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NASA - Materials Manufactured from 3D Printed Synthetic Biology Arrays

NASA - Materials Manufactured from 3D Printed Synthetic Biology Arrays | SynBioFromLeukipposInstitute | Scoop.it
Materials Manufactured from 3D Printed Synthetic Biology Arrays
Gerd Moe-Behrens's insight:

Team:
Diana Gentry, NASA Ames Research Center, SGE, Samson Phan, Stanford University, Lynn J. Rothschild (POC), NASA Ames Research Center, SGE

"The Problem

Complex, biologically derived materials (such as wood and silk) often have extremely useful properties. However, their use in space-related applications is hampered by two primary drawbacks: Expensive, specific production. Many of these materials can only be produced as part of significant support ecosystem. For example, spider silk can only be produced by providing a contained, sustainable habitat and appropriate food for selected species of spiders, and can then only be harvested in relatively small quantities by a laborious human-intensive process. These overhead requirements simply add too much upmass for a potential Mars habitat mission. Limited manufacturing compatibility. Collecting and processing many such materials (for example, cotton) requires specialized equipment that adds impractical upmass or resource requirements to a potential self-contained habitat. Many cannot be worked with modern micro-scale manufacturing techniques at all (e.g., wood), limiting their use in creating potentially useful composite structures.  The VisionUsing structured arrays of biologically engineered cells to deposit or excrete biological materials in a specified composite pattern creating novel biomaterials and biocomposites.Complex, biologically derived materials (such as wood and silk) often have extremely useful properties but their use in space-related applications is hampered by expensive production, and the limited manufacturing compatibility with space (e.g., upmass and resource requirements.) Many cannot be worked with micro-scale manufacturing techniques (e.g., wood).The innovation of this project is the application of synthetic biology to 3D printing technology. Their combination presents significant challenges. Potential impactIf successful, this application would dramatically expand manufacturing capabilities on Earth and in space: In situ resource utilization. The ability to make a far greater range of materials and products out of the limited basic resource palette offered by existing in situ resource extraction techniques. Reduced equipment and material upmass for off-Earth habitats. Production of a wide variety of ready-to-use highly specialized construction materials (radiation hardened, compressive/tensile, light or dense) from an extremely low starting mass, allowing for flexible production of working and living spaces tailored to off planet environments. Structured biomaterial production. New ready-to-use macro, micro, and molecular manufacturing techniques for traditional materials such as wood, including finely calibrated microstructures. New and novel biocomposite creation. The ability to create completely novel material composites from any base material that ...."



 http://1.usa.gov/11dTVgv

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Synthetic Biology - Google+

Synthetic Biology - Google+ | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

The new digital age, the rise of the imdivid, patient empowerment and participatory medicine

We are facing due to +Eric Schmidt `s new book a major cultural change with the imdivid as a major player (see this interesting interview http://nyti.ms/18KcAcv and the book: ‘The New Digital Age,’ by Eric Schmidt and Jared Cohenhttp://nyti.ms/17OtPdc). Social networks are the reason. Billions of people have got a voice.

This change will affect many aspects of society. This has also impact for my area of interest: medical applications of #syntheticbiology  
Due to the advances in wearable electronics and the cultural change described above, we are getting a new type of patient. A person, collecting many biomedical health and fitness data. We see an emerging field of participatory medicine (see eg http://participatorymedicine.org). The patient is one of the most underestimated resources in healthcare. People are starting to use mobile devices to build their internet of me with their own data. What we see with Google glasses, Nike fuel band, Lark, Pebble, Apples up coming iWatch is just the top of the ice mountain. We see a field on the horizon which held huge premisses both for the patient and the entrepreneur.

We will need to develop special wearable health and medical bioelectronics for this kind of patient. An exiting area for synthetic biology.

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Synthetic Networks: Oscillators and Toggle Switches for Escherichia coli - Springer

Synthetic Networks: Oscillators and Toggle Switches for Escherichia coli - Springer | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

*Synthetic Networks: Oscillators and Toggle Switches for Escherichia coli* 

http://bit.ly/11e8qSq

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Students as Collaborators in Systems Biology Research

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*Students as Collaborators in Systems Biology Research*

by
Susan McClatchy, Deborah McGann, Robert Gotwals, Amanda Baskett,  Gary Churchill

"In his 1854 speech at the University of Lille, Louis Pasteur stated "In the fields of observation, chance favors only the prepared mind." Preparation for scientific inquiry is critical for the future of research, yet opportunities are rare in the early stages of education. This discrepancy can be resolved by immersing students in genuine research activities as early as possible. We have created an experience for high school students to engage in and contribute to ongoing research. We prepare students to formulate and test hypotheses using computational tools and data collected in our laboratory, or available from public repositories."


http://bit.ly/118Z1uC

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Robust synchronization control scheme of a population of nonlinear stochastic synthetic genetic oscillators under intrinsic and extrinsic molecular noise via quorum sensing

Robust synchronization control scheme of a population of nonlinear stochastic synthetic genetic oscillators under intrinsic and extrinsic molecular noise via quorum sensing | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

*Robust synchronization control scheme of a population of nonlinear stochastic synthetic genetic oscillators under intrinsic and extrinsic molecular noise via quorum sensing*

by
Bor-Sen Chen and Chih-Yuan Hsu

"Collective rhythms of gene regulatory networks have been a subject of considerable interest for biologists and theoreticians, in particular the synchronization of dynamic cells mediated by intercellular communication. Synchronization of a population of synthetic genetic oscillators is an important design in practical applications, because such a population distributed over different host cells needs to exploit molecular phenomena simultaneously in order to emerge a biological phenomenon. However, this synchronization may be corrupted by intrinsic kinetic parameter fluctuations and extrinsic environmental molecular noise. ...." 

http://1.usa.gov/15pD3I7

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The egg, The inside story of a cell

The egg, The inside story of a cell | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

by
Manuela Monti, Carlo Alberto Redi

"The egg, a fantastic little laboratory of molecular biology, has played a crucial role in redefining modern biology by moving it from the description of living things to the synthesis of living things (synthetic biology). Over the centuries, many hypotheses have been advanced concerning the egg's role in reproduction — from the preformation theory until von Baer's discovery to the present, with the 2012 Nobel Prize for Physiology or Medicine celebrating the egg as a totipotent stem cell able to reprogram fully differentiated somatic nuclei. The molecular dissection of its cytoplasmic components makes the egg an ideal bioreactor for several biotechnological applications, including pharmacological and food production sciences. In addition to its ubiquitous contribution to the worldwide diet, the egg, a powerful symbol, pervades philosophy, art, religion, and idiomatic expressions."

http://bit.ly/11erUcO

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Microscopic computing in cells and with self-assembling DNA tiles

Microscopic computing in cells and with self-assembling DNA tiles | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

by
ARTEM KAZNATCHEEV 

"One of the three goals of natural algorithms is to implement computers in non-electronic media. In cases like quantum computing, the goal is to achieve a qualitatively different form of computing, but other times (as with most biological computing) the goal is just to recreate normal computation (or a subset of it) at a different scale or in more natural ways. Of course, these two approaches aren’t mutually exclusive! Imagine how great it would be if we could grow computers on the level of cells, or smaller. For starters, this approach could revolutionize health-care: you could program some of your own cells to sense and record your internal environment and release drugs only when necessary. It could also alter how we manufacture things; if you throught 3D printers are cool, what if you could program nanoscale assemblies?

To start, it is important to understand what cells can already compute. For Luca Cardelli — first presentation on the second day of the 2nd workshop on Natural Algorithms and the Sciences — computation is the primary function of biology and so asking “what does the cell cycle switch computes” is perfectly natural. In an agent-based model of chemical reactions that you might see inside the membrane of a P-system, Cardelli & Csikász-Nagy (2012) showed that the cell cycle switch robustly implements the Angluin, Aspnes, and Eisenstat (2008) approximate majority algorithm from distributed computing. The goal of approximate majority is to figure out how to switch a cell from expressing some A and B to expressing only A or only B depending on which is in the majority of the initial configuration. Cardelli’s result is stunning since the approximate majority algorithm is optimal for a fault-tolerant implementation where agents are drawn uniformly at random to interact, and since the simplest network to implement it for an artificial cell system has the same structure as the empirically observed biological network. I would like to know if this sort of complex function could emerge in Valiant’s (2009) machine learning model of evolvability. Cardelli & Csikász-Nagy (2012) rely primarily on simulations to establish their results, but do not succumb to the curse of computing and present an analytic treatment...."

http://bit.ly/12kk18U

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Gen9 Launches GeneBytes™ to Enable Gene-Scale Synthetic Biology

Gen9, Inc., a pioneer in the development of scalable technologies for synthesizing and assembling DNA, today announced the commercial availability of GeneBytes™ DNA constructs, or gene fragments, manufactured at lengths ranging from 1,000 to 3,000...
Gerd Moe-Behrens's insight:

Gen9 Launches GeneBytes™ to Enable Gene-Scale Synthetic Biology http://bit.ly/1765q1K

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Emerging tools for synthetic genome design

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by
Lee BR, Cho S, Song Y, Kim SC, Cho BK.

"Synthetic biology is an emerging discipline for designing and synthesizing predictable, measurable, controllable, and transformable biological systems. These newly designed biological systems have great potential for the development of cheaper drugs, green fuels, biodegradable plastics, and targeted cancer therapies over the coming years. Fortunately, our ability to quickly and accurately engineer biological systems that behave predictably has been dramatically expanded by significant advances in DNA-sequencing, DNA-synthesis, and DNA-editing technologies. Here, we review emerging technologies and methodologies in the field of building designed biological systems, and we discuss their future perspectives."

http://bit.ly/19jZ8ec

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Environment and Planning A abstract

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The socionatural engineering of reductionist metaphors: a political ecology of synthetic biology http://bit.ly/172Q12i

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Putting the Patient at the Center of Care by Dr. Larry Chu

Gerd Moe-Behrens's insight:

I just followed an awesome lecture:

*Putting the Patient at the Center of Care by Dr. Larry Chu*

Patient centric medicine
The patient is in charge
The patient owns her or his own data.....

A great cultural change

The patient the most underestimated resource in healthcare

The video also mention some really great resources:

http://participatorymedicine.org
http://www.pcori.org
http://www.ahrq.gov

http://medicinex.stanford.edu

Video Link

http://bit.ly/12K3OoC

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IGEM Nepal 2013 for Synthetic Biology

IGEM Nepal 2013 for Synthetic Biology | SynBioFromLeukipposInstitute | Scoop.it
Synthetic biology is the design and construction of biological devices and systems for useful... (RT @SynBioCnsltg: Introducing the 1st Nepali #iGEM team - result of a @SynBiocnsltg project to bring #SynBio to developing countries.
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Modular, rule-based modeling for the design of eukaryotic synthetic gene circuit

Modular, rule-based modeling for the design of eukaryotic synthetic gene circuit | SynBioFromLeukipposInstitute | Scoop.it
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A step closer to artificial livers

A step closer to artificial livers | SynBioFromLeukipposInstitute | Scoop.it
Researchers identify compounds that help liver cells grow outside the body.
Gerd Moe-Behrens's insight:

by
Anne Trafton

Prometheus, the mythological figure who stole fire from the gods, was punished for this theft by being bound to a rock. Each day, an eagle swept down and fed on his liver, which then grew back to be eaten again the next day.  Modern scientists know there is a grain of truth to the tale, says MIT engineer Sangeeta Bhatia: The liver can indeed regenerate itself if part of it is removed. However, researchers trying to exploit that ability in hopes of producing artificial liver tissue for transplantation have repeatedly been stymied: Mature liver cells, known as hepatocytes, quickly lose their normal function when removed from the body.  “It’s a paradox because we know liver cells are capable of growing, but somehow we can’t get them to grow” outside the body, says Bhatia, the John and Dorothy Wilson Professor of Health Sciences and Technology and Electrical Engineering and Computer Science at MIT, a senior associate member of the Broad Institute and a member of MIT’s Koch Institute for Integrative Cancer Research and Institute for Medical Engineering and Science. Now, Bhatia and colleagues have taken a step toward that goal. In a paper appearing in the June 2 issue of Nature Chemical Biology, they have identified a dozen chemical compounds that can help liver cells not only maintain their normal function while grown in a lab dish, but also multiply to produce new tissue. ...."


http://bit.ly/15zaHvB

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Roy J. Carver Charitable Trust Funds New Research Focus at IGB | The Institute for Genomic Biology

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Transposon-Based and Plasmid-Based Genetic Tools for Editing Genomes of Gram-Negative Bacteria - Springer

Transposon-Based and Plasmid-Based Genetic Tools for Editing Genomes of Gram-Negative Bacteria - Springer | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

*Transposon-Based and Plasmid-Based Genetic Tools for Editing Genomes of Gram-Negative Bacteria* 

http://bit.ly/11vnUjY

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Microbial production of lactate-containing polyesters

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by

Yang JE, Choi SY, Shin JH, Park SJ, Lee SY.

"Due to our increasing concerns on environmental problems and limited fossil resources, biobased production of chemicals and materials through biorefinery has been attracting much attention. Optimization of the metabolic performance of microorganisms, the key biocatalysts for the efficient production of the desired target bioproducts, has been achieved by metabolic engineering. Metabolic engineering allowed more efficient production of polyhydroxyalkanoates, a family of microbial polyesters. More recently, non-natural polyesters containing lactate as a monomer have also been produced by one-step fermentation of engineered bacteria. Systems metabolic engineering integrating traditional metabolic engineering with systems biology, synthetic biology, protein/enzyme engineering through directed evolution and structural design, and evolutionary engineering, enabled microorganisms to efficiently produce natural and non-natural products. Here, we review the strategies for the metabolic engineering of microorganisms for the in vivo biosynthesis of lactate-containing polyesters and for the optimization of whole cell metabolism to efficiently produce lactate-containing polyesters. Also, major problems to be solved to further enhance the production of lactate-containing polyesters are discussed."

http://1.usa.gov/17bFFx1

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Synthetic Biology Meets Analog Circuitry

Shirts and Stuff http://www.zazzle.com/qdragon Follow us on Twitter https://twitter.com/BrainstormSci Like us on Facebook http://www.facebook.com/brainstormn...
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Brief video: Synthetic Biology Meets Analog Circuitry http://bit.ly/18zQVDP

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Responsible conduct of synthetic biology

Terry Johnson of UC Berkeley and Synberc provides a perspective on the unique features of synthetic biology that require special consideration above and beyo...
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Video 12 min Responsible conduct of synthetic biology http://bit.ly/10IOU0w

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Meeker: The next ten years will be about wearable computing and personal data

Meeker: The next ten years will be about wearable computing and personal data | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

This is the frame under which the biological computer will work on:

 

*Meeker: The next ten years will be about wearable computing and personal data*

by
by Tom Krazit

"The photo wars aren’t over, but a shift is about to take place in terms of the content we upload and share to the internet, according to Kleiner Perkins’ Mary Meeker and her trademark Powerpoint slides at D11. After years of uploading each and every photo to the web, we’re about to start uploading personal data and sound files to the web in greater and greater numbers as wearable computing develops.

 Meeker’s annual attempt to present more than 100 slides in 10 minutes is a little tough on the eyes, but a few key trends emerged Wednesday at D11 (the full deck is embedded below): 500 million photos are being uploaded and shared each day, doubling year over year as Snapchat turns into a real phenomenon. But photo-sharing is relatively mature compared to…Video, which as Janko noted earlier today is on a tear. At the moment, video growth is being spurred by short-form video sharing like Vine and Dropcam, Meeker said.Both of those content types, however, are relatively well understood compared to the next big wave: sound files and data from wearable computers. That’s because we’re at the cusp of a computing shift in which wearables take precedent over mobile.Fitness and health data will be a huge percentage of that personal data, Meeker said, as more and more people realize how behavioral shifts can improve their health and how new devices can help people track those behaviors.The platform change to wearables will help create that world, Meeker said. While the past ten years have been about mobile computing and the ten years before that were about the PC, the next ten years will be about wearable computers with sensors......."

http://bit.ly/11zJj1f ;
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Tuning the Dials of Synthetic Biology

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by
James A. J. Arpino, Edward J. Hancock, James Anderson, Mauricio Barahona, Guy-Bart V. Stan, Antonis Papachristodoulou and Karen Polizzi

"Synthetic Biology is the "Engineering of Biology" - it aims to use a forward-engineering design cycle based on specifications, modelling, analysis, experimental implementation, testing and validation to modify natural or design new, synthetic biology systems so that they behave in a predictable fashion. Motivated by the need for truly plug-and-play synthetic biological components we present a comprehensive review of ways in which the various parts of a biological system can be modified systematically. In particular, we review the list of 'dials' that are available to the designer and discuss how they can be modelled, tuned and implemented. The dials are categorized according to whether they operate at the global, transcriptional, translational or post translational level and the resolution that they operate at. We end this review with a discussion on the relative advantages and disadvantages of some dials over others."


http://bit.ly/143s9Fl

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Decisive noise : noisy intercellular signalling analysed and enforced through synthetic biology

intercellular signalling ; noise ; synthetic biology ; quorum sensing ; systems biology
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PhD thesis by
 Victoria Jane Jackson

(congratulations!)

"Individual cells in a genetically identical population, exposed to the same environment, can show great variation in their protein expression levels. This is due to noise, which is inherent in many biological processes, due in part to the low molecule numbers and probabilistic interactions which lead to stochasticity. Much of the work in the field of noise and its propagation in gene expression networks, whether it is experimental, modelling or theoretical, has been conducted on networks/systems that occur within a single cell. However, cells do not exist solely in isolation and understanding how cells are able to coordinate their behaviour despite this noise is an interesting area of expansion for the field. In this study, a synthetic intercellular communication system was designed that allows the investigation of how noise is propagated in intercellular communication. The communication system consists of separate sender and receiver cells incorporating components of the Lux quorum sensing system of Vibrio fischeri. The sender cell was designed so that the production of the signalling molecule, 3-oxohexanoyl homoserine lactone, is able to be controlled by addition of isopropyl-β-D-thio-galactoside (IPTG) and monitored via a reporter gene. The receiver cell was designed with a dual reporter system to enable the response of the cell to the signalling molecule to be monitored and the intrinsic and extrinsic noise contributions to the total noise to be calculated. Sender and the receiver cells were engineered in Escherichia coli. The functionality of the receiver cells was tested in the presence of known concentrations of the signalling molecule. The population response and the noise characteristics of the receiver cells in the homogeneous environment were determined from single cell measurements. The functionality of the sender cells was tested in the presence of a range of IPTG concentrations and the induction of expression from the LacI-repressible promoter was monitored. Mathematical models of the system were developed. Stochastic simulations of the models were used to investigate any unexplained behaviour seen in the characterisation of the cells. The full functionality of the intercellular communication system was then tested by growing the receiver in the collected media of the induced sender cells. The response of the receiver cells to the signalling molecule in the media was again characterised using single cell measurements of the reporter expression levels. The analysis of mixed populations of the sender and receiver cells was hampered by the technical limitations of the instruments used for the single cell measurements. Difficulties were encountered in simultaneous and specific measurement of the three reporter genes. Two methods for overcoming this issue were proposed using microscopy, and one of these methods was shown to have potential in overcoming the issue."


 http://bit.ly/17nHNT7

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Advancing bacteriophage-based microbial diagnostics with synthetic biology

Advancing bacteriophage-based microbial diagnostics with synthetic biology | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

by

Timothy K. Lu, Jayson Bowers and Michael S. Koeris

"Synthetic biology is an emerging engineering field focused on designing artificial biological systems with novel functionalities for use in therapeutics, basic science, biotechnology, and diagnostics [1,2]. Continuous advancements in DNA synthesis and sequencing technologies coupled with new techniques for genomic modification and assembly have opened the door for harnessing the power and diversity of biology for applications. For example, natural bacteriophage products, such as ListShield (Intralytix) and Agriphage (Omnilytics), are commercially available for reducing unwanted bacterial contamination. Natural bacteriophages can be genetically modified to deliver engineered payloads into bacteria, thus selectively functionalizing target bacterial populations to produce active biomolecules. This strategy can endow bacteriophages with the ability to efficiently destroy bacterial biofilms or increase the bactericidal efficacy of antibiotics used in combination with phages by many orders of magnitude [3]. In addition, bacteriophages can be engineered as near-real-time microbial diagnostics by using them to transform target bacteria into factories for detectable molecules..."


http://bit.ly/114egWn

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Bio-Hackers, Get Ready

Bio-Hackers, Get Ready | SynBioFromLeukipposInstitute | Scoop.it
Gerd Moe-Behrens's insight:

by
KIM-MAI CUTLER

"When I speak to technical founders, they often look back with fondness to days of tinkering with a Commodore 64 or Hypercard.

 But perhaps tomorrow’s founders will experiment with a very different kind of code — the genetic code that underlies how everything from one-celled organisms to humans develop and behave. A pair of companies in San Francisco’s SOMA neighborhood and Tel Aviv are positioning themselves as the “Wintel” of the bio-hacking era. One company, called Genome Compiler, builds software for designing synthetic life forms, while the other, Cambrian Genomics, is experimenting with ways to cheaply laser print DNA. Like the old Microsoft-Intel relationship of the PC era, they believe they have the symbiotic relationship necessary to usher in a new era where anybody can inexpensively create their own life forms. Genome Compiler is backed with $3 million in funding, including $2 million from Autodesk. Cambrian is funded by Founders Fund, Felicis Ventures and Draper Associates. “We are democratizing creation,” said Genome Compiler co-founder Omri Amirav-Drory. “Cells are nothing more than a computer, running a program and the program is the genetic code. The code is DNA. The software are the chromosomes. The hardware is the wetware.”..."


 http://tcrn.ch/Zp8hjG

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