Van Oudenaarden Lab:Internal - Revision history

Alexander at 15:10, 1 March 2010

2010-03-01T15:10:46Z

←Older revision		Revision as of 15:10, 1 March 2010
Line 4:		Line 4:
	<br /> Reagents list<br />[[Van_Oudenaarden_Lab:Enzymes \| Restriction enzymes]] (-20C fridge)<br /> Chores list<br/>		<br /> Reagents list<br />[[Van_Oudenaarden_Lab:Enzymes \| Restriction enzymes]] (-20C fridge)<br /> Chores list<br/>
	[[Van_Oudenaarden_Lab:Books \| Books in the lab]]<br/>[http://singlemoleculefish.com/] Single Molecule FISH		[[Van_Oudenaarden_Lab:Books \| Books in the lab]]<br/>[http://singlemoleculefish.com/] Single Molecule FISH
-	~~<br />[[Van_Oudenaarden_Lab:TFProjectElegans \| '''''C. elegans'' TF project''' ]]~~	+
	----		----
	Checklist for 68-311 tissue culture room maintenance:<br /><br />		Checklist for 68-311 tissue culture room maintenance:<br /><br />

Alexander at 21:45, 28 February 2010

2010-02-28T21:45:58Z

←Older revision		Revision as of 21:45, 28 February 2010
Line 4:		Line 4:
	<br /> Reagents list<br />[[Van_Oudenaarden_Lab:Enzymes \| Restriction enzymes]] (-20C fridge)<br /> Chores list<br/>		<br /> Reagents list<br />[[Van_Oudenaarden_Lab:Enzymes \| Restriction enzymes]] (-20C fridge)<br /> Chores list<br/>
	[[Van_Oudenaarden_Lab:Books \| Books in the lab]]<br/>[http://singlemoleculefish.com/] Single Molecule FISH		[[Van_Oudenaarden_Lab:Books \| Books in the lab]]<br/>[http://singlemoleculefish.com/] Single Molecule FISH
		+	<br />[[Van_Oudenaarden_Lab:TFProjectElegans \| '''''C. elegans'' TF project''' ]]
	----		----
	Checklist for 68-311 tissue culture room maintenance:<br /><br />		Checklist for 68-311 tissue culture room maintenance:<br /><br />

Arjunraj at 15:55, 9 December 2009

2009-12-09T15:55:32Z

←Older revision		Revision as of 15:55, 9 December 2009
Line 4:		Line 4:
	<br /> Reagents list<br />[[Van_Oudenaarden_Lab:Enzymes \| Restriction enzymes]] (-20C fridge)<br /> Chores list<br/>		<br /> Reagents list<br />[[Van_Oudenaarden_Lab:Enzymes \| Restriction enzymes]] (-20C fridge)<br /> Chores list<br/>
	[[Van_Oudenaarden_Lab:Books \| Books in the lab]]<br/>[http://singlemoleculefish.com/] Single Molecule FISH		[[Van_Oudenaarden_Lab:Books \| Books in the lab]]<br/>[http://singlemoleculefish.com/] Single Molecule FISH
		+	----
		+	Checklist for 68-311 tissue culture room maintenance:<br /><br />
		+
		+	Mark empty CO2 tanks<br />
		+	Fill out log sheet for CO2 tanks<br />
		+	<br />
		+
		+	Emergency contact information: <br />
		+	Chris Ng, Fraenkel Lab 68-317 <br />
		+	cwng@mit.edu<br />
		+	253-2042<br />
		+	<br />
		+
		+	Deepika Dinesh, Fraenkel Lab 68-317 <br />
		+	dpk_d@mit.edu, db21gn@gmail.com <br />
		+	452-2086<br />
		+	<br />
		+
		+	Yanna Zheng, AvO Lab 68-353 <br />
		+	617-955-6488<br />
		+	<br />
		+
		+	Other TC facilities in building 68: <br />
		+	Burge Lab<br />
		+	Lab phones: 253-7039, 253-6726<br />
		+
		+
	----		----
	<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.		<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.

Apratim Sahay at 21:47, 10 April 2009

2009-04-10T21:47:27Z

←Older revision		Revision as of 21:47, 10 April 2009
Line 1:		Line 1:
	<div style="text-align: left;">		<div style="text-align: left;">
	----		----
		+	<br />[[Van_Oudenaarden_Lab:ImProToo \| '''Image Processing Tools''' ]]
	<br /> Reagents list<br />[[Van_Oudenaarden_Lab:Enzymes \| Restriction enzymes]] (-20C fridge)<br /> Chores list<br/>		<br /> Reagents list<br />[[Van_Oudenaarden_Lab:Enzymes \| Restriction enzymes]] (-20C fridge)<br /> Chores list<br/>
-	[[Van_Oudenaarden_Lab:Books \| Books in the lab~~]]<br />[[Van_Oudenaarden_Lab:ImProToo \| Image Processing Tools~~ ]] <br/>[http://singlemoleculefish.com/] Single Molecule FISH	+	[[Van_Oudenaarden_Lab:Books \| Books in the lab]]<br/>[http://singlemoleculefish.com/] Single Molecule FISH
	----		----
	<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.		<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.

Apratim Sahay at 20:21, 10 April 2009

2009-04-10T20:21:26Z

←Older revision		Revision as of 20:21, 10 April 2009
Line 2:		Line 2:
	----		----
	<br /> Reagents list<br />[[Van_Oudenaarden_Lab:Enzymes \| Restriction enzymes]] (-20C fridge)<br /> Chores list<br/>		<br /> Reagents list<br />[[Van_Oudenaarden_Lab:Enzymes \| Restriction enzymes]] (-20C fridge)<br /> Chores list<br/>
-	[[Van_Oudenaarden_Lab:Books \| Books in the lab]]<br />[[Van_Oudenaarden_Lab:ImProToo \| Image Processing Tools ]]	+	[[Van_Oudenaarden_Lab:Books \| Books in the lab]]<br />[[Van_Oudenaarden_Lab:ImProToo \| Image Processing Tools ]] <br/>[http://singlemoleculefish.com/] Single Molecule FISH
	----		----
-	<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>	+	<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>
	----		----
	<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 />
	----		----
	<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>

Apratim Sahay at 19:34, 10 April 2009

2009-04-10T19:34:14Z

←Older revision		Revision as of 19:34, 10 April 2009
Line 2:		Line 2:
	----		----
	<br /> Reagents list<br />[[Van_Oudenaarden_Lab:Enzymes \| Restriction enzymes]] (-20C fridge)<br /> Chores list<br/>		<br /> Reagents list<br />[[Van_Oudenaarden_Lab:Enzymes \| Restriction enzymes]] (-20C fridge)<br /> Chores list<br/>
-	[[Van_Oudenaarden_Lab:Books \| Books in the lab]]<br />[[Van_Oudenaarden_Lab:~~Image Processing~~ \| Image Processing Tools ]]	+	[[Van_Oudenaarden_Lab:Books \| Books in the lab]]<br />[[Van_Oudenaarden_Lab:ImProToo \| Image Processing Tools ]]
	----		----
	<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>		<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>

Apratim Sahay at 19:33, 10 April 2009

2009-04-10T19:33:19Z

←Older revision		Revision as of 19:33, 10 April 2009
Line 2:		Line 2:
	----		----
	<br /> Reagents list<br />[[Van_Oudenaarden_Lab:Enzymes \| Restriction enzymes]] (-20C fridge)<br /> Chores list<br/>		<br /> Reagents list<br />[[Van_Oudenaarden_Lab:Enzymes \| Restriction enzymes]] (-20C fridge)<br /> Chores list<br/>
-	[[Van_Oudenaarden_Lab:Books \| Books in the lab]]<br />[[Van_Oudenaarden_Lab:~~ImProToo~~ \| Image Processing Tools ]]	+	[[Van_Oudenaarden_Lab:Books \| Books in the lab]]<br />[[Van_Oudenaarden_Lab:Image Processing \| Image Processing Tools ]]
	----		----
	<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>		<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>

Christoph Engert at 21:47, 6 April 2009

2009-04-06T21:47:30Z

←Older revision		Revision as of 21:47, 6 April 2009
Line 2:		Line 2:
	----		----
	<br /> Reagents list<br />[[Van_Oudenaarden_Lab:Enzymes \| Restriction enzymes]] (-20C fridge)<br /> Chores list<br/>		<br /> Reagents list<br />[[Van_Oudenaarden_Lab:Enzymes \| Restriction enzymes]] (-20C fridge)<br /> Chores list<br/>
-	[[Van_Oudenaarden_Lab:Books \| Books in the lab]]	+	[[Van_Oudenaarden_Lab:Books \| Books in the lab]]<br />[[Van_Oudenaarden_Lab:ImProToo \| Image Processing Tools ]]
	----		----
-	<span style="font-style: italic~~;"><br />Internal Wikis:<br /><div style="margin-left: 40px;"> Image Processing Solutions <br /><br /><span style="font-weight: bold~~;"><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>	+	<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>
	----		----
	<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 />
	----		----
	<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>

Christoph Engert at 21:42, 6 April 2009

2009-04-06T21:42:58Z

←Older revision		Revision as of 21:42, 6 April 2009
Line 4:		Line 4:
	[[Van_Oudenaarden_Lab:Books \| Books in the lab]]		[[Van_Oudenaarden_Lab:Books \| Books in the lab]]
	----		----
-	<span style="font-style: italic;"><br />Internal Wikis:<br /><div style="margin-left: 40px;"> Image Processing Solutions <br /><br /><span style="font-weight: bold;"><big><span style="font-weight: bold;"></span></big>~~</span>]~~ 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>	+	<span style="font-style: italic;"><br />Internal Wikis:<br /><div style="margin-left: 40px;"> Image Processing Solutions <br /><br /><span style="font-weight: bold;"><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>
	----		----
	<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 />
	----		----
	<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>

Christoph Engert at 21:42, 6 April 2009

2009-04-06T21:42:31Z

←Older revision		Revision as of 21:42, 6 April 2009
Line 4:		Line 4:
	[[Van_Oudenaarden_Lab:Books \| Books in the lab]]		[[Van_Oudenaarden_Lab:Books \| Books in the lab]]
	----		----
-	<span style="font-style: italic;"><br />Internal Wikis:<br /><div style="margin-left: 40px;"> Image Processing Solutions <span style="font-weight: bold;"><big><span style="font-weight: bold;"></span></big></span>] 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>	+	<span style="font-style: italic;"><br />Internal Wikis:<br /><div style="margin-left: 40px;"> Image Processing Solutions <br /><br /><span style="font-weight: bold;"><big><span style="font-weight: bold;"></span></big></span>] 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 /><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 />
	----		----
	<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>