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Biological Pathways and the Semantic Web

Biological Pathways and the Semantic Web | SynBioFromLeukipposInstitute | Scoop.it
Biological Pathways and the Semantic Web...

WikiPathways (www.wikipathways.org) is a community-driven pathway resource [1-3]. It is inspired by Wikipedia and aims at capturing knowledge about biological pathways in such a way that it can be used for data analysis. For the Innovative Medicine Initiative project Open PHACTS [4], we expose the contents of WikiPathways in semantic web format. We are taking a multi-pronged approach, selecting different ontologies to capture diverse aspects of semantics. As an established pathway ontology, BioPAX [5] forms the bulk of the semantics for the actual pathway content, but we also use other specialized ontologies to capture the semantics of curators, authors, and other WikiPathways-specific meta data.

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Synthetic biology firms becoming attractive to investors – Midven

Synthetic biology firms becoming attractive to investors – Midven | SynBioFromLeukipposInstitute | Scoop.it
The team behind Midven's Rainbow Seed Fund, a £24m early stage venture capital pot for UK tech companies, said synthetic biology is now providing an "exciting investment opportunity".
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Synthetic biology firms becoming attractive to investors – Midven - Insider Media | CodonOps

Synthetic biology firms becoming attractive to investors – Midven - Insider Media | CodonOps | SynBioFromLeukipposInstitute | Scoop.it
Synthetic biology firms becoming attractive to investors – MidvenInsider MediaCompanies in the field of synthetic biology were developing out of the laboratory and into the commercial world, according to Dr Andrew Muir, Rainbow Seed Fund's...
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Synthetic biology: Biocircuits in synchrony

Synthetic biology: Biocircuits in synchrony | SynBioFromLeukipposInstitute | Scoop.it

A major goal of synthetic biology is to build reliable, predictable networks of molecular and cellular components that can work as new biological devices capable of, for example, sensing chemicals, manufacturing drugs or even fighting disease. However, achieving such goals entails the production of complex synthetic biocircuits, which requires synchronization of multiple components. Although synchronization is well established in electronics1, synchronizing living cells is a major challenge, because it demands correlation of different phenomena that may be taking place on different temporal and spatial scales. (...) Prindle et al. report that such coupling has been achieved in cells of the bacterium Escherichia coli.


Synthetic biology: Biocircuits in synchrony
Ricard Solé & Javier Macía

Nature (2014)

http://dx.doi.org/10.1038/nature13224 ;


Rapid and tunable post-translational coupling of genetic circuits
Arthur Prindle, Jangir Selimkhanov, Howard Li, Ivan Razinkov, Lev S. Tsimring & Jeff Hasty
Nature (2014)

http://dx.doi.org/10.1038/nature13238


Via Complexity Digest
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Systems and synthetic biology approaches to cell division

Systems and synthetic biology approaches to cell division | SynBioFromLeukipposInstitute | Scoop.it
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Socrates Logos's curator insight, February 4, 12:48 PM

by
Alireza Mashaghi • Cees Dekker

"Cells proliferate by division into similar daughter cells, a process that lies at the heart of cell biol- ogy. Extensive research on cell division has led to the identification of the many components and control ele- ments of the molecular machinery underlying cellular division. Here we provide a brief review of prokaryotic and eukaryotic cell division and emphasize how new approa- ches such as systems and synthetic biology can provide valuable new insight."

http://bit.ly/1aZrcI6

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Rewiring Nature With Synthetic Biology - Discover Magazine

Rewiring Nature With Synthetic Biology - Discover Magazine | SynBioFromLeukipposInstitute | Scoop.it
Rewiring Nature With Synthetic Biology
Discover Magazine
Bioengineer Drew Endy shares his vision to reprogram biology as a precision manufacturer — and possibly change civilization as we know it. By Anil Ananthaswamy.
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#iEthereum

An easy to use Ethereum iPhone and iWatch implementation for the…

#iEthereum <br/><br/>An easy to use Ethereum iPhone and iWatch implementation for the… | SynBioFromLeukipposInstitute | Scoop.it
#iEthereum

An easy to use Ethereum iPhone and iWatch implementation for the general public

If you like the project you can donate BTC here… - Gerd Moe-Behrens - Google+
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▶ Saclay - YouTube

This is the presentation video of Paris Saclay iGEM team in the communication workshop organized by Paris Bettencourt iGEM team in the French iGEM meeting 20...
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Applications of computational modeling in metabolic engineering of yeast

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Advances and Computational Tools towards Predictable Design in Biological Engineering

Advances and Computational Tools towards Predictable Design in Biological Engineering | SynBioFromLeukipposInstitute | Scoop.it

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Socrates Logos's insight:

by
Pasotti L, Zucca S.

"The design process of complex systems in all the fields of engineering requires a set of quantitatively characterized components and a method to predict the output of systems composed by such elements. This strategy relies on the modularity of the used components or the prediction of their context-dependent behaviour, when parts functioning depends on the specific context. Mathematical models usually support the whole process by guiding the selection of parts and by predicting the output of interconnected systems. Such bottom-up design process cannot be trivially adopted for biological systems engineering, since parts function is hard to predict when components are reused in different contexts. This issue and the intrinsic complexity of living systems limit the capability of synthetic biologists to predict the quantitative behaviour of biological systems. The high potential of synthetic biology strongly depends on the capability of mastering this issue. This review discusses the predictability issues of basic biological parts (promoters, ribosome binding sites, coding sequences, transcriptional terminators, and plasmids) when used to engineer simple and complex gene expression systems in Escherichia coli. A comparison between bottom-up and trial-and-error approaches is performed for all the discussed elements and mathematical models supporting the prediction of parts behaviour are illustrated."

 http://bit.ly/1tHXAFj

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chein cherry's curator insight, August 28, 9:42 PM

wish it is dazzling enough

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CytoComp Dapp - building a decentralized company on top of Ethereum

CytoComp Dapp - building a decentralized company on top of Ethereum | SynBioFromLeukipposInstitute | Scoop.it
Socrates Logos's insight:

As you might know, I am CEO of a startup called CytoComp http://www.cytocomp.com We are focusing on building a microprocessor from biological parts.

I am interested to build the company structure in a decentralized manner. I would like to discuss how one can do this on top of Ethereum https://www.ethereum.org. Especially interesting subjects are IP, crowd sourced project development, micro payments for crowd sourced micro contributions, distributed location of coworkers, crowd funding of project ideas, crowd shares, contracts, in general tot figure out how a working company structure on top of Ethereum will look like.
Looking forward to discuss.


bit.ly/1ly7PLv 

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Synthetic Biology Gone Wild? Probably Not. An interview with Tom Ellis. | Synthetic Biology Community

Synthetic Biology Gone Wild? Probably Not. An interview with Tom Ellis. | Synthetic Biology Community | SynBioFromLeukipposInstitute | Scoop.it
By Prashant Bhat The first annual Synthetic Biology: Engineering, Evolution & Design (SEED) conference was held last month in Manhattan Beach, CA. Both (Synthetic Biology Gone Wild? Probably Not.
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A Love Button for the Internet / ChangeTip

ChangeTip makes it easy to send and receive money online. Tip people, businesses and organizations by mentioning a recipient, @changetip, and an amount.
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Kitchen Counter Biohacking

Kitchen Counter Biohacking | SynBioFromLeukipposInstitute | Scoop.it
Kitchen counter biohacking is easy, fun and you can do it too.
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Crowdsourcing Synthetic Biology - Citizen Science Salon | DiscoverMagazine.com

Crowdsourcing Synthetic Biology - Citizen Science Salon | DiscoverMagazine.com | SynBioFromLeukipposInstitute | Scoop.it
Biology + Engineering = Synthetic Biology (Image Credit: Shutterstock / Tarchyishnik Andrei ) At first glance, the terms ‘synthetic’ and ‘biology’ seem lik (Check out these DIY synthetic biology projects: http://t.co/0zoAC6oDsf...
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Synthetic biology A protein code to target RNA - Nature.com

Synthetic biology A protein code to target RNA
Nature.com
The genetic code, by which RNA sequence is translated into protein, was a seminal discovery in molecular biology.
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Synthetic biology Mini Symposium

Synthetic biology Mini Symposium | SynBioFromLeukipposInstitute | Scoop.it
1st Baojian Ding Synthetic biology Mini Symposium February 13th 2014
Blue Hall, Ecology B... (Synthetic Biology Mini Symposium in Lund 13 Feb!...
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Transcription Activator-like Effectors: A Toolkit for Synthetic Biology - ACS Synth. Biol.

Transcription Activator-like Effectors: A Toolkit for Synthetic Biology - ACS Synth. Biol. | SynBioFromLeukipposInstitute | Scoop.it

(via T. Lahaye, thx)

Moore et al, 2014

Transcription activator-like effectors (TALEs) are proteins secreted by Xanthomonas bacteria to aid the infection of plant species. TALEs assist infections by binding to specific DNA sequences and activating the expression of host genes. Recent results show that TALE proteins consist of a central repeat domain, which determines the DNA targeting specificity and can be rapidly synthesized de novo. Considering the highly modular nature of TALEs, their versatility, and the ease of constructing these proteins, this technology can have important implications for synthetic biology applications. Here, we review developments in the area with a particular focus on modifications for custom and controllable gene regulation.


Via dromius
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dromius's curator insight, March 13, 4:30 AM

Table 2 gives an overview over assembly methods and their required time effort.

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Broad-host-range vector system for synthetic biology and ...

Broad-host-range vector system for synthetic biology and ... | SynBioFromLeukipposInstitute | Scoop.it
Abstract. Inspired by the developments of synthetic biology and the need for improved genetic tools to exploit cyanobacteria for the production of renewable bioproducts, we developed a versatile platform for the construction of ...
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iEthereum

iEthereum | SynBioFromLeukipposInstitute | Scoop.it
Socrates Logos's insight:

iEthereum

This is a new Project I started : An easy to use Ethereum iPhone and iWatch implementation for the general public. You are welcome to join me. Please follow me on GiyHub 
http://bit.ly/1pfxovB

If you like to support me, my BTC address is:

1KnikzSG7fnRfG76DxjLZyrbvw8fS9nisw

I think ethereum is a great platform for biohacker and for Ethereum is the platform I will use for my CytoComp project see building a decentralized company: http://bit.ly/1qSEScZ (An ethereum Dapp implementing of the structure of an organization wherein the decision making authority does not sit with a central figure or group designed for all organizations with interest in such structure)  and DNA analysis Dapp ( Ethereum Dapp for secure sharing and analysis of your personal DNA data both for self trackers and people with diseases with underlying genetic alterations)http://bit.ly/1B4J5xP

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[MAJOR ANNOUNCEMENT] Reddcoin to implement new algorithm Proof-of-Stake-Velocity • /r/reddCoin

[MAJOR ANNOUNCEMENT] Reddcoin to implement new algorithm Proof-of-Stake-Velocity • /r/reddCoin | SynBioFromLeukipposInstitute | Scoop.it
Socrates Logos's insight:


I am following tight the developments at Reddcoin - I think their idea of a social currency where you can show your love of a contributor in social media with a tip. Today ReddCoin announced a paper where they further develop their ideas.

A new social currency model by Reddit - this can potentially revolutionize science publishing. We can direct publish and can get payment, if we have done great work - instead of that the authors have to pay and publishing companies make the big money....

*Proof of Stake Velocity: Building the Social Currency of the Digital Age*

by
Larry Ren

"Proof of Stake Velocity (PoSV) is proposed as an alternative to Proof of Work (PoW) and Proof of Stake (PoS) to secure the peer-to-peer network and confirm transactions of Reddcoin, a cryptocurrency created specifi- cally to facilitate social interactions in the digital age. PoSV is designed to encourage both ownership (Stake) and activity (Velocity) which directly correspond to the two main functions of Reddcoin as a real currency: store of value and medium of exchange. Reddcoin can also function as the unit of account in heterogeneous social context. The technological aspects of PoSV are presented after a detailed review of existing designs. The eco- nomic aspects of Reddcoin are then analysed. Finally the unique position of Reddcoin as a digital social currency in the competitive landscape of cryptocurrencies is discussed."

 http://bit.ly/VSlfG6

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SynBio Axlr8r demo day makes history (video)

SynBio Axlr8r demo day makes history (video) | SynBioFromLeukipposInstitute | Scoop.it
After months of work, the SynBio Axlr8r demo day at the Science Gallery in Dublin made history as the first of its kind in the world.
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DIYbio Toronto

DIYbio.to #ScienceHack

Thursday, Sep 18, 2014, 6:30 PM

Synbiota Inc.
35 Liberty St. Suite #105 Toronto, ON

13 biophilians Attending

Heya DIYbio.to family! I’m pleased to announce two wetlab workshops I’m organizing that will run in September. We’re going to do a DIYbio.to #ScienceHack See https://sciencehack.synbiota.com/ These wetlab workshops involve learning: (1) how to rationally design DNA, assemble your DNA design using real DNA, and; (2) then booting up your assembled DN...

Check out this Meetup →

Heya DIYbio.to family! I’m pleased to announce two wetlab workshops I’m organizing that will run in September. We’re going to do a DIYbio.to #ScienceHack See https://sciencehack.synbiota.com/
These we
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What would be a great coin name used for paying DNA analysis and synthethesis? - Looking forward to your suggestions

What would be a great coin name used for paying DNA analysis and synthethesis? - Looking forward to your suggestions | SynBioFromLeukipposInstitute | Scoop.it

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Socrates Logos's insight:
*What would be a great coin name used for paying DNA analysis and synthethesis - Looking forward to your suggestions*

I am thinking about a DApp for Ethereum https://www.ethereum.org
There are certain aspects my CytoComp project where I see solutions in Bitcoin 2.0 / BlockChain technology.
DNA sequencing and synthesis plays a central role in synthetic biology.
One problem is the secure sharing and analysis of DNA data. It is possible to track the identity of a person from shared DNA sequences without an identifier http://www.sciencemag.org/content/339/6117/321.abstract. As genomics play an increasingly important role in modern medicine, this is a major problem. DNA data are highly sensitive and sequencing information has a huge potential for misuse. I think it is possible to use BlockChain technology to securely share these kind of data P2P.
Moreover, DNA data are huge files and will in the future need increasing computing power to be rapidly analyzed. The design of DNA sequences might also sometimes need larger computing power. I see the option to chop up these large DNA data files and analyze these parts by utilizing secure multiparty computing. I think platforms like Ethereum are well suited to build a secure DNA analysis app.
A token, specific coin would be great to use in this system in order to pay for expenses.
Thus as a starting point, please share your thoughts and suggest a name.
BTW if anybody is interested to join such a project - let me know.
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Self Healing with Synthetic Biology

Self Healing with Synthetic Biology | SynBioFromLeukipposInstitute | Scoop.it
Today, I wanted to provide some context to spark a discussion on using living organisms as supplements in structures to make them self-healing. I saw a piece on self-healing concrete that was...
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I need your help!

I need your help! | SynBioFromLeukipposInstitute | Scoop.it
Socrates Logos's insight:

If you like my #synbio  curating and projects, please support me with #bitcoin  donation. I need your support in order to continue!

Thanks so much!

Adress
1KnikzSG7fnRfG76DxjLZyrbvw8fS9nisw

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