TABASCO - Revision history

Endy: /* Examples */

2011-05-06T16:46:37Z

Examples

←Older revision		Revision as of 16:46, 6 May 2011
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	== Examples ==		== Examples ==
-	[http://~~web~~.~~mit~~.~~edu~~/~~~skosuri~~/~~www~~/t7-~~tabascoweb~~.mov QuickTime] movie showing TABASCO being used to simulate gene expression for the first 1500 seconds of bacteriophage T7 development.	+	[http://www.biomedcentral.com/content/download/supplementary/1471-2105-8-480-s1.mov QuickTime] movie showing TABASCO being used to simulate gene expression for the first 1500 seconds of bacteriophage T7 development.

Endy: /* Software and Installation */

2011-05-06T16:45:39Z

Software and Installation

←Older revision		Revision as of 16:45, 6 May 2011
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	===Installation instructions (for Unix systems)===		===Installation instructions (for Unix systems)===
-	#Download the [http://~~model~~.~~mit~~.~~edu~~/~~Tabasco~~/~~tabasco~~.~~tar.gz~~ extractable archive].	+	#Download the [http://www.biomedcentral.com/content/supplementary/1471-2105-8-480-s3.zip extractable archive (.zip file)].
	#Extract the archive using the following command: <pre> tar -xvzf tabasco.tar.gz </pre>		#Extract the archive using the following command: <pre> tar -xvzf tabasco.tar.gz </pre>
	#*Windows users should be able to use WinZip or other free programs (or download [http://www.cygwin.com/ Cygwin] to make the process more unix like)		#*Windows users should be able to use WinZip or other free programs (or download [http://www.cygwin.com/ Cygwin] to make the process more unix like)

Endy: /* Software */

2008-12-10T18:44:17Z

Software

←Older revision		Revision as of 18:44, 10 December 2008
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	== Software and Installation ==		== Software and Installation ==
	===Software===		===Software===
-	The software for Tabasco is freely available here with the publication, via ~~Additional File #3:~~ [http://www.biomedcentral.com/content/supplementary/1471-2105-8-480-s3.zip .zip file]	+	The software for Tabasco is freely available here with the publication, via [http://www.biomedcentral.com/content/supplementary/1471-2105-8-480-s3.zip Additional File #3 (.zip file)]

	The simulator was only tested on [http://java.sun.com/j2se/1.4.2/ J2SE version 1.4.2] and higher. A basic knowledge of running Java programs is needed. Generally one can either download the source, and then compile it using a java compiler to create byte code or download the precompiled byte code above.		The simulator was only tested on [http://java.sun.com/j2se/1.4.2/ J2SE version 1.4.2] and higher. A basic knowledge of running Java programs is needed. Generally one can either download the source, and then compile it using a java compiler to create byte code or download the precompiled byte code above.

Endy: /* Software */

2008-12-10T18:43:31Z

Software

←Older revision		Revision as of 18:43, 10 December 2008
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	== Software and Installation ==		== Software and Installation ==
	===Software===		===Software===
-	The software for Tabasco is freely available here with the publication, via Additional File #3:~~<br>~~	+	The software for Tabasco is freely available here with the publication, via Additional File #3: [http://www.biomedcentral.com/content/supplementary/1471-2105-8-480-s3.zip .zip file]
-	[http://www.biomedcentral.com/content/supplementary/1471-2105-8-480-s3.zip \| .zip file]	+

	The simulator was only tested on [http://java.sun.com/j2se/1.4.2/ J2SE version 1.4.2] and higher. A basic knowledge of running Java programs is needed. Generally one can either download the source, and then compile it using a java compiler to create byte code or download the precompiled byte code above.		The simulator was only tested on [http://java.sun.com/j2se/1.4.2/ J2SE version 1.4.2] and higher. A basic knowledge of running Java programs is needed. Generally one can either download the source, and then compile it using a java compiler to create byte code or download the precompiled byte code above.

Endy: /* Software */

2008-12-10T18:43:12Z

Software

←Older revision		Revision as of 18:43, 10 December 2008
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	===Software===		===Software===
	The software for Tabasco is freely available here with the publication, via Additional File #3:<br>		The software for Tabasco is freely available here with the publication, via Additional File #3:<br>
-	http://www.biomedcentral.com/1471-2105/8/480~~/additional/~~	+	[http://www.biomedcentral.com/content/supplementary/1471-2105-8-480-s3.zip \| .zip file]

	The simulator was only tested on [http://java.sun.com/j2se/1.4.2/ J2SE version 1.4.2] and higher. A basic knowledge of running Java programs is needed. Generally one can either download the source, and then compile it using a java compiler to create byte code or download the precompiled byte code above.		The simulator was only tested on [http://java.sun.com/j2se/1.4.2/ J2SE version 1.4.2] and higher. A basic knowledge of running Java programs is needed. Generally one can either download the source, and then compile it using a java compiler to create byte code or download the precompiled byte code above.

Endy: /* Software */

2008-12-10T18:41:38Z

Software

←Older revision		Revision as of 18:41, 10 December 2008
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	== Software and Installation ==		== Software and Installation ==
	===Software===		===Software===
-	The software for Tabasco is freely available here~~:<br>~~	+	The software for Tabasco is freely available here with the publication, via Additional File #3:<br>
-	~~[http://model.mit.edu/Tabasco/TabascoWeb.tar.gz Extractable archive of all code~~, ~~documentation, and examples] <br>~~	+	http://www.biomedcentral.com/1471-2105/8/480/additional/
-	~~[http~~:~~//model.mit.edu/Tabasco/source Java Source Files]~~ <br>	+
-	[http://~~model~~.~~mit~~.~~edu~~/~~Tabasco~~/~~doc~~/ ~~Javadoc Documentation] <br>~~	+
-	~~[http:~~//~~model.mit.edu/Tabasco/classes Compiled Java Byte Code] <br>~~	+

	The simulator was only tested on [http://java.sun.com/j2se/1.4.2/ J2SE version 1.4.2] and higher. A basic knowledge of running Java programs is needed. Generally one can either download the source, and then compile it using a java compiler to create byte code or download the precompiled byte code above.		The simulator was only tested on [http://java.sun.com/j2se/1.4.2/ J2SE version 1.4.2] and higher. A basic knowledge of running Java programs is needed. Generally one can either download the source, and then compile it using a java compiler to create byte code or download the precompiled byte code above.

Endy: /* Summary */

2008-01-24T00:08:00Z

Summary

←Older revision		Revision as of 00:08, 24 January 2008
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	{{EndyLab}}		{{EndyLab}}
	== Summary ==		== Summary ==
-	TABASCO is a simulator created to address the problem of simulating gene expression at single-base resolution. By defining the logic of transcription and translation rules a priori such as initiation, elongation, termination, and interactions of polymerases and proteins, Tabasco automatically traverses the state of the system as it develops and thus makes simulation at such high resolution computationally feasible. Tabasco was designed to allow us to better understand bacteriophage gene expression. In general, Tabasco would be useful to those interested in explicitly simulating hypotheses of protein-DNA interactions and their relation to gene expression (e.g., eukaryotic gene expression initiation). A research article ~~(BMC Bioinformatics 2007, 8:480doi:10.1186/1471-2105-8-480)~~ describing Tabasco has been [http://www.biomedcentral.com/1471-2105/8/480/ published].	+	TABASCO is a simulator created to address the problem of simulating gene expression at single-base resolution. By defining the logic of transcription and translation rules a priori such as initiation, elongation, termination, and interactions of polymerases and proteins, Tabasco automatically traverses the state of the system as it develops and thus makes simulation at such high resolution computationally feasible. Tabasco was designed to allow us to better understand bacteriophage gene expression. In general, Tabasco would be useful to those interested in explicitly simulating hypotheses of protein-DNA interactions and their relation to gene expression (e.g., eukaryotic gene expression initiation). A research article describing Tabasco has been [http://www.biomedcentral.com/1471-2105/8/480/ published] (BMC Bioinformatics 2007, 8:480 doi:10.1186/1471-2105-8-480).

	== Note regarding trademark ==		== Note regarding trademark ==

Endy: /* Summary */

2008-01-24T00:07:35Z

Summary

←Older revision		Revision as of 00:07, 24 January 2008
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	{{EndyLab}}		{{EndyLab}}
	== Summary ==		== Summary ==
-	TABASCO is a simulator created to address the problem of simulating gene expression at single-base resolution. By defining the logic of transcription and translation rules a priori such as initiation, elongation, termination, and interactions of polymerases and proteins, Tabasco automatically traverses the state of the system as it develops and thus makes simulation at such high resolution computationally feasible. Tabasco was designed to allow us to better understand bacteriophage gene expression. In general, Tabasco would be useful to those interested in explicitly simulating hypotheses of protein-DNA interactions and their relation to gene expression (e.g., eukaryotic gene expression initiation). A research article describing Tabasco has been [http://www.biomedcentral.com/1471-2105/8/480/ published].	+	TABASCO is a simulator created to address the problem of simulating gene expression at single-base resolution. By defining the logic of transcription and translation rules a priori such as initiation, elongation, termination, and interactions of polymerases and proteins, Tabasco automatically traverses the state of the system as it develops and thus makes simulation at such high resolution computationally feasible. Tabasco was designed to allow us to better understand bacteriophage gene expression. In general, Tabasco would be useful to those interested in explicitly simulating hypotheses of protein-DNA interactions and their relation to gene expression (e.g., eukaryotic gene expression initiation). A research article (BMC Bioinformatics 2007, 8:480doi:10.1186/1471-2105-8-480) describing Tabasco has been [http://www.biomedcentral.com/1471-2105/8/480/ published].

	== Note regarding trademark ==		== Note regarding trademark ==

Endy: /* Summary */

2008-01-24T00:06:56Z

Summary

←Older revision		Revision as of 00:06, 24 January 2008
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	{{EndyLab}}		{{EndyLab}}
	== Summary ==		== Summary ==
-	TABASCO is a simulator created to address the problem of simulating gene expression at single-base resolution. By defining the logic of transcription and translation rules a priori such as initiation, elongation, termination, and interactions of polymerases and proteins, Tabasco automatically traverses the state of the system as it develops and thus makes simulation at such high resolution computationally feasible. Tabasco was designed to allow us to better understand bacteriophage gene expression. In general, Tabasco would be useful to those interested in explicitly simulating hypotheses of protein-DNA interactions and their relation to gene expression (e.g., eukaryotic gene expression initiation).	+	TABASCO is a simulator created to address the problem of simulating gene expression at single-base resolution. By defining the logic of transcription and translation rules a priori such as initiation, elongation, termination, and interactions of polymerases and proteins, Tabasco automatically traverses the state of the system as it develops and thus makes simulation at such high resolution computationally feasible. Tabasco was designed to allow us to better understand bacteriophage gene expression. In general, Tabasco would be useful to those interested in explicitly simulating hypotheses of protein-DNA interactions and their relation to gene expression (e.g., eukaryotic gene expression initiation). A research article describing Tabasco has been [http://www.biomedcentral.com/1471-2105/8/480/ published].

	== Note regarding trademark ==		== Note regarding trademark ==

Endy: /* Note regarding trademark */

2007-11-21T20:01:36Z

Note regarding trademark

←Older revision		Revision as of 20:01, 21 November 2007
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	== Note regarding trademark ==		== Note regarding trademark ==
-	Our use of the word TABASCO here refers to a simulator of gene expression systems, or other systems comprised of elementary chemical reaction events that can be ordered along one or more dimensions. The origins of our use of the word were as an acronym, abbreviating the words “Transcription And Binding And Serious Computational Overhead.” The word “Tabasco” is also a registered trademark of the McIlhenny Company for use in connection with pepper sauces, clothing, and other consumer products. The TABASCO simulator is neither affiliated with nor sponsored or endorsed by the ~~[http://www.tabasco.com/~~ McIlhenny Company] and our use of the TABASCO name is not intended to suggest any such affiliation, sponsorship, or endorsement. “Tabasco” can also refer to a [http://en.wikipedia.org/wiki/Tabasco state in Mexico.]	+	Our use of the word TABASCO here refers to a simulator of gene expression systems, or other systems comprised of elementary chemical reaction events that can be ordered along one or more dimensions. The origins of our use of the word were as an acronym, abbreviating the words “Transcription And Binding And Serious Computational Overhead.” The word “Tabasco” is also a registered trademark of the [http://www.tabasco.com/ McIlhenny Company] for use in connection with pepper sauces, clothing, and other consumer products. The TABASCO simulator is neither affiliated with nor sponsored or endorsed by the McIlhenny Company and our use of the TABASCO name is not intended to suggest any such affiliation, sponsorship, or endorsement. “Tabasco” can also refer to a [http://en.wikipedia.org/wiki/Tabasco state in Mexico.]

	== People ==		== People ==