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Latest news on complex systems in life sciences, engineering, education and government
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Biomolecular computing systems: principles, progress and potential

Published in Nature by Yaakov Benenson

"The task of information processing, or computation, can be performed by natural and man-made 'devices'. Man-made computers are made from silicon chips, whereas natural 'computers', such as the brain, use cells and molecules. Computation also occurs on a much smaller scale in regulatory and signalling pathways in individual cells and even within single biomolecules. Indeed, much of what we recognize as life results from the remarkable capacity of biological building blocks to compute in highly sophisticated ways. Rational design and engineering of biological computing systems can greatly enhance our ability to study and to control biological systems. Potential applications include tissue engineering and regeneration and medical treatments. This Review introduces key concepts and discusses recent progress that has been made in biomolecular computing." Learn more at: http://bit.ly/Ll8Lg2 ;

(Note you will need a Nature login or need to purchase the paper)


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Data Science Summit Videos | Greenplum

Data Science Summit Videos | Greenplum | Complex Insight  - Understanding our world | Scoop.it

A number of videos from the 2012 Data Science Summit via Greenplum that are worth watching. (useful selection from 2011 as well). The Data Science Summit brings together thought leaders from academia, the social enterprise, start-ups, and the public sector to help attendees explore and define their path forward in  our emergeing big data-driven world. Through data mining, statistics, advanced analytics and innovative visualizations, data scientists are drawing insights from the abundance of structured and unstructured data. Learn more.

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Debating a Proposed Moratorium On Synthetic Biology Research | Ali | Intersect: The Stanford Journal of Science, Technology and Society

by Sanna J. Ali : "This essay explores the ethical issues surrounding the public policy debate of imposing a moratorium on synthetic biology research. In particular, this article explores the risks of synthetic biology research, including those of safety, intellectual property rights, and a shift in the global economy, while assessing whether these risks are dangerous enough to call for a moratorium." http://bit.ly/LhPZcH


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ACM A.M. Turing Centenary Celebration

ACM A.M. Turing Centenary Celebration | Complex Insight  - Understanding our world | Scoop.it

Thanks to Franz Dill (Eponymous Pickle blog) for this link. On Friday, June 15 and Saturday, June 16, more than 30 Turing Award recipients will gather to commemorate the 100th anniversary of Alan Turing's birth with personal remembrances, talks, and panel discussions. The ACM is webcasting the entire event live (and a stream will be available after the event).  This is a great way to get an insisight into computing's past and future, from the unique perspectives of its pioneers and leading contemporary thinkers. Please note that all times listed are Pacific Daylight Time (PDT). Worth Watching.

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Economics and Morality: Paul Krugman’s Framing.

Economics and Morality: Paul Krugman’s Framing. | Complex Insight  - Understanding our world | Scoop.it

Markets are not provided by nature. They are constructed — by laws, rules, and institutions. All of these have moral bases of one sort or another. Hence, all markets are moral, according to someone’s sense of morality. The only question is, Whose morality? In contemporary America, it is conservative versus progressive morality that governs forms of economic policy. The systems of morality behind economic policies need to be discussed. Learn more...

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Mind Wobbles - A Totally Awesome Systems Biology Blog by Allyson Lister, Newcastle Uni.

Mind Wobbles - A Totally Awesome Systems Biology Blog by Allyson Lister, Newcastle Uni. | Complex Insight  - Understanding our world | Scoop.it

Awesome post on systems biology by Allyson Lister  a PhD student at Newcastle University. Her Blog "The Mind Wobbles" - should be high on systems biologists and computational modellers reading list.

 

Sample: There are four main areas of study in systems biology research: (i) the structure (e.g. interactions and pathways) of a system; (ii) how a system behaves over time, or its dynamics; (iii) the method of controlling and modulating the system; and (iv) the design method, or the deliberate progress using well defined design principles. These four properties are strongly tied to the quantitative modelling aspect of systems biology, and illustrate the importance of such models. However, models are of limited use to either people or computers if they do not have structured biological annotations to provide context. For instance, until SBML  models are annotated by the BioModels team, elements often contain short-hand, biologically irrelevant names and descriptions in computationally incompatible free text. While attaching additional biological knowledge to quantitative models is not a requirement for their simulation, without such annotations model sharing, interpretation of simulation results, integration and reuse becomes nearly impossible [9]. Therefore the addition of biologically relevant, computationally accessible metadata will not only enhance the semantics of a model but provide a method of unambiguously identifying its elements.  Read More...

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Ian Abbott Donnelly , European CTO, Smart Cities IBM: visualising solutions for smart cities

Ian Abbott Donnelly , European CTO, Smart Cities IBM: visualising solutions for smart cities | Complex Insight  - Understanding our world | Scoop.it

Cities are systems of systems, with things interacting in interesting ways. How do we work with them to make things better. Smart cities aren't about growth - they're about prosperity. They're about making insightful decisions, predicting problems, and co-ordinating resources to operate effectively.

Peterborough is one of the UK"s leading cities for sustainability. They're gathering huge amounts of data, but very little of its is being sued by business or public sector decision makers. So they're trying to produce it in new forms. They create visualisations to make the information more accessible. For exampe - a visualisation of water meter use. Learn more..

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Cleantech Insights | A Smarter City is Not Enough: Better Brains, Better Hearts

Cleantech Insights | A Smarter City is Not Enough: Better Brains, Better Hearts | Complex Insight  - Understanding our world | Scoop.it

Great blog post by Greg Neichin on the smarter city movement.

 

It is this stark contrast between the emerging, and deservedly warranted, enthusiasm for smart cities initiatives and the reality of the lives of many living in the squalor and sprawl of the world’s mega cities that demands attention. The world’s poor vastly outnumber the world’s rich and smarter cities will be cities that are not only smart and data-driven, but truly sustainable for all of their inhabitants, not just those with smart phones.

 

Much like the sustainability movement encouraged corporations to not only think about their carbon footprint, but also about employee, supplier, and community welfare, so too, the smart cities movement should be based on organizing principles that are holistic in nature. As we as technologists continue to do our part to enhance the intelligence available to public officials and individual citizens, let us never forget that we are doing this out of a fundamental drive to raise the standard of living for all and to make tomorrow’s mega-cities sustainable, healthy, vibrant ecosystems.

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Dinosaurs made extinct by Big Data:

Dinosaurs made extinct by Big Data: | Complex Insight  - Understanding our world | Scoop.it

 Nice article on comparing big data  with MoneyBall movie which ends with the excellent summation: This is ultimately going to be the story of Big Data: A big data set well analyzed beats a hunch every time.. learn more.

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Stochastic simulations of a synthetic bacteria... [BMC Syst Biol. 2012] - PubMed - NCBI

Research paper by Biliouris K, Babson D, Schmidt-Dannert C, Kaznessis Y.


BACKGROUND:
The field of synthetic biology has greatly evolved and numerous functions can now be implemented by articially engineered cells carrying the appropriate genetic information. However, in order for the cells to robustly perform complex or multiple tasks, co-operation between them may be necessary.  In this paper, the team model a synthetic ecosystem comprising of bacteria and yeast that communicate with and benefit from each other using small diffusible molecules using stochastic modeling. The stochastic model captures the relevant intra-cellular and inter-cellular interactions taking place in and between the eukaryotic and prokaryotic cells. Integration of well-characterized molecular regulatory elements into these two microbes allows for communication through quorum sensing. The way that the model is built allows for studying the dynamics of any system consisting of two species communicating with one another via chemical signals and therefore is of interest to a wide domain and may potentially drive the experimental design of various synthetic heterogeneous ecosystems.". A provisional full version of the paper is available at: http://www.biomedcentral.com/content/pdf/1752-0509-6-58.pdf


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Study: Universal gene for life missing from volcanic microbes (Wired UK)

Study: Universal gene for life missing from volcanic microbes (Wired UK) | Complex Insight  - Understanding our world | Scoop.it
ThermoDBP potentially usefully in #syntheticbiology:

*Study: Universal gene for life missing from volcanic microbes*

by
Liat Clark
"A DNA-binding protein which is supposedly present in all life on Earth is absent from certain microbes found living near volcanoes, a study says. The discovery challenges our present knowledge of the fundamental basis of living organisms.

In the place of the single-stranded DNA-binding protein (SSB), the single cell organism Thermoproteales has another gene, now named ThermoDBP. The functionality of the gene is not yet clear. However, the study, published in the Proceedings of the National Academy of Sciences (PNAS) journal, suggests it could be useful in the fields of biotechnology and synthetic biology.

"All cells, whether they are microbial or human, have some things in common," says Malcolm White of the University of St Andrews' School of Biology, one of the paper's authors. "These are the fundamental components or building blocks which were present in the first cells and have been passed on over 3.5 billion years. However, we have discovered that a gene normally thought to be absolutely essential and conserved throughout every form of life, is in fact lost in one group of volcanic bugs, and replaced by a completely novel gene."....". Learn more..

 


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A search engine for social networks based on the behavior of ants

A search engine for social networks based on the behavior of ants | Complex Insight  - Understanding our world | Scoop.it

Research at Carlos III University in Madrid is developing an algorithm, based on ants' behavior when they are searching for food, which accelerates the search for relationships among elements that are present in social networks.

 

One of the main technical questions in the field of social networks, whose use is becoming more and more generalized, consists in locating the chain of reference that leads from one person to another, from one node to another. The greatest challenges that are presented in this area is the enormous size of these networks and the fact that the response must be rapid, given that the final user expects results in the shortest time possible. In order to find a solution to this problem, these researchers from UC3M have developed an algorithm SoSACO, which accelerates the search for routes between two nodes that belong to a graph that represents a social network.

 

The way SoSACO works was inspired by behavior that has been perfected over thousands of years by one of the most disciplined insects on the planet when they search for food. In general, the algorithms used by colonies of ants imitate how they are capable of finding the path between the anthill and the source of food by secreting and following a chemical trail, called a pheromone, which is deposited on the ground. "In this study – the authors explain – other scented trails are also included so that the ants can follow both the pheromone as well as the scent of the food, which allows them to find the food source much more quickly". The main results of this research, which was carried out by Jessica Rivero in UC3M's Laboratorio de Bases de Datos Avanzadas (The Advanced Data Bases Laboratory - LABDA) as part of her doctoral thesis, are summarized in a scientific article published in the journal Applied Intelligence. "The early results show that the application of this algorithm to real social networks obtains an optimal response in a very short time (tens of milliseconds)", Jessica Rivero states.


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Sensor search engine developed - Scottish Headlines - Fife Today

Sensor search engine developed - Scottish Headlines - Fife Today | Complex Insight  - Understanding our world | Scoop.it

Scientists at the University of Glasgow's School of Computing Science are developing a new internet search engine which will use information from sensors in the real world to deliver results. The SMART project will be built upon an open-source search engine technology known as Terrier in development at the university since 200. 4. The SMART engine will be able to answer high-level queries by automatically identifying cameras, microphones and other sensors that can contribute to the query, then synthesising results stemming from distributed sources in an intelligent way. SMART builds upon the existing concept of 'smart cities', physical spaces which are covered in an array of intelligent sensors which communicate with each other and can be searched for information. Researchers expect that that SMART will be tested in a real city by 2014. Learn more...

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Biologists grow human-eye precursor from stem cells

Biologists grow human-eye precursor from stem cells | Complex Insight  - Understanding our world | Scoop.it

A stem-cell biologist has had an eye-opening success in his latest effort to mimic mammalian organ development in vitro. Yoshiki Sasai of the RIKEN Center for Developmental Biology (CBD) in Kobe, Japan, has grown the precursor of a human eye in the lab. Learn more...

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Temporal percolation of the susceptible network in an epidemic spreading

L. D. Valdez, P. A. Macri, L. A. Braunstein
(Submitted on 13 Jun 2012)
In this work, we study the evolution of the susceptible individuals during the spread of an epidemic modeled by the susceptible-infected-recovered (SIR) process spreading on top of complex networks. Using a edge-based compartmental approach and percolation tools, we find that the network composed by susceptible individuals undergoes a dynamic node percolation transition with a time dependent control parameter. We show that there exists a critical time $t_c$ above which the giant susceptible cluster is destroyed. As a consequence, in order to protect a large fraction of the susceptible individuals, any mitigation strategy should be implemented before this critical time $t_c$. Our theoretical results are confirmed by extensive simulations of the SIR process.


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Informatics, Biology Team Demonstrates Role of Foreign DNA Strands in Life-Supporting Bacteria

From - Lab Manager Magazine® : An Indiana University team of researchers has conducted the most in-depth and diverse genetic analysis of the defense systems that trillions of micro-organisms in the human body use to fend off viruses. Led by IU Bloomington assistant professor of informatics and computing Yuzhen Ye, the team of bioinformaticists and biologists reconstructed arrays of clusters of regularly interspaced short palindromic repeats -- CRISPRs -- which function as immune systems to the bacteria that play a vital role in human health. Between genomic repeats, CRISPR locations carry short strands of foreign DNA called spacers, which provide a history of past exposures to outside invaders like plasmids and bacteriophages (viruses that infect bacteria), and allow the bacteria to fight off viruses they have already encountered. This is an incredibly interesting piece of research and demonstrates the applications of CRISPRs to tracing the virus exposure of individuals  and it indicates the importance of effective identification and characterization of CRISPR loci to the study of the dynamic ecology of microbiomes and human health.  Learn more...

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About PAXsims

About PAXsims | Complex Insight  - Understanding our world | Scoop.it

The PaxSims blog is devoted to the development and effective use of simulation-based learning concerning issues of conflict, peacebuilding, and development in fragile and conflict-affected states, as well as to the policy of application of gaming and simulation techniques. If you are using agent based models or complex systems related simulations for policy modelling or development then the PAXsims blog should be on your essential reading list. Learn more...

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The evolution of simulation | Datacenter Dynamics

The evolution of simulation | Datacenter Dynamics | Complex Insight  - Understanding our world | Scoop.it

One of our previous 3D simulation tools was used for simulation based planning and training by Airbus (A380) and Boeing (787) so this article on Datacenter Dynamics was very much of interest. In recent years advancements in technology and reduction of costs have made simulation a differentiator in the aerospace market. Deals are often made on an aircraft’s time to market and the ability of the end user to customize their purchase and achieve fuel efficiency and rapid turn around time are key factors in fleet purchase decisions. This is a good article on how Airbus are using simulation and high performance computing (HPC) to drive results and enable advanced designs. Learn more

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Mathematical Model Developed to Predict Malaria Outbreaks: Open Malaria Warning (OMaWa)

Mathematical Model Developed to Predict Malaria Outbreaks: Open Malaria Warning (OMaWa) | Complex Insight  - Understanding our world | Scoop.it

Ethiopian and Norwegian researchers have developed a mathematical model that can identify conditions that increase the likelihood of a malaria outbreak up to two months ahead of its occurrence.The computer model, Open Malaria Warning (OMaWa), incorporates hydrological, meteorological, mosquito-breeding and land-use data to determine when and where outbreaks are likely to occur. Unlike earlier models which simplified key components of the malariy outbreak cycle - the OmaWa model is delivering better results. Learn more..


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SourceForge.net: PyCX Project: PyCX 0.2 now available

SourceForge.net: PyCX Project: PyCX 0.2 now available | Complex Insight  - Understanding our world | Scoop.it

The PyCX Project aims to develop an online repository of simple, crude, yet easy-to-understand Python sample codes for dynamic complex systems simulations, including iterative maps, cellular automata, dynamical networks and agent-based models. Learn more...


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Flash Drives Replace Disks At Amazon, Facebook, Dropbox

Flash Drives Replace Disks At Amazon, Facebook, Dropbox | Complex Insight  - Understanding our world | Scoop.it

The unsexy part of big data to most news folks is where the data actually gets stored. Good article at Wired on increasing use of solid state drives (SSD) to replace traditional disk drives. SSD's are currently more expensive and have some other limitations but they offer speed and versatility over traditional disk drives and as a result are starting to get adopted into the big name data centers. Interesting article - learn more...

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Craig Venter : ‪Synthetic Biology‬ talk at Nasa Ames

Craig Venter : ‪Synthetic Biology‬ talk at Nasa Ames | Complex Insight  - Understanding our world | Scoop.it

NASA Ames uses software we have helped develop in a bunch of different roles (something we are very proud of). One of the coolest things about working with NASA Ames (other than just what they do)is the sheer generosity they have in sharing information.  This is a great talk by Craig Venter on Synthetic Biology given to teams at Nasa Ames.

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*MODELING AND DESIGN TOOLS FOR SYNTHETIC BIOLOGY*

Given the experiements we are doing with TinkerCell and other tools this article by

JURIJS MEITALOVS, NATALJA BULIPOPA, OLESJA KOVALONOKA is very much of  interest. The paper reviews several computational tools for application in synthetic biology. Recently developed computational tools, for instance, for gap-filling, orphan reaction searching, metabolic engineering, pathway analysing, gene engineering, metabolic reconstruction and others are reviewed and their functionality described. Some tools have similar functionality and some tools can be used for different tasks. Tools for comparison were chosen from the most cited scientific literature. Learn more:

http://bit.ly/KTbIaG


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John Carmack is making a virtual reality headset, $500 kits available soon, video interview inside | PC Gamer

John Carmack is making a virtual reality headset, $500 kits available soon, video interview inside  | PC Gamer | Complex Insight  - Understanding our world | Scoop.it

John Carmack is one of the best graphics programmers in the game industry. His research and development work has tended to pioneer a number of new techniques that later become mainstream. It was with interest to learn that he is currently re-examining virtual reality head mounted displays.  The videos explain where he is at and what the state of development is. If you are interested in display technology and remember the original promise of headsets for certain applications this is well worth watching. Learn more...

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Core Python Programming, 2nd Edition | Free eBook Share

Core Python Programming, 2nd Edition | Free eBook Share | Complex Insight  - Understanding our world | Scoop.it
It combines the power of compiled languages with the simplicity and rapid development of scripting languages. In Core Python Programming, Second Edition, leading Python developer and trainer Wesley Chun helps you ...

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