This months edition of Bio::Blogs is now available at Duncan's blog and it is mostly focused on (bio)engineering. Click the link for a summary of interesting things that were blogged about in the past month.
I will be hosting issue number 20 here in the blog, without a clear topic. Possibly with some emphasis on data integration. Email your top picks of the month until the end of March to bioblogs at gmail .com
Showing posts with label synthetic biology. Show all posts
Showing posts with label synthetic biology. Show all posts
Saturday, March 08, 2008
Sunday, March 02, 2008
Design, mutate and freze
Drew Endy talked about engineering biology for Edge. Most of the emphasis is still on standardization of biological parts and the importance of simplifying the process of creating a biological function. Still it would be nice to hear from him some new ideas about establishing processes of engineering biology. His whole speech seems focused on creating the hacker culture in biology. To transpose all the same concepts that would allow us to re-create the explosive growth of tinkering and production that we saw for electronics and computer programing within the biological sciences.
I agree with most of what he says, that we should: 1)focus on method development; 2)work on a registry of parts and 3) foster an "open source"/hacker culture in synthetic biology. In this text he did not mention for example the importance of modeling but it is implicit in the standardization of parts. Once you have a computer simulation of the process you wish to engineer that you should be able to reach into the parts list to implement it. The problem with this concept of standardized parts is the complexity that Drew Endy dislikes so much. There is still no way around it. We can take a part that has been very well defined in E. coli, plug into a yeast plasmid and it might not work at all.
If we are still far way from the ideal plug and play maybe we could try to take advantage of what biology can do very well, to evolve to a suitable solution. I would argue that we should develop engineering protocols that could take advantage of the evolutionary process.
<insert rambling>
Lets say we want to implement a function and I know beforehand that I will not be able to get perfect parts to implement it. Can we design this function in a way that it will have a large funnel of attraction for the design properties that I am interested in ? Are there biological parts that are more amenable to a directed evolutionary experiment to reach that design goal ? How can I increase the mutation rate for a controlled period of time and only for the stretch of DNA that I want to evolve ? Maybe it is possible to place the parts in a plasmid and have the replication of this plasmid be under a different polymerase that is more error prone ?
</insert rambling>
If we could answer some of these questions (maybe we have already), we could design the function of interest (modeling), pull parts that would be close to the solution, mutate/select until the best design is achieved and then freeze it by reducing the generation of diversity in some way.
Further reading:
Synthetic biology: promises and challenges
Molecular Systems Biology 3 Article number: 158 doi:10.1038/msb4100202
I agree with most of what he says, that we should: 1)focus on method development; 2)work on a registry of parts and 3) foster an "open source"/hacker culture in synthetic biology. In this text he did not mention for example the importance of modeling but it is implicit in the standardization of parts. Once you have a computer simulation of the process you wish to engineer that you should be able to reach into the parts list to implement it. The problem with this concept of standardized parts is the complexity that Drew Endy dislikes so much. There is still no way around it. We can take a part that has been very well defined in E. coli, plug into a yeast plasmid and it might not work at all.
If we are still far way from the ideal plug and play maybe we could try to take advantage of what biology can do very well, to evolve to a suitable solution. I would argue that we should develop engineering protocols that could take advantage of the evolutionary process.
<insert rambling>
Lets say we want to implement a function and I know beforehand that I will not be able to get perfect parts to implement it. Can we design this function in a way that it will have a large funnel of attraction for the design properties that I am interested in ? Are there biological parts that are more amenable to a directed evolutionary experiment to reach that design goal ? How can I increase the mutation rate for a controlled period of time and only for the stretch of DNA that I want to evolve ? Maybe it is possible to place the parts in a plasmid and have the replication of this plasmid be under a different polymerase that is more error prone ?
</insert rambling>
If we could answer some of these questions (maybe we have already), we could design the function of interest (modeling), pull parts that would be close to the solution, mutate/select until the best design is achieved and then freeze it by reducing the generation of diversity in some way.
Further reading:
Synthetic biology: promises and challenges
Molecular Systems Biology 3 Article number: 158 doi:10.1038/msb4100202
Thursday, August 09, 2007
First issue of IET Synthetic Biology
The first issue of (yet) another journal related to systems&synthetic biology is now online. IET Synthetic Biology will be freely available during this year. This issue covers several works from iGEM and the editorial is worth a read to have a look at the future direction of the journal.
In addition to conventional research and review articles, we see an important need for practical articles describing technical advances and innovative methods useful in synthetic biology. We will encourage submission of technical articles that might describe novel BioBrick components, construction techniques, characterisation of a new biological circuit, new software or a practical ‘hands-on’ guide to the construction of new instrumentation or a biological device.
In addition to the print journal, we are developing associated web resources. These will include a repository of online video resources, specialised review material and research tools for synthetic biology.
Some journals tracking similar fields:
Molecular Systems Biology
BMC Systems Biology
Systems and Synthetic Biology
HSFP Journal
IET Systems Biology
The first issue of (yet) another journal related to systems&synthetic biology is now online. IET Synthetic Biology will be freely available during this year. This issue covers several works from iGEM and the editorial is worth a read to have a look at the future direction of the journal.
In addition to conventional research and review articles, we see an important need for practical articles describing technical advances and innovative methods useful in synthetic biology. We will encourage submission of technical articles that might describe novel BioBrick components, construction techniques, characterisation of a new biological circuit, new software or a practical ‘hands-on’ guide to the construction of new instrumentation or a biological device.
In addition to the print journal, we are developing associated web resources. These will include a repository of online video resources, specialised review material and research tools for synthetic biology.
Some journals tracking similar fields:
Molecular Systems Biology
BMC Systems Biology
Systems and Synthetic Biology
HSFP Journal
IET Systems Biology
Monday, June 25, 2007
Synthetic Biology 3.0
I am not attending the 3rd edition of the Synthetic Biology conference but there are several bloggers attending and reporting.
The Seven Stones
Nature Newsblog (part I and part II)
The ETC blog (intro and part I)
I am not attending the 3rd edition of the Synthetic Biology conference but there are several bloggers attending and reporting.
The Seven Stones
Nature Newsblog (part I and part II)
The ETC blog (intro and part I)
Friday, March 16, 2007
Systems and Synthetic biology RSS pipe
Here is the RSS feed for a Yahoo pipe combining and filtering papers mostly about synthetic and systems biology. There are three systems biology journals directly combined into the feed. Unfortunately I could not find the RSS feeds for IET Systems Biology so it is not included. On top of these are added selected papers from Nature tittles, PLoS titles, Cell, PNAS, Science and Genome Biology. The filtering is done using some typical key words that might be associated to Systems and Synthetic biology. Here is a simple illustration of how it works:
I still have to test the pipe for some time and tweak the filters, but it is enough to get an idea of the things that can be done with these pipes. Like the pipe before you can clone this and change the filters and journals as you like.
Here is the RSS feed for a Yahoo pipe combining and filtering papers mostly about synthetic and systems biology. There are three systems biology journals directly combined into the feed. Unfortunately I could not find the RSS feeds for IET Systems Biology so it is not included. On top of these are added selected papers from Nature tittles, PLoS titles, Cell, PNAS, Science and Genome Biology. The filtering is done using some typical key words that might be associated to Systems and Synthetic biology. Here is a simple illustration of how it works:
I still have to test the pipe for some time and tweak the filters, but it is enough to get an idea of the things that can be done with these pipes. Like the pipe before you can clone this and change the filters and journals as you like.
Wednesday, March 14, 2007
Quick Links
Deepak recorded his first podcast. Even if I am not a big fan of podcasts, I found it interesting to hear. Maybe it could serve as platform for a radio version of his blog. The idea of doing interviews would be really nice. In general I prefer reading because I can do it much faster than listening. Next year, when I go back to doing more bench work I will probably try consuming podcast while working.
(Via Deepak, Roland, and Konrad) Freebase is a very promising new web service. For those who have heard about semantic web, it will look familiar. They want to organize data by allowing users to add metadata to the information stored on the site. This will be great for aggregation of content and data mining. For science it could serve as place to deposit and organize data for collaborative projects.
(Via BioHacking) Microsoft has announced the winners of the first award for computational challenges in Synthetic Biology. Six projects were awarded a total of $570,000 (USD) to develop tools for synthetic biology.
(Via Jason Stajich) My own favorite model organism database (SGD) has created a wiki for community annotation. Anyone interested in S. cerevisiae biology, methods, reagents and strains can go there and help populate the wiki.
Deepak recorded his first podcast. Even if I am not a big fan of podcasts, I found it interesting to hear. Maybe it could serve as platform for a radio version of his blog. The idea of doing interviews would be really nice. In general I prefer reading because I can do it much faster than listening. Next year, when I go back to doing more bench work I will probably try consuming podcast while working.
(Via Deepak, Roland, and Konrad) Freebase is a very promising new web service. For those who have heard about semantic web, it will look familiar. They want to organize data by allowing users to add metadata to the information stored on the site. This will be great for aggregation of content and data mining. For science it could serve as place to deposit and organize data for collaborative projects.
(Via BioHacking) Microsoft has announced the winners of the first award for computational challenges in Synthetic Biology. Six projects were awarded a total of $570,000 (USD) to develop tools for synthetic biology.
(Via Jason Stajich) My own favorite model organism database (SGD) has created a wiki for community annotation. Anyone interested in S. cerevisiae biology, methods, reagents and strains can go there and help populate the wiki.
Thursday, March 01, 2007
Craig Venter in Colbert Report
(via Drew Endy in SynBio discuss list) Here is mister Craig Venter in Colbert Report promoting synthetic biology and the personal genome (in a funny way).
Let's hope that Synthetic Biology does not get over hyped. The public might start reacting negatively to these technologies if they grow too fast or if they don't deliver what they promise.
(via Drew Endy in SynBio discuss list) Here is mister Craig Venter in Colbert Report promoting synthetic biology and the personal genome (in a funny way).
Let's hope that Synthetic Biology does not get over hyped. The public might start reacting negatively to these technologies if they grow too fast or if they don't deliver what they promise.
Tuesday, February 27, 2007
The future impact of genome synthesis
The synthesis blog pointed to a detailed report discussing the economical importance of impending advances in biological engineering. The study, supported by DOE, DuPont Corporation and The Berkley Nanosciences Nanoengineering Institute tries to cover the main driving forces for biotechnology innovation, it's possible future applications and economical impact. The last chapter is dedicated to envisioning future scenarios for synthetic biology based on different assumptions about important factors that could determine the progress of this technology.
While the scenarios described in the end of the report might be useful to track the speed and mode of evolution of this emerging technology, the most relevant section for life scientists is arguably the one discussing possible applications of genome synthesis.
There are three main applications listed:
Chemicals: Engineering new production pathways and creating new products
Energy: Opening new biological routes for energy transformation
Synthetic Vaccines: Opportunities for rapid-response biosecurity
The best examples of synthetic biology research have consisted up to now mostly of simple toy examples. Usually simple circuits are created and studied to detail but few have obvious immediate practical applications. Are we currently at the inflection point, were synthetic biology research will produce more practical applications or is the complexity of living systems still too large a barrier ?
One example of the use of synthetic biology in chemical production is the work of Dae-Kyun Ro and colleagues in the Keasling lab (free PDF). They re-engineered S. cerevisiae to produce artemisinic acid, a precursor of the malaria drug Artemisinin.
Keasling is also one of the researchers involved in the Helios project. An effort directed at developing technology for solar fuel generation (in the form of biofuel). The project is also headed by Nobel prize laureate Steve Chu that explains the project in this video presentation.
The synthesis blog pointed to a detailed report discussing the economical importance of impending advances in biological engineering. The study, supported by DOE, DuPont Corporation and The Berkley Nanosciences Nanoengineering Institute tries to cover the main driving forces for biotechnology innovation, it's possible future applications and economical impact. The last chapter is dedicated to envisioning future scenarios for synthetic biology based on different assumptions about important factors that could determine the progress of this technology.
While the scenarios described in the end of the report might be useful to track the speed and mode of evolution of this emerging technology, the most relevant section for life scientists is arguably the one discussing possible applications of genome synthesis.
There are three main applications listed:
Chemicals: Engineering new production pathways and creating new products
Energy: Opening new biological routes for energy transformation
Synthetic Vaccines: Opportunities for rapid-response biosecurity
The best examples of synthetic biology research have consisted up to now mostly of simple toy examples. Usually simple circuits are created and studied to detail but few have obvious immediate practical applications. Are we currently at the inflection point, were synthetic biology research will produce more practical applications or is the complexity of living systems still too large a barrier ?One example of the use of synthetic biology in chemical production is the work of Dae-Kyun Ro and colleagues in the Keasling lab (free PDF). They re-engineered S. cerevisiae to produce artemisinic acid, a precursor of the malaria drug Artemisinin.
Keasling is also one of the researchers involved in the Helios project. An effort directed at developing technology for solar fuel generation (in the form of biofuel). The project is also headed by Nobel prize laureate Steve Chu that explains the project in this video presentation.
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