Synthetic Biology:Tools - Revision history

Sam Kapp: /* DNA Tools */

2013-04-18T07:04:40Z

DNA Tools

←Older revision		Revision as of 07:04, 18 April 2013
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	**Web tool for converting between sequence file formats.		**Web tool for converting between sequence file formats.

-	*[http://www.genomecompiler.com/ Genome Compiler] by Genome Compiler	+	*[http://www.genomecompiler.com/?utm_source=syntheticbiology.org/tools Genome Compiler] by Genome Compiler
	**Genome Compiler is the industry's most user friendly genetic engineering design tool. It allows you to manipulate genetic information; from genes to plasmids to whole genomes. You can rapidly access extensive libraries of genetic parts, and easily order your final design from a variety of providers.		**Genome Compiler is the industry's most user friendly genetic engineering design tool. It allows you to manipulate genetic information; from genes to plasmids to whole genomes. You can rapidly access extensive libraries of genetic parts, and easily order your final design from a variety of providers.
	**Some of the key features include: a user-friendly workspace for handling genetic constructs of all sizes, a powerful gene search capability with lightning fast NCBI access, a built-in constructs library that includes a parts registry, vectors-plasmids, complete genomes, as well as seamless collaboration through the Genome Compiler Cloud. Additionally you can drag components between layers and projects (in multiple tabs), design genetic constructs across tightly integrated layers; operon/part level, amino acid, and DNA, perform re-annotation and reverse complement, employ automatic sequence detection to point out restriction enzymes and protein sub-domains.		**Some of the key features include: a user-friendly workspace for handling genetic constructs of all sizes, a powerful gene search capability with lightning fast NCBI access, a built-in constructs library that includes a parts registry, vectors-plasmids, complete genomes, as well as seamless collaboration through the Genome Compiler Cloud. Additionally you can drag components between layers and projects (in multiple tabs), design genetic constructs across tightly integrated layers; operon/part level, amino acid, and DNA, perform re-annotation and reverse complement, employ automatic sequence detection to point out restriction enzymes and protein sub-domains.

Sam Kapp: /* DNA Tools */

2013-04-04T07:44:58Z

DNA Tools

←Older revision		Revision as of 07:44, 4 April 2013
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	*[http://synbio.mit.edu/tools/converter.cgi File format converter] by [[Austin Che]]		*[http://synbio.mit.edu/tools/converter.cgi File format converter] by [[Austin Che]]
	**Web tool for converting between sequence file formats.		**Web tool for converting between sequence file formats.
		+
		+	*[http://www.genomecompiler.com/ Genome Compiler] by Genome Compiler
		+	**Genome Compiler is the industry's most user friendly genetic engineering design tool. It allows you to manipulate genetic information; from genes to plasmids to whole genomes. You can rapidly access extensive libraries of genetic parts, and easily order your final design from a variety of providers.
		+	**Some of the key features include: a user-friendly workspace for handling genetic constructs of all sizes, a powerful gene search capability with lightning fast NCBI access, a built-in constructs library that includes a parts registry, vectors-plasmids, complete genomes, as well as seamless collaboration through the Genome Compiler Cloud. Additionally you can drag components between layers and projects (in multiple tabs), design genetic constructs across tightly integrated layers; operon/part level, amino acid, and DNA, perform re-annotation and reverse complement, employ automatic sequence detection to point out restriction enzymes and protein sub-domains.

	*[http://www.genedesign.org/ GeneDesign] by Boeke lab		*[http://www.genedesign.org/ GeneDesign] by Boeke lab
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	** DeviceEditor: a visual DNA design canvas that serves as front-end for j5		** DeviceEditor: a visual DNA design canvas that serves as front-end for j5
	** VectorEditor: a visual DNA editing and annotation tool		** VectorEditor: a visual DNA editing and annotation tool
-	** The j5 and DeviceEditor software has been exclusively licensed to [http://teselagen.com TeselaGen Biotechnologies] for commercial use and distribution.	+	** The j5 and DeviceEditor software has been exclusively licensed to [http://teselagen.com TeselaGen Biotechnologies] for commercial use and distribution.

	===RNA Tools===		===RNA Tools===

Nathan J. Hillson: /* General Tools */

2012-10-05T20:07:38Z

General Tools

←Older revision		Revision as of 20:07, 5 October 2012
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	** Try out the integrated online tools, including DNA sequence editing and annotation (Vector Editor) and auto-aligning sequencing trace files against a template.		** Try out the integrated online tools, including DNA sequence editing and annotation (Vector Editor) and auto-aligning sequencing trace files against a template.
	** Follow a link to the underlying open-source software source code.		** Follow a link to the underlying open-source software source code.
		+
		+	* [http://parpar.jbei.org PaR-PaR Laboratory Automation Platform]
		+	** PaR-PaR allows researchers to use liquid-handling robots effectively, enabling experiments that would not have been considered previously. After minimal training, a biologist can independently write complicated protocols for a robot within an hour.
	</div>		</div>
	{{Synthetic biology bottom}}		{{Synthetic biology bottom}}

Nathan J. Hillson at 18:17, 5 August 2012

2012-08-05T18:17:48Z

←Older revision		Revision as of 18:17, 5 August 2012
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	**Free-to-academics tool for sequence analysis and data management.		**Free-to-academics tool for sequence analysis and data management.

-	*[http://j5.jbei.org j5 ~~and~~ DeviceEditor ~~BioCAD~~] online tools	+	*[http://j5.jbei.org j5, DeviceEditor, and VectorEditor] online tools
-	** j5: DNA assembly design automation for (combinatorial) SLIC/Gibson/CPEC and Golden Gate assembly methods	+	** j5: DNA assembly design automation for (combinatorial) flanking homology (e.g., SLIC/Gibson/CPEC/SLiCE/yeast) and type IIs-mediated (e.g., Golden Gate/FX cloning) assembly methods
	** DeviceEditor: a visual DNA design canvas that serves as front-end for j5		** DeviceEditor: a visual DNA design canvas that serves as front-end for j5
		+	** VectorEditor: a visual DNA editing and annotation tool
		+	** The j5 and DeviceEditor software has been exclusively licensed to [http://teselagen.com TeselaGen Biotechnologies] for commercial use and distribution.

	===RNA Tools===		===RNA Tools===

Nathan J. Hillson at 00:28, 17 February 2012

2012-02-17T00:28:46Z

←Older revision		Revision as of 00:28, 17 February 2012
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	*[http://j5.jbei.org j5 and DeviceEditor BioCAD] online tools		*[http://j5.jbei.org j5 and DeviceEditor BioCAD] online tools
-	** j5: DNA assembly design automation for ~~the~~ SLIC/Gibson/CPEC and ~~(combinatorial)~~ Golden Gate assembly methods	+	** j5: DNA assembly design automation for (combinatorial) SLIC/Gibson/CPEC and Golden Gate assembly methods
	** DeviceEditor: a visual DNA design canvas that serves as front-end for j5		** DeviceEditor: a visual DNA design canvas that serves as front-end for j5

Nathan J. Hillson: /* DNA Tools */

2011-06-02T22:18:56Z

DNA Tools

←Older revision		Revision as of 22:18, 2 June 2011
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	**Free-to-academics tool for sequence analysis and data management.		**Free-to-academics tool for sequence analysis and data management.

-	*[http://jbei~~-exwebapp~~.~~lbl.gov/j5~~ j5 and DeviceEditor BioCAD] online tools	+	*[http://j5.jbei.org j5 and DeviceEditor BioCAD] online tools
	** j5: DNA assembly design automation for the SLIC/Gibson/CPEC and (combinatorial) Golden Gate assembly methods		** j5: DNA assembly design automation for the SLIC/Gibson/CPEC and (combinatorial) Golden Gate assembly methods
	** DeviceEditor: a visual DNA design canvas that serves as front-end for j5		** DeviceEditor: a visual DNA design canvas that serves as front-end for j5

Nathan J. Hillson: /* General Tools */

2011-04-07T00:26:49Z

General Tools

←Older revision		Revision as of 00:26, 7 April 2011
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	**Open repository of BioBricks; the place for all your standard biological parts.		**Open repository of BioBricks; the place for all your standard biological parts.

-	* The public instance of the [https://public.~~jbeir~~.org JBEI Registry]	+	* The public instance of the [https://public-registry.jbei.org JBEI Registry]
	** A DNA part, plasmid, microbial strain, and Arabidopsis Seed online repository with physical sample tracking capabilities		** A DNA part, plasmid, microbial strain, and Arabidopsis Seed online repository with physical sample tracking capabilities
	** A site where you can explore the various features of the JBEI Registry software, and even get some work done!		** A site where you can explore the various features of the JBEI Registry software, and even get some work done!

Nathan J. Hillson: /* General Tools */

2011-01-06T01:35:22Z

General Tools

←Older revision		Revision as of 01:35, 6 January 2011
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	*[http://parts.mit.edu/ Registry of Standard Biological Parts] by MIT		*[http://parts.mit.edu/ Registry of Standard Biological Parts] by MIT
	**Open repository of BioBricks; the place for all your standard biological parts.		**Open repository of BioBricks; the place for all your standard biological parts.
		+
		+	* The public instance of the [https://public.jbeir.org JBEI Registry]
		+	** A DNA part, plasmid, microbial strain, and Arabidopsis Seed online repository with physical sample tracking capabilities
		+	** A site where you can explore the various features of the JBEI Registry software, and even get some work done!
		+	** Try out the integrated online tools, including DNA sequence editing and annotation (Vector Editor) and auto-aligning sequencing trace files against a template.
		+	** Follow a link to the underlying open-source software source code.
	</div>		</div>
	{{Synthetic biology bottom}}		{{Synthetic biology bottom}}

Nathan J. Hillson: /* DNA Tools */

2011-01-06T01:33:59Z

DNA Tools

←Older revision		Revision as of 01:33, 6 January 2011
Line 55:		Line 55:
	*[http://www.invitrogen.com/content.cfm?pageid=10373 Vector NTI] by Informax, Inc.		*[http://www.invitrogen.com/content.cfm?pageid=10373 Vector NTI] by Informax, Inc.
	**Free-to-academics tool for sequence analysis and data management.		**Free-to-academics tool for sequence analysis and data management.
		+
		+	*[http://jbei-exwebapp.lbl.gov/j5 j5 and DeviceEditor BioCAD] online tools
		+	** j5: DNA assembly design automation for the SLIC/Gibson/CPEC and (combinatorial) Golden Gate assembly methods
		+	** DeviceEditor: a visual DNA design canvas that serves as front-end for j5

	===RNA Tools===		===RNA Tools===

Notadoctor: /* DNA Tools */

2010-02-11T06:00:15Z

DNA Tools

←Older revision		Revision as of 06:00, 11 February 2010
Line 33:		Line 33:

	*[http://www.genedesign.org/ GeneDesign] by Boeke lab		*[http://www.genedesign.org/ GeneDesign] by Boeke lab
-	**Collection of online tools for codon optimization and shuffling, restriction site editing, and so on.	+	**Collection of online (and some command line) tools for codon optimization and shuffling, restriction site editing, and so on.

	*[https://www.dna20.com/tools/genedesigner.php GeneDesigner] by DNA2.0		*[https://www.dna20.com/tools/genedesigner.php GeneDesigner] by DNA2.0