Main Page - Revision history

Murray: /* The Nucleus Developer Cell Platform */

2026-06-27T16:23:05Z

The Nucleus Developer Cell Platform

← Older revision		Revision as of 09:23, 27 June 2026
Line 99:		Line 99:
	The Nucleus platform uses the OpenMTA<ref>https://www.openplant.org/openmta. Retrieved 19 Jul 2025.</ref> material transfer agreement, developed as a collaborative effort led by the BioBricks Foundation and OpenPlant, which allows open sharing of DNA with attribution (similar to an open source software license). Nucleus also uses the CERN Open Hardware License - Permission <ref> https://gitlab.com/ohwr/project/cernohl/-/wikis/uploads/3eff4154d05e7a0459f3ddbf0674cae4/cern_ohl_p_v2.txt. Retrieved 19 Jul 2025</ref> for distribution of modules and protocols. Documentation of Nucleus modules are done via Developer Notes<ref> https://devnotes.bnext.bio. Retrieved 19 Jul 2025</ref>, an open access, short form mechanism for scientific communication.		The Nucleus platform uses the OpenMTA<ref>https://www.openplant.org/openmta. Retrieved 19 Jul 2025.</ref> material transfer agreement, developed as a collaborative effort led by the BioBricks Foundation and OpenPlant, which allows open sharing of DNA with attribution (similar to an open source software license). Nucleus also uses the CERN Open Hardware License - Permission <ref> https://gitlab.com/ohwr/project/cernohl/-/wikis/uploads/3eff4154d05e7a0459f3ddbf0674cae4/cern_ohl_p_v2.txt. Retrieved 19 Jul 2025</ref> for distribution of modules and protocols. Documentation of Nucleus modules are done via Developer Notes<ref> https://devnotes.bnext.bio. Retrieved 19 Jul 2025</ref>, an open access, short form mechanism for scientific communication.

	A more detailed discussion of the developer cell concept, including the subsystem architecture and scaling path, is given on the [[~~Developer~~ cells]] page.		A more detailed discussion of the developer cell concept, including the subsystem architecture and scaling path, is given on the [[developer cells]] page.

	== References ==		== References ==
	<references />		<references />

Murray: /* The Nucleus Developer Cell Platform */

2026-06-27T16:22:45Z

The Nucleus Developer Cell Platform

← Older revision		Revision as of 09:22, 27 June 2026
Line 98:		Line 98:

	The Nucleus platform uses the OpenMTA<ref>https://www.openplant.org/openmta. Retrieved 19 Jul 2025.</ref> material transfer agreement, developed as a collaborative effort led by the BioBricks Foundation and OpenPlant, which allows open sharing of DNA with attribution (similar to an open source software license). Nucleus also uses the CERN Open Hardware License - Permission <ref> https://gitlab.com/ohwr/project/cernohl/-/wikis/uploads/3eff4154d05e7a0459f3ddbf0674cae4/cern_ohl_p_v2.txt. Retrieved 19 Jul 2025</ref> for distribution of modules and protocols. Documentation of Nucleus modules are done via Developer Notes<ref> https://devnotes.bnext.bio. Retrieved 19 Jul 2025</ref>, an open access, short form mechanism for scientific communication.		The Nucleus platform uses the OpenMTA<ref>https://www.openplant.org/openmta. Retrieved 19 Jul 2025.</ref> material transfer agreement, developed as a collaborative effort led by the BioBricks Foundation and OpenPlant, which allows open sharing of DNA with attribution (similar to an open source software license). Nucleus also uses the CERN Open Hardware License - Permission <ref> https://gitlab.com/ohwr/project/cernohl/-/wikis/uploads/3eff4154d05e7a0459f3ddbf0674cae4/cern_ohl_p_v2.txt. Retrieved 19 Jul 2025</ref> for distribution of modules and protocols. Documentation of Nucleus modules are done via Developer Notes<ref> https://devnotes.bnext.bio. Retrieved 19 Jul 2025</ref>, an open access, short form mechanism for scientific communication.

			A more detailed discussion of the developer cell concept, including the subsystem architecture and scaling path, is given on the [[Developer cells]] page.

	== References ==		== References ==
	<references />		<references />

Murray: /* Synthetic Cell Subsystems */

2026-06-27T15:50:40Z

Synthetic Cell Subsystems

← Older revision		Revision as of 08:50, 27 June 2026
Line 68:		Line 68:
	* '''Regulation and Logic''': The [[Regulation Subsystem]] maintains the internal environment of the cell and is responsible for providing robustness in the presence of uncertainty as well as allowing the design of the dynamics of the cell. The [[Logic Subsystem]] is responsible for implementing internal logic that can control the operations of the synthetic cell. In its simplest form, it carries out logical operations such as AND and OR functions, but more complex logic including finite state machines can also be used if needed.		* '''Regulation and Logic''': The [[Regulation Subsystem]] maintains the internal environment of the cell and is responsible for providing robustness in the presence of uncertainty as well as allowing the design of the dynamics of the cell. The [[Logic Subsystem]] is responsible for implementing internal logic that can control the operations of the synthetic cell. In its simplest form, it carries out logical operations such as AND and OR functions, but more complex logic including finite state machines can also be used if needed.
	* '''Metabolism''': The [[Metabolic Subsystem]] provides the energy required for the cell to operate. It can either consist of a mechanism for directly transferring energy from an external source or it can convert energy from one form into another.		* '''Metabolism''': The [[Metabolic Subsystem]] provides the energy required for the cell to operate. It can either consist of a mechanism for directly transferring energy from an external source or it can convert energy from one form into another.
	* '''Motility and Adhesion''': The [[~~Motility~~ Subsystem]] is responsible for generating forces in a what that allows a synthetic cell to move in its environment. The [[Adhesion Subsystem]] is used to attach a synthetic cell to other synthetic cells or other objects in the environment.		* '''Motility and Adhesion''': The [[Mechanical Actuation Subsystem]] is responsible for generating forces in a what that allows a synthetic cell to exert forces or move in its environment. The [[Adhesion Subsystem]] is used to attach a synthetic cell to other synthetic cells or other objects in the environment.

	Which of these systems is present depends on the applications needs of the synthetic cell. We note that in the synthetic cells described here, we do not include a replication subsystem, since we are focused on non-replicating synthetic cells.		Which of these systems is present depends on the applications needs of the synthetic cell. We note that in the synthetic cells described here, we do not include a replication subsystem, since we are focused on non-replicating synthetic cells.

Murray: /* Why Are Synthetic Cells a Good Way to Get There? */

2026-06-27T11:45:50Z

Why Are Synthetic Cells a Good Way to Get There?

← Older revision		Revision as of 04:45, 27 June 2026
Line 38:		Line 38:

	A major drawback of the synthetic cell approach versus more conventional approaches to engineering biology is that we have to re-invent all of the major subsystems from scratch. In particular, the need to "reinvent" metabolism is a major hurdle: natural cells come with the ability to metabolize carbon sources and turn them into energy and the other materials need for the cell to function. Synthetic cells must import the natural metabolic subsystem, reinvent metabolism, or find a different method for providing the power required to operate. The last approach seems to most plausible, but is an example of the significant challenges that must be overcome in order to make synthetic cells a viable alternative to genetically modified organisms.		A major drawback of the synthetic cell approach versus more conventional approaches to engineering biology is that we have to re-invent all of the major subsystems from scratch. In particular, the need to "reinvent" metabolism is a major hurdle: natural cells come with the ability to metabolize carbon sources and turn them into energy and the other materials need for the cell to function. Synthetic cells must import the natural metabolic subsystem, reinvent metabolism, or find a different method for providing the power required to operate. The last approach seems to most plausible, but is an example of the significant challenges that must be overcome in order to make synthetic cells a viable alternative to genetically modified organisms.
			These challenges — context dependence, resource limits, and evolutionary instability — become more acute as system complexity grows; see [[Scalability Challenges in Biological Engineering]] for a detailed discussion.

	=== More Achievable Starting Points (MVPs) ===		=== More Achievable Starting Points (MVPs) ===

Murray: /* Modeling and Specifications */

2025-09-13T04:51:01Z

Modeling and Specifications

← Older revision		Revision as of 21:51, 12 September 2025
Line 77:		Line 77:
	Throughout this wiki, Python-based simulation models will be used to illustrate the dynamic characteristics of the subsystems and to build computational representations of interconnected subsystems. We will make use of the BioCRNpyler package<ref name="biocrnpyler">https://biocrnpyler.readthedocs.org. Retrieved 13 Sep 2025</ref>, a software framework and library designed to aid in the rapid construction of models from common motifs, such as molecular components, biochemical mechanisms and parameter sets. These parts can be reused and recombined to rapidly generate chemical reaction network (CRN) models in diverse chemical contexts at varying levels of model complexity.		Throughout this wiki, Python-based simulation models will be used to illustrate the dynamic characteristics of the subsystems and to build computational representations of interconnected subsystems. We will make use of the BioCRNpyler package<ref name="biocrnpyler">https://biocrnpyler.readthedocs.org. Retrieved 13 Sep 2025</ref>, a software framework and library designed to aid in the rapid construction of models from common motifs, such as molecular components, biochemical mechanisms and parameter sets. These parts can be reused and recombined to rapidly generate chemical reaction network (CRN) models in diverse chemical contexts at varying levels of model complexity.

	BioCRNpyler compiles high-level specifications into detailed CRN models saved as SBML. Specifications may include: biomolecular ~~Components~~, modeling assumptions (~~Mechanisms~~), biochemical context (~~Mixtures~~), and ~~Parameters~~. BioCRNpyler is written in Python with a flexible object-oriented design, extensive documentation, and detailed examples to allow for easy model construction by modelers as well as customization and extension by developers. BioCRNpyler make use of the following abstractions (see the BioCRNpyler<ref name=biocrnpyler/> documentation for more details):		BioCRNpyler compiles high-level specifications into detailed CRN models saved as SBML. Specifications may include: biomolecular components, modeling assumptions (mechanisms), biochemical context (mixtures), and parameters. BioCRNpyler is written in Python with a flexible object-oriented design, extensive documentation, and detailed examples to allow for easy model construction by modelers as well as customization and extension by developers. BioCRNpyler make use of the following abstractions (see the BioCRNpyler<ref name=biocrnpyler/> documentation for more details):

	* '''Species''' and '''Reactions''' make up a CRN and are the output of BioCRNpyler compilation. Many sub-classes exist, such as ComplexSpecies and reactions with different kinds of rate function (e.g. mass-action, Hill functions, etc).		* '''Species''' and '''Reactions''' make up a CRN and are the output of BioCRNpyler compilation. Many sub-classes exist, such as ComplexSpecies and reactions with different kinds of rate function (e.g. mass-action, Hill functions, etc).

Murray: /* Modeling and Specifications */

2025-09-13T04:40:04Z

Modeling and Specifications

← Older revision		Revision as of 21:40, 12 September 2025
Line 75:		Line 75:
	[[Image:BioCRNpyler_Overview.png\|thumb\|400px\|The hierarchical organization of classes in the BioCRNpyler framework. Arrows represent compilation. From https://biocrnpyler.readthedocs.org]]		[[Image:BioCRNpyler_Overview.png\|thumb\|400px\|The hierarchical organization of classes in the BioCRNpyler framework. Arrows represent compilation. From https://biocrnpyler.readthedocs.org]]

	Throughout this wiki, Python-based simulation models will be used to illustrate the dynamic characteristics of the subsystems and to build computational representations of interconnected subsystems. We will make use of the BioCRNpyler package<ref name="biocrnpyler"> https://~~buildacell~~.~~github~~.~~com/biocrnpyler~~. Retrieved ~~19 Jul~~ 2025</ref>, a software framework and library designed to aid in the rapid construction of models from common motifs, such as molecular components, biochemical mechanisms and parameter sets. These parts can be reused and recombined to rapidly generate chemical reaction network (CRN) models in diverse chemical contexts at varying levels of model complexity.		Throughout this wiki, Python-based simulation models will be used to illustrate the dynamic characteristics of the subsystems and to build computational representations of interconnected subsystems. We will make use of the BioCRNpyler package<ref name="biocrnpyler">https://biocrnpyler.readthedocs.org. Retrieved 13 Sep 2025</ref>, a software framework and library designed to aid in the rapid construction of models from common motifs, such as molecular components, biochemical mechanisms and parameter sets. These parts can be reused and recombined to rapidly generate chemical reaction network (CRN) models in diverse chemical contexts at varying levels of model complexity.

	BioCRNpyler compiles high-level specifications into detailed CRN models saved as SBML. Specifications may include: biomolecular Components, modeling assumptions (Mechanisms), biochemical context (Mixtures), and Parameters. BioCRNpyler is written in Python with a flexible object-oriented design, extensive documentation, and detailed examples to allow for easy model construction by modelers as well as customization and extension by developers. BioCRNpyler make use of the following abstractions (see the BioCRNpyler<ref name=biocrnpyler/> documentation for more details):		BioCRNpyler compiles high-level specifications into detailed CRN models saved as SBML. Specifications may include: biomolecular Components, modeling assumptions (Mechanisms), biochemical context (Mixtures), and Parameters. BioCRNpyler is written in Python with a flexible object-oriented design, extensive documentation, and detailed examples to allow for easy model construction by modelers as well as customization and extension by developers. BioCRNpyler make use of the following abstractions (see the BioCRNpyler<ref name=biocrnpyler/> documentation for more details):

Murray: /* More Achievable Starting Points (MVPs) */

2025-08-30T12:00:44Z

More Achievable Starting Points (MVPs)

← Older revision		Revision as of 05:00, 30 August 2025
Line 48:		Line 48:

	* '''Synthetic Cells as Replacements for EMERs'''. Engineered Microbes for Environmental Release (EMERs) are an emerging application area in synthetic biology with applications in agriculture, remediation, biomining, and therapeutics (animals or humans). EMERs can be challenging to use due to regulations governing the release of genetically modified organisms, in particular because they are often intended for open release, and so conventional containments strategies for genetically engineered organisms are not applicable. Replacing EMERs with (non-replicating) synthetic cells could provide a safer and more predictable method for carrying out existing biological functions such as nitrogen fixation, phenol degradation, or waste processing.		* '''Synthetic Cells as Replacements for EMERs'''. Engineered Microbes for Environmental Release (EMERs) are an emerging application area in synthetic biology with applications in agriculture, remediation, biomining, and therapeutics (animals or humans). EMERs can be challenging to use due to regulations governing the release of genetically modified organisms, in particular because they are often intended for open release, and so conventional containments strategies for genetically engineered organisms are not applicable. Replacing EMERs with (non-replicating) synthetic cells could provide a safer and more predictable method for carrying out existing biological functions such as nitrogen fixation, phenol degradation, or waste processing.

			[[Synthetic cell demonstrations\|Current demonstrations]] of synthetic cells are primarily oriented at demonstrating basic capabilities.

	=== What About Recreating Life? ===		=== What About Recreating Life? ===

Murray: /* Why Are Synthetic Cells a Good Way to Get There? */

2025-08-30T11:17:01Z

Why Are Synthetic Cells a Good Way to Get There?

← Older revision		Revision as of 04:17, 30 August 2025
Line 32:		Line 32:

	=== Why Are Synthetic Cells a Good Way to Get There? ===		=== Why Are Synthetic Cells a Good Way to Get There? ===

			[[Image:syncell_whitespace.png\|400px\|thumb\|alt=DARPA white space chart\|"White space" chart, showing a possible path to engineering biology at scale using synthetic cells. Figure courtesy Richard Murray, 2025 (CC BY).]]

	One of the hypothesis of the synthetic cell movement is that building from the "bottom up" is more "engineerable" (predictable, robust, scaleable) than other approaches to building complex biomachines. The most obvious alternative is genetically modifying living organisms, and this is where the majority of work in synthetic biology currently takes place. But our record in engineering complex biological circuits and pathways in living organisms is not great: the most complex systems we have been able to to engineer to date have at most dozens of individually engineered components (see, for example, Srinivasan and Smolke, ''Science'', 2020<ref>P. Srinivasan and C. D. Smolke. [https://www.nature.com/articles/s41586-020-2650-9 "Biosynthesis of medicinal tropane alkaloids in yeast"]. ''Nature'' 585(7826):614–19, 2020. DOI: 10.1038/s41586-020-2650-9.</ref>), versus the millions of engineered components that are part of a cell phone, an airplane, or the power grid. One reason this might be the case is that when we engineer living systems, we are fighting against billions of years of evolution that have fine-tuned the organism we are engineering to carry out its specific function in nature, and we don't yet have the understanding or insight to modify that function in a way that is predictable, robust, and scaleable.		One of the hypothesis of the synthetic cell movement is that building from the "bottom up" is more "engineerable" (predictable, robust, scaleable) than other approaches to building complex biomachines. The most obvious alternative is genetically modifying living organisms, and this is where the majority of work in synthetic biology currently takes place. But our record in engineering complex biological circuits and pathways in living organisms is not great: the most complex systems we have been able to to engineer to date have at most dozens of individually engineered components (see, for example, Srinivasan and Smolke, ''Science'', 2020<ref>P. Srinivasan and C. D. Smolke. [https://www.nature.com/articles/s41586-020-2650-9 "Biosynthesis of medicinal tropane alkaloids in yeast"]. ''Nature'' 585(7826):614–19, 2020. DOI: 10.1038/s41586-020-2650-9.</ref>), versus the millions of engineered components that are part of a cell phone, an airplane, or the power grid. One reason this might be the case is that when we engineer living systems, we are fighting against billions of years of evolution that have fine-tuned the organism we are engineering to carry out its specific function in nature, and we don't yet have the understanding or insight to modify that function in a way that is predictable, robust, and scaleable.

Murray: /* How Could Synthetic Cells Be Useful? */

2025-08-15T12:10:59Z

How Could Synthetic Cells Be Useful?

← Older revision		Revision as of 05:10, 15 August 2025
Line 16:		Line 16:

	== How Could Synthetic Cells Be Useful? ==		== How Could Synthetic Cells Be Useful? ==

			This section summarizes some of the potential applications for synthetic cells. The [[Synthetic Cell Applications]] page has a more detailed analysis of current and future applications of synthetic cells.

	=== Long Term Vision: Building Biological Machines at Scale ===		=== Long Term Vision: Building Biological Machines at Scale ===

Murray: /* Why Are Synthetic Cells a Good Way to Get There? */

2025-07-19T14:58:26Z

Why Are Synthetic Cells a Good Way to Get There?

← Older revision		Revision as of 07:58, 19 July 2025
Line 31:		Line 31:
	=== Why Are Synthetic Cells a Good Way to Get There? ===		=== Why Are Synthetic Cells a Good Way to Get There? ===

	One of the hypothesis of the synthetic cell movement is that building from the "bottom up" is more "engineerable" (predictable, robust, scaleable) than other approaches to building complex biomachines. The most obvious alternative is genetically modifying living organisms, and this is where the majority of work in synthetic biology currently takes place. But our record in engineering complex biological circuits and pathways in living organisms is not great: the most complex systems we have been able to to engineer to date have at most dozens of individually engineered components (see, for example, ~~X et al~~, Science, ~~2022~~<ref>P. Srinivasan and C. D. Smolke. "Biosynthesis of medicinal tropane alkaloids in yeast." ''Nature'' 585(7826):614–19, 2020. DOI: 10.1038/s41586-020-2650-9.</ref>), versus the millions of engineered components that are part of a cell phone, an airplane, or the power grid. One reason this might be the case is that when we engineer living systems, we are fighting against billions of years of evolution that have fine-tuned the organism we are engineering to carry out its specific function in nature, and we don't yet have the understanding or insight to modify that function in a way that is predictable, robust, and scaleable.		One of the hypothesis of the synthetic cell movement is that building from the "bottom up" is more "engineerable" (predictable, robust, scaleable) than other approaches to building complex biomachines. The most obvious alternative is genetically modifying living organisms, and this is where the majority of work in synthetic biology currently takes place. But our record in engineering complex biological circuits and pathways in living organisms is not great: the most complex systems we have been able to to engineer to date have at most dozens of individually engineered components (see, for example, Srinivasan and Smolke, ''Science'', 2020<ref>P. Srinivasan and C. D. Smolke. [https://www.nature.com/articles/s41586-020-2650-9 "Biosynthesis of medicinal tropane alkaloids in yeast"]. ''Nature'' 585(7826):614–19, 2020. DOI: 10.1038/s41586-020-2650-9.</ref>), versus the millions of engineered components that are part of a cell phone, an airplane, or the power grid. One reason this might be the case is that when we engineer living systems, we are fighting against billions of years of evolution that have fine-tuned the organism we are engineering to carry out its specific function in nature, and we don't yet have the understanding or insight to modify that function in a way that is predictable, robust, and scaleable.

	A major drawback of the synthetic cell approach versus more conventional approaches to engineering biology is that we have to re-invent all of the major subsystems from scratch. In particular, the need to "reinvent" metabolism is a major hurdle: natural cells come with the ability to metabolize carbon sources and turn them into energy and the other materials need for the cell to function. Synthetic cells must import the natural metabolic subsystem, reinvent metabolism, or find a different method for providing the power required to operate. The last approach seems to most plausible, but is an example of the significant challenges that must be overcome in order to make synthetic cells a viable alternative to genetically modified organisms.		A major drawback of the synthetic cell approach versus more conventional approaches to engineering biology is that we have to re-invent all of the major subsystems from scratch. In particular, the need to "reinvent" metabolism is a major hurdle: natural cells come with the ability to metabolize carbon sources and turn them into energy and the other materials need for the cell to function. Synthetic cells must import the natural metabolic subsystem, reinvent metabolism, or find a different method for providing the power required to operate. The last approach seems to most plausible, but is an example of the significant challenges that must be overcome in order to make synthetic cells a viable alternative to genetically modified organisms.