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Video: Dig the three minute introduction. Script by Claudia Vickers, Animation by Orlando Mee, Produced by Stephan Kern
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Amazon.com: Creating Life in the Lab: How New Discoveries in Synthetic Biology Make a Case for the Creator (Reasons to Believe) (9780801072093): Fazale Rana: Books...
"Modern scientific and engineering research relies heavily on computer programs, which analyze experimental data and run simulations. In fact, you would be hard-pressed to find a scientific paper (outside of pure theory) that didn’t involve code in some way. Unfortunately, most code written for research remains closed, even if the code itself is the subject of a published scientific paper. According to an editorial in Nature, this hinders reproducibility, a fundamental principle of the scientific method...."
"....The field of synthetic biology also poses a number of challenges for patent law and public policy. One of the most important questions patent experts (such as Professor Graham Dutfield) are asking is whether synthetic biology is too different from previous biotechnologies to apply existing objections to the patenting of living things.
In addition to considering patentability of synthetic biology, patent offices and courts will have to consider the novelty, inventiveness and utility of the claimed inventions and scope of the claims, in light of the scientific knowledge in this field.
In the United States, patent applications for synthetic biology have fallen into two broad categories:1) biological tools, methods and products.2) computer programs. This includes software for design of biological devices and programs for analysis of biochemical activity within cells.
Some US patent applications have focused on the construction of a synthetic cell. Scientists at the J Craig Venter Institute, for example, have filed applications for patents on a minimal bacterial genome, a synthetic genome and a method of installing a genome into a cell.
Other US patent applications have involved the creation of useful biological products from cells, such as Jay D. Keasling and colleagues’ production of a malaria drug precursor in a genetically modified cell.
There are also patent applications for various methods of biofuel production....."
As reported in the online version of Nature Structural & Molecular Biology on Feb. 5, researchers have produced 3-D images of the protein system that works to repair DNA.
Synthetic Biology Project launched a web Synthetic Biology Scorecard, to track federal & non-federal efforts to improve the governance of synthetic biology research.
Clotho is for engineering synthetic biological systems and managing the data which is used to create them. It also provides a mechanism to begin the process of creating standardized data, algorithms, and methodologies for synthetic biology.
Data Access Client
The Data Access Client is the human-centered interface of the BIOFAB's electronic datasheets. It is a rich internet application (RIA) that provides user-friendly access to the design and performance of BIOFAB parts and constructs.Click Here to Start the Data Access ClientVersion 2.0 alphaReleased on 9-23-2011This is a stable release of the application. The data and information gathered with this version are correct, but are being curated and enhanced.Gene Designer
DNA2.0's Gene Designer is a free computer-aided design (CAD) tool that is able to directly import BIOFAB part design and performance.Click Here to Download Gene DesignerData Analysis and Simulation Tools
You are able to import BIOFAB part design and performance into popular data analysis and simulation tools like R, MATLAB, and Mathematica.ExampleClick Here to Download an Example Mathematica NotebookIf you do not own a copy of Mathematica, you can view the example notebook using the Wolfram CDF Player which can be downloaded free of charge.Click here to get information about the Wolfram CDF Player.Data Access Web Service
The Data Access Web Service is the application interface (API) of the BIOFAB's electronic datasheets. It is a RESTful web service that provides the design and performance of BIOFAB parts and constructs. The data and information are in machine-readable formats.Version 2.0 alphaReleased on 10-11-2011This is a stable release of the application. The data and information gathered with this version are correct, but are being curated and enhanced.DocumentationUse Cases, Requirements, Comments, and Feedback
Issue TrackingContact UsSource Code
BIOFAB @ GitHub
ProgrammableWeb.com keeps you up to date with web mashups and APIs:
"Biofab Data Access API: The service provides access to a repository of data collections documenting annotated parts, which are DNA sequences with a single known biological function. Datasets support local research while also promoting consistency across researchers. Datasets are or will be in compliance with the Synthetic Biology Open Language (SBOL) standard.
API methods support retrieval of raw data listing annotated parts, as well as collections encompassing subsets of the total repository. Methods also allow retrieval of DNA sequence constructs and construct designs."
"In 2008, a paper on Synthetic Biology and biosecurity was published. The author, (Dr. Markus Schmidt from the Organization for International Dialogue and Management of Conflicts) is one of the figures who have been involved the most in the biosecurity scene and, recently, in the implications that Synthetic Biology has in the matter..."
"A researcher specialising in architecture and synthetic biology, Rachel Armstrong imagines a future with building materials that function as part of living systems. New Scientist caught up with her to talk about her new TED book, Living Architecture.
What is wrong with today’s architecture?The issue with modern architecture is that it is imagined through the framework and technology of the machine. We even think of ourselves as machines. Machines are good at taking resources and making objects but they’re impenetrable to the environment and they are extremely wasteful.
Currently, the best our architecture can be is carbon-neutral. You are looking to nature to go one step further?If we change our world view from being centred on machines to being centred on ecology, it starts to become a lot easier to imagine what kinds of technology might complement this approach. The natural world is full of examples: algae technology, the use of trees like baobabs as toilets and the living root bridges of Cherrapungi, north eastern India. But they don’t fit well into an urban environment and they don’t respond fast enough for the lifestyle we demand.
Are you advocating we go back to some bucolic agrarian-based existence?Not at all - more like a symbiotic approach between nature and existing structures and technology.
What sort of technologies do you have in mind?I have been looking at applying synthetic biology to environmental problems."
free ebook by Nature
From Tweets to publication....
Circuits in Synthetic Biology One of the concepts that runs through synthetic biology is that of circuits. They are often compared to circuits in electronics but the analogy is not perfect and there are significant differences between the two.
"For the past decade, scientists have been pursuing cancer treatments based on RNA interference — a phenomenon that offers a way to shut off malfunctioning genes with short snippets of RNA. However, one huge challenge remains: finding a way to efficiently deliver the RNA.
Most of the time, short interfering RNA (siRNA) — the type used for RNA interference — is quickly broken down inside the body by enzymes that defend against infection by RNA viruses.
“It’s been a real struggle to try to design a delivery system that allows us to administer siRNA, especially if you want to target it to a specific part of the body,” says Paula Hammond, the David H. Koch Professor in Engineering at MIT.
Hammond and her colleagues have now come up with a novel delivery vehicle in which RNA is packed into microspheres so dense that they withstand degradation until they reach their destinations. The new system, described Feb. 26 in the journal Nature Materials, knocks down expression of specific genes as effectively as existing delivery methods, but with a much smaller dose of particles...."
"Hacking Medicine’s purpose is to bring together the most excited and innovative thinkers in the Boston area and come out at the end with actionable projects and passionate teams.Our 2nd hackathon will be held on February 25th and 26th at the Media Lab at MIT. To view past events, please see go here.We’re capping participation at 80 people to ensure focus and a productive distribution of expertise. The body will be made up of engineers, students, physicians, and entrepreneurs....
We’re collecting massive data like never before – about patients, hospitals, treatments, and more. What are the best ways to extract meaningful information from this data? How can we best apply what we learn to make real changes?2. Biosensing & Biostimulation
The technology that drives sensors has become cheap, crazy cheap. How can we best use these new sensors (which are sometimes also stimulation) to capture and record new kinds of data or design new tests to detect diagnose disease more accurately than ever before?3. Healthcare Automation
Any practicing doctor will tell you how tedious and formulaic certain parts of practice can be. What parts of healthcare practice are least addressed by modern technology?4. Synthetic Biology
Groundbreaking research into the development of new medicines from the earth’s natural resources will be the focus of a symposium in March, hosted by the University of Aberdeen.
“The role of natural products and synthetic biology in drug discovery” symposium will bring together academics and industry representatives from across the UK, working in biomedicine and biotechnology.
Registration is now being invited for the event which is hosted by the University’s Marine Biodiscovery Centre and will take place on March 21, 2012.
Synthetic biology is in the process of inventing itself and its ownership regimes. There are currently two dominant approaches to ownership and sharing in the field. The work of the J. Craig Venter Institute is grounded in molecular biology and in gene patenting.
Parts-based approaches to synthetic biology, in contrast, are inspired by engineering, open source software and distributed innovation, and they are building new communities to help further this agenda. Despite these differences, the two approaches make very similar use of informational and computational metaphors. They both also have a place in a vision for the future of synthetic biology as a ‘diverse ecology’ of the open and the proprietary. It remains to be seen whether such a diverse ecology will be sustainable, whether synthetic biology will go down the patenting route taken by previous biotechnologies, or whether novel forms of ownership and sharing will emerge. Which path is taken will depend on the success of synthetic biology in achieving both its technical objectives and its social innovations.
"Better medicines, carbon neutral fuels, cheaper food, and a cleaner environment—who could be against that? Well, quite a few people, as it turns out.
Last week, a research team led by private human genome sequencer J. Craig Venter announced that they had created the world’s first synthetic self-replicating bacteria. Among other things, synthetic biologists are aiming to create a set of standardized biological parts that can be mixed and matched the way off-the-shelf microchips, hard drives, and screens can be combined to create a computer. The goal is to produce novel organisms that excrete biofuels, clean up toxic spills, strip clogged arteries of cholesterol, rapidly produce vaccines, grow more photosynthetically efficient crops, and manufacture eco-friendly plastics. In an early success, UC Berkeley biologist Jay Keasling used synthetic biology techniques to engineer micro-organisms to produce at much lower cost the anti-malaria drug artemisinin in 2004.
Eventually, bioengineers will no longer be limited to just moving around and tweaking genes discovered in nature, but instead would develop never-before-seen genes. “With the tools of synthetic biology, we don’t have to just accept what Nature has given us,” Keasling often says.
But nowadays, every technological breakthrough is accompanied with ethical handwringing and dire warnings about unintended consequences, and synthetic biology is no exception...."
The funds will support the development of the Clotho software platform for synthetic biology.
The service provides access to a repository of data collections documenting annotated parts, which are DNA sequences with a single known biological function. Datasets support local research while also promoting consistency across researchers. Datasets are or will be in compliance with the Synthetic Biology Open Language (SBOL) standard.
API methods support retrieval of raw data listing annotated parts, as well as collections encompassing subsets of the total repository. Methods also allow retrieval of DNA sequence constructs and construct designs.
Engineers at Harvard have demonstrated a new kind of tunable color filter that uses optical nanoantennas to obtain precise control of color output.
BIOMOD is a bio-molecular design competition that provides undergraduates an opportunity to systematically engineer biomolecules on the nanometer scale. Focus areas may include—but are not limited to—biomolecular robotics, biomolecular logic and computing, and structural bionanotechnology. It is funded by the Wyss Institute at Harvard University, with additional support from corporate sponsors.
In this interview, Shawn Douglas, Biomod's organizing director answers the following questions:1. What is Biomod?2. What is DNA nanotechnology, and how does DNA origami fit in?3. Why DNA nanotechnology?4. What is expected of the teams?5. What new designs an we expect to see?
For more information, go to biomod.net.
"We describe a site-specific recombination-based tandem assembly (SSRTA) method for reconstruction of biological parts in synthetic biology. The system was catalyzed by Streptomyces phage φBT1 integrase, which belongs to the large serine recombinase subfamily. This one-step approach was efficient and accurate, and able to join multiple DNA molecules in vitro in a defined order. Thus, it could have applications in constructing metabolic pathways and genetic networks."
Organovo's 3-D printer creates human tissues that could help speed drug discovery.
"In a small clean room tucked into the back of San Diego–based startup Organovo, Chirag Khatiwala is building a thin layer of human skeletal muscle. He inserts a cartridge of specially prepared muscle cells into a 3-D printer, which then deposits them in uniform, closely spaced lines in a petri dish. This arrangement allows the cells to grow and interact until they form working muscle tissue that is nearly indistinguishable from something removed from a human subject.
The technology could fill a critical need. Many potential drugs that seem promising when tested in cell cultures or animals fail in clinical trials because cultures and animals are very different from human tissue. Because Organovo's product is so similar to human tissue, it could help researchers identify drugs that will fail long before they reach clinical trials, potentially saving drug companies billions of dollars. So far, Organovo has built tissue of several types, including cardiac muscle, lung, and blood vessels."