes | Restriction enzymes]] (-20C fridge)<br /> Chores list<br/>
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[[Van_Oudenaarden_Lab:Books | Books in the lab]]<br/>[http://singlemoleculefish.com/] Single Molecule FISH
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<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>
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Checklist for 68-311 tissue culture room maintenance:<br /><br />
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Mark empty CO2 tanks<br />
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Fill out log sheet for CO2 tanks<br />
 +
<br />
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Emergency contact information: <br />
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Chris Ng, Fraenkel Lab 68-317 <br />
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cwng@mit.edu<br />
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253-2042<br />
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<br />
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Deepika Dinesh, Fraenkel Lab 68-317 <br />
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dpk_d@mit.edu, db21gn@gmail.com <br />
 +
452-2086<br />
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<br />
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Yanna Zheng, AvO Lab 68-353 <br />
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617-955-6488<br />
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<br />
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Other TC facilities in building 68: <br />
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Burge Lab<br />
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Lab phones: 253-7039, 253-6726<br />
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<span style="font-style: italic;"><big><span style="font-weight: bold;"></span></big>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>
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<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 /><br />
<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 /><br />
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<div style="text-align: right;">additions, corrections, &c: [mailto:mokelly@mit.edu <mokelly@mit.edu>]<br /> </div> </div> </div>
<div style="text-align: right;">additions, corrections, &c: [mailto:mokelly@mit.edu <mokelly@mit.edu>]<br /> </div> </div> </div>

Current revision



Image Processing Tools
Reagents list
Restriction enzymes (-20C fridge)
Chores list
Books in the lab
[1] Single Molecule FISH


Checklist for 68-311 tissue culture room maintenance:

Mark empty CO2 tanks
Fill out log sheet for CO2 tanks

Emergency contact information:
Chris Ng, Fraenkel Lab 68-317
cwng@mit.edu
253-2042

Deepika Dinesh, Fraenkel Lab 68-317
dpk_d@mit.edu, db21gn@gmail.com
452-2086

Yanna Zheng, AvO Lab 68-353
617-955-6488

Other TC facilities in building 68:
Burge Lab
Lab phones: 253-7039, 253-6726



Online tools:
NebCutter V2.0 Restriction and other DNA analysis, with great GUI.
Primer3 Primer design tool best for creating compatible primer pairs for a given template.
Netprimer Primer test tool. Verify melting temperatures, hairpins, dimerization, &c of final primer designs.
NCBI National Center for Biotechnology Information
Entrez Biology search engine, e.g. for looking up protein and DNA sequences by name
PubMed Literature search
BLAST Basic Local Alignment Search Tool, for DNA/protein alignment and comparison, primer verification, etc.
Google Scholar Most general literature search tool.

Freeware:
WinGene Tool for analyzing nucleotide sequences. Best for reverse complements and primer checks.
MFI For converting flow cytometer output files to ASCII. Simple free registration.
OpenOffice.org Open source office environment, fully compatible (well, almost) with MS Office, including Powerpoint.
Open Perl IDE Open source Integrated Development environment for Perl. Easy to set up and use.
ActivePerl Easy installation for running Perl scripts in Windows; necessary for Open Perl IDE.

Perl scripts:
deannotate_dna.pl A useful script for annotating and editing DNA sequences. This file provides documentation and an example.
cytometry.zip Package of scripts and executables for quickly processing raw flow cytometer files into a table of histograms. Consult Michael on its use.


Protocols:
General
E. Coli
Yeast
Cyanobacteria


additions, corrections, &c: <mokelly@mit.edu>
Personal tools