Computational Tools - Revision history

Johannes W. Dietrich: /* SimThyr */

2013-02-09T20:35:23Z

SimThyr

←Older revision		Revision as of 20:35, 9 February 2013
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	SBW (Systems Biology Workbench)		SBW (Systems Biology Workbench)

		+	== SimThyr==
		+	http://simthyr.sf.net
		+	'''Johannes W. Dietrich'''
		+
		+	SimThyr is a continuous numeric simulation program for thyroid homeostasis. It is based on a parametrically isomorphic model of the overall system. Applications of this program cover research, including development of hypotheses, and education of students in biology and medicine, nurses and patients.

	== SynBioSS==		== SynBioSS==

Nathan J. Hillson: /* DeviceEditor */

2012-08-05T18:20:13Z

DeviceEditor

←Older revision		Revision as of 18:20, 5 August 2012
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	'''Joanna Chen, Douglas Densmore, Timothy Ham, Zinovii Dmytriv		'''Joanna Chen, Douglas Densmore, Timothy Ham, Zinovii Dmytriv

-	A web-based bioCAD software tool, DeviceEditor, provides a graphical design environment that mimics the intuitive visual whiteboard design process practiced in biological laboratories. The key innovations of DeviceEditor include visual combinatorial library design, direct integration with scar-less multi-part DNA assembly design automation, and a graphical user interface for the creation and modification of design specification rules. DeviceEditor liberates researchers from DNA base-pair manipulation, and enables users to create successful prototypes using standardized, functional, and visual abstractions. Open and documented software interfaces support further integration of DeviceEditor with other bioCAD tools and software platforms. DeviceEditor saves researcher time and institutional resources through correct-by-construction design, the automation of tedious tasks, design reuse, and the minimization of DNA assembly costs.	+	A web-based bioCAD software tool, DeviceEditor, provides a graphical design environment that mimics the intuitive visual whiteboard design process practiced in biological laboratories. The key innovations of DeviceEditor include visual combinatorial library design, direct integration with scar-less multi-part DNA assembly design automation, and a graphical user interface for the creation and modification of design specification rules. DeviceEditor liberates researchers from DNA base-pair manipulation, and enables users to create successful prototypes using standardized, functional, and visual abstractions. Open and documented software interfaces support further integration of DeviceEditor with other bioCAD tools and software platforms. DeviceEditor saves researcher time and institutional resources through correct-by-construction design, the automation of tedious tasks, design reuse, and the minimization of DNA assembly costs. The DeviceEditor software has been exclusively licensed to [http://teselagen.com TeselaGen Biotechnologies] for commercial use and distribution.

	==VectorEditor==		==VectorEditor==

Nathan J. Hillson: /* j5 */

2012-08-05T18:19:47Z

←Older revision		Revision as of 18:19, 5 August 2012
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	'''Nathan J. Hillson		'''Nathan J. Hillson

-	Recent advances in Synthetic Biology have yielded standardized and automatable DNA assembly protocols that enable a broad range of biotechnological research and development. Unfortunately, the experimental design required for modern scar-less multipart DNA assembly methods is frequently laborious, time-consuming, and error-prone. A web-based software tool, j5, automates the design of scar-less multipart DNA assembly protocols including SLIC, Gibson, CPEC, and Golden Gate. The key innovations of the j5 design process include cost optimization, leveraging DNA synthesis when cost-effective to do so, the enforcement of design specification rules, hierarchical assembly strategies to mitigate likely assembly errors, and the instruction of manual or automated construction of scar-less combinatorial DNA libraries. j5 can be used to build combinatorial libraries and applied to the preparation of linear gene deletion cassettes. These innovations save researchers time and effort, reduce the frequency of user design errors and off-target assembly products, decrease research costs, and enable scar-less multipart and combinatorial DNA construction at scales unfeasible without computer-aided design.	+	Recent advances in Synthetic Biology have yielded standardized and automatable DNA assembly protocols that enable a broad range of biotechnological research and development. Unfortunately, the experimental design required for modern scar-less multipart DNA assembly methods is frequently laborious, time-consuming, and error-prone. A web-based software tool, j5, automates the design of scar-less multipart DNA assembly protocols including SLIC, Gibson, CPEC, and Golden Gate. The key innovations of the j5 design process include cost optimization, leveraging DNA synthesis when cost-effective to do so, the enforcement of design specification rules, hierarchical assembly strategies to mitigate likely assembly errors, and the instruction of manual or automated construction of scar-less combinatorial DNA libraries. j5 can be used to build combinatorial libraries and applied to the preparation of linear gene deletion cassettes. These innovations save researchers time and effort, reduce the frequency of user design errors and off-target assembly products, decrease research costs, and enable scar-less multipart and combinatorial DNA construction at scales unfeasible without computer-aided design. The j5 software has been exclusively licensed to [http://teselagen.com TeselaGen Biotechnologies] for commercial use and distribution.

	==DeviceEditor==		==DeviceEditor==

Michal Galdzicki: /* iGEM Software */

2012-06-13T02:54:31Z

iGEM Software

←Older revision		Revision as of 02:54, 13 June 2012
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	'''Michal Galdzicki'''		'''Michal Galdzicki'''

-	A reference collection of iGEM software projects 2007-2011. This is a compilation of all the software projects large and small created throughout the iGEM competition. On this site you can find the description of the computational tool ~~created~~, a link to the project page and source code.	+	A reference collection of iGEM software projects 2007-2011. This is a compilation of all the software projects large and small created throughout the iGEM competition. On this site you can find the description of the computational tool, a link to the project page and source code.

Michal Galdzicki: /* iGEM Software */

2012-06-13T02:53:52Z

iGEM Software

←Older revision		Revision as of 02:53, 13 June 2012
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	'''Michal Galdzicki'''		'''Michal Galdzicki'''

-	A reference collection of iGEM software projects 2007-2011. This is a compilation of all the software projects large and small created throughout the iGEM competition.	+	A reference collection of iGEM software projects 2007-2011. This is a compilation of all the software projects large and small created throughout the iGEM competition. On this site you can find the description of the computational tool created, a link to the project page and source code.

Michal Galdzicki at 02:49, 13 June 2012

2012-06-13T02:49:58Z

←Older revision		Revision as of 02:49, 13 June 2012
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	https://public-registry.jbei.org/static/vesa/VectorEditor.html		https://public-registry.jbei.org/static/vesa/VectorEditor.html
	'''Zinovii Dmytriv, Timothy Ham, Hector Plahar, Joanna Chen		'''Zinovii Dmytriv, Timothy Ham, Hector Plahar, Joanna Chen
-

	Open source, web based cross platform and cross browser DNA sequence editing and analysis tool.		Open source, web based cross platform and cross browser DNA sequence editing and analysis tool.
		+
		+	==iGEM Software==
		+	http://igem.synbioreview.com/
		+	'''Michal Galdzicki'''
		+
		+	A reference collection of iGEM software projects 2007-2011. This is a compilation of all the software projects large and small created throughout the iGEM competition.

Nathan J. Hillson at 16:55, 17 February 2012

2012-02-17T16:55:23Z

←Older revision		Revision as of 16:55, 17 February 2012
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	A web-based bioCAD software tool, DeviceEditor, provides a graphical design environment that mimics the intuitive visual whiteboard design process practiced in biological laboratories. The key innovations of DeviceEditor include visual combinatorial library design, direct integration with scar-less multi-part DNA assembly design automation, and a graphical user interface for the creation and modification of design specification rules. DeviceEditor liberates researchers from DNA base-pair manipulation, and enables users to create successful prototypes using standardized, functional, and visual abstractions. Open and documented software interfaces support further integration of DeviceEditor with other bioCAD tools and software platforms. DeviceEditor saves researcher time and institutional resources through correct-by-construction design, the automation of tedious tasks, design reuse, and the minimization of DNA assembly costs.		A web-based bioCAD software tool, DeviceEditor, provides a graphical design environment that mimics the intuitive visual whiteboard design process practiced in biological laboratories. The key innovations of DeviceEditor include visual combinatorial library design, direct integration with scar-less multi-part DNA assembly design automation, and a graphical user interface for the creation and modification of design specification rules. DeviceEditor liberates researchers from DNA base-pair manipulation, and enables users to create successful prototypes using standardized, functional, and visual abstractions. Open and documented software interfaces support further integration of DeviceEditor with other bioCAD tools and software platforms. DeviceEditor saves researcher time and institutional resources through correct-by-construction design, the automation of tedious tasks, design reuse, and the minimization of DNA assembly costs.
		+
		+	==VectorEditor==
		+	https://public-registry.jbei.org/static/vesa/VectorEditor.html
		+	'''Zinovii Dmytriv, Timothy Ham, Hector Plahar, Joanna Chen
		+
		+
		+	Open source, web based cross platform and cross browser DNA sequence editing and analysis tool.

Nathan J. Hillson at 16:46, 17 February 2012

2012-02-17T16:46:47Z

←Older revision		Revision as of 16:46, 17 February 2012
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	design using their own physical protocol, which we exemplify by already incorporating three alternative effective energy functions.Our versatile software will allow synthetic biologists using physical		design using their own physical protocol, which we exemplify by already incorporating three alternative effective energy functions.Our versatile software will allow synthetic biologists using physical
	models to use a standard molecular dynamics software for protein design.		models to use a standard molecular dynamics software for protein design.
		+
		+	==j5==
		+	http://j5.jbei.org
		+	'''Nathan J. Hillson
		+
		+	Recent advances in Synthetic Biology have yielded standardized and automatable DNA assembly protocols that enable a broad range of biotechnological research and development. Unfortunately, the experimental design required for modern scar-less multipart DNA assembly methods is frequently laborious, time-consuming, and error-prone. A web-based software tool, j5, automates the design of scar-less multipart DNA assembly protocols including SLIC, Gibson, CPEC, and Golden Gate. The key innovations of the j5 design process include cost optimization, leveraging DNA synthesis when cost-effective to do so, the enforcement of design specification rules, hierarchical assembly strategies to mitigate likely assembly errors, and the instruction of manual or automated construction of scar-less combinatorial DNA libraries. j5 can be used to build combinatorial libraries and applied to the preparation of linear gene deletion cassettes. These innovations save researchers time and effort, reduce the frequency of user design errors and off-target assembly products, decrease research costs, and enable scar-less multipart and combinatorial DNA construction at scales unfeasible without computer-aided design.
		+
		+	==DeviceEditor==
		+	http://j5.jbei.org
		+	'''Joanna Chen, Douglas Densmore, Timothy Ham, Zinovii Dmytriv
		+
		+	A web-based bioCAD software tool, DeviceEditor, provides a graphical design environment that mimics the intuitive visual whiteboard design process practiced in biological laboratories. The key innovations of DeviceEditor include visual combinatorial library design, direct integration with scar-less multi-part DNA assembly design automation, and a graphical user interface for the creation and modification of design specification rules. DeviceEditor liberates researchers from DNA base-pair manipulation, and enables users to create successful prototypes using standardized, functional, and visual abstractions. Open and documented software interfaces support further integration of DeviceEditor with other bioCAD tools and software platforms. DeviceEditor saves researcher time and institutional resources through correct-by-construction design, the automation of tedious tasks, design reuse, and the minimization of DNA assembly costs.

Salis at 22:32, 25 August 2010

2010-08-25T22:32:07Z

←Older revision		Revision as of 22:32, 25 August 2010
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	For more detailed information, please refer to the recent papers [http://dx.doi.org/doi:10.1093/bioinformatics/btp029 ProMoT: Modular Modeling for Systems Biology] and		For more detailed information, please refer to the recent papers [http://dx.doi.org/doi:10.1093/bioinformatics/btp029 ProMoT: Modular Modeling for Systems Biology] and
	[http://dx.doi.org/10.1093/bioinformatics/btn330 Computational design of synthetic gene circuits with composable parts] or the synthetic biology research page [http://www.csb.ethz.ch/research/synthetic Synthetic Biology at ETH Zurich].		[http://dx.doi.org/10.1093/bioinformatics/btn330 Computational design of synthetic gene circuits with composable parts] or the synthetic biology research page [http://www.csb.ethz.ch/research/synthetic Synthetic Biology at ETH Zurich].
		+
		+	== Ribosome Binding Site (RBS) Calculator ==
		+	http://salis.psu.edu/software
		+	''Howard Salis, Ethan Mirsky, and Christopher Voigt, Nature Biotechnology, v27, 2009''
		+
		+	The Ribosome Binding Site (RBS) Calculator is an engineering design method that predicts the translation initiation rate of a protein coding sequence in bacteria. You can use the RBS Calculator to generate synthetic ribosome binding site sequences and to rationally control the production rate of any protein in bacteria from 0.1 to 100,000+ on a proportional scale.
		+
		+	Relevant paper: [http://www.nature.com/nbt/journal/v27/n10/abs/nbt.1568.html Automated design of synthetic ribosome binding sites to control protein expression]

	== RoVerGeNe ==		== RoVerGeNe ==

Douglas Densmore: /* Clotho */

2009-11-14T03:08:40Z

Clotho

←Older revision		Revision as of 03:08, 14 November 2009
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	==Clotho==		==Clotho==
-	http://~~biocad-server~~.~~eecs~~.~~berkeley.edu/wiki/index.php/Clotho_Development~~	+	http://www.clothocad.org
	'''Douglas Densmore, J. Christopher Anderson, Alberto Sangiovanni-Vincentelli'''		'''Douglas Densmore, J. Christopher Anderson, Alberto Sangiovanni-Vincentelli'''