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Python and GIS Resources | GIS Lounge

Python and GIS Resources | GIS Lounge | Complex Insight  - Understanding our world | Scoop.it
Find resources to web sites about Python scripting to use in GIS. Learn how to use Python to expand your geographic information system.
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Complex Insight  - Understanding our world
Latest news on complex systems in life sciences, engineering, education and government
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CUDA Toolkit

CUDA Toolkit | Complex Insight  - Understanding our world | Scoop.it
The NVIDIA® CUDA® Toolkit provides a comprehensive development environment for C and C++ developers building GPU-accelerated applications. The CUDA Toolkit includes a compiler for NVIDIA GPUs, math libraries, and tools for debugging and optimizing the performance of your applications.
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New CUDA 6 toolkit release with 64-bit arm support, improved CUDA Fortran for scientific aplications, replay features in visual profiler and nvprof and a new BLAS GPU library cublasXT that scales across GPUs. A lot of goodness for compute developers - available here: https://developer.nvidia.com/cuda-downloads

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Are Agent-Based Models the Future of Macroeconomics?

Are Agent-Based Models the Future of Macroeconomics? | Complex Insight  - Understanding our world | Scoop.it
A couple months back, Mark Buchannan wrote an article in which he argued that ABMs might be a productive way of trying to understand the economy.  In fact, he went a bit further – he said that ABMs...
ComplexInsight's insight:

Been a while since we published anything on economics but with over 20 years experience building agent based models - we are suckers for articles that encourage people to discover them as thinking tools. Good explanation on how agent based models fit into economic forecasting.

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Why HIV Virions Have Low Numbers of Envelope Spikes: Implications for Vaccine Development

Why HIV Virions Have Low Numbers of Envelope Spikes: Implications for Vaccine Development | Complex Insight  - Understanding our world | Scoop.it
From molecules to physiology
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Interesting paper on structural protien envelope spikes in HIV related viruses and their relation to autoimmune response and implications for vaccine development by John Schiller and Bryce Chackerian. 

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Programmable on-chip DNA compartments as artificial cells


Via Socrates Logos
ComplexInsight's insight:

At Radcliffe Institute of Advanced Study at Harvard, Roy Bar-Ziv is expanding his research to explore the paradigm of programmable on-chip DNA compartments as artificial cells, in which the essential reactions of living cells encoded in DNA take place inside miniaturized compartments fabricated in silicon. Understanding the emergent properties of these compartments may lead to assembly of artificial cells capable of computation, autonomous sensing, and replication, with applications in future technologies.

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Socrates Logos's curator insight, August 14, 2:25 PM

by
Eyal Karzbrun, Alexandra M. Tayar, Vincent Noireaux, Roy H. Bar-Ziv

"The assembly of artificial cells capable of executing synthetic DNA programs has been an important goal for basic research and biotechnology. We assembled two-dimensional DNA compartments fabricated in silicon as artificial cells capable of metabolism, programmable protein synthesis, and communication. Metabolism is maintained by continuous diffusion of nutrients and products through a thin capillary, connecting protein synthesis in the DNA compartment with the environment. We programmed protein expression cycles, autoregulated protein levels, and a signaling expression gradient, equivalent to a morphogen, in an array of interconnected compartments at the scale of an embryo. Gene expression in the DNA compartment reveals a rich, dynamic system that is controlled by geometry, offering a means for studying biological networks outside a living cell."

 http://bit.ly/1qaF0k3

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Limits on fundamental limits to computation

An indispensable part of our personal and working lives, computing has also become essential to industries and governments. Steady improvements in computer hardware have been supported by periodic doubling of transistor densities in integrated circuits over the past fifty years. Such Moore scaling now requires ever-increasing efforts, stimulating research in alternative hardware and stirring controversy. To help evaluate emerging technologies and increase our understanding of integrated-circuit scaling, here I review fundamental limits to computation in the areas of manufacturing, energy, physical space, design and verification effort, and algorithms. To outline what is achievable in principle and in practice, I recapitulate how some limits were circumvented, and compare loose and tight limits. Engineering difficulties encountered by emerging technologies may indicate yet unknown limits.

 

Limits on fundamental limits to computation
Igor L. Markov
Nature 512, 147–154 (14 August 2014) http://dx.doi.org/10.1038/nature13570


Via Complexity Digest
ComplexInsight's insight:

Discussion of limits is key to creating new ideas - Igor Markov's paper is worth reading for exploring lmitations and engineering implications and to trigger off new discussions and ideas. Worth reading.

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Internet of Things Gains Real World Traction - Automation World

Internet of Things Gains Real World Traction - Automation World | Complex Insight  - Understanding our world | Scoop.it
E&T magazine Internet of Things Gains Real World Traction Automation World More than many other such pronouncements, this statement, made by Jim Robinson of Intel's Internet of Things Group, during a panel discussion at National Instruments' NI...
ComplexInsight's insight:

While IoT is going  through its peak on the hype cycle - stories such as this from Airbus regarding instrumenting the entire production process highlight many of the possibilities. As with any long term technology change, IoT is better described and extrapolated from  the small deploymnent stories that indicate its real future. as opposed to the analyst and booster hype. 

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Are fish far more intelligent than we realize?

Are fish far more intelligent than we realize? | Complex Insight  - Understanding our world | Scoop.it
They don't have a three-second memory. And one researcher thinks we've been dramatically underestimating their intelligence all along.
ComplexInsight's insight:

Culum Brown's research into fish behaviour is deeply revealing both for the insights into aquatic life and into human prejudice regarding other species capabilities.  Good article on vox.com regarding fish sentience, perception and behavioural evolution - worth reading.

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Artificial Life 14

Artificial Life 14 | Complex Insight  - Understanding our world | Scoop.it

ALIFE 14, the Fourteenth International Conference on the Synthesis and Simulation of Living Systems, presents the current state of the art of Artificial Life—the highly interdisciplinary research area on artificially constructed living systems, including mathematical, computational, robotic, and biochemical ones. The understanding and application of such generalized forms of life, or “life as it could be,” have been producing significant contributions to various fields of science and engineering.
This volume contains papers that were accepted through rigorous peer reviews for presentations at the ALIFE 14 conference. The topics covered in this volume include: Evolutionary Dynamics; Artificial Evolutionary Ecosystems; Robot and Agent Behavior; Soft Robotics and Morphologies; Collective Robotics; Collective Behaviors; Social Dynamics and Evolution; Boolean Networks, Neural Networks and Machine Learning; Artificial Chemistries, Cellular Automata and Self-Organizing Systems; In-Vitro and In-Vivo Systems; Evolutionary Art, Philosophy and Entertainment; and Methodologies.

 

Artificial Life 14

Proceedings of the Fourteenth International Conference on the Synthesis and Simulation of Living Systems

Edited by Hiroki Sayama, John Rieffel, Sebastian Risi, René Doursat and Hod Lipson

http://mitpress.mit.edu/books/artificial-life-14


Via Complexity Digest
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I remember reading the first one of these and my imagination being captured by Chris Langton's introduction. Look forward to reading this one.

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Gigantic Ocean Vortices Seen From Space Could Change Climate Models | Science | WIRED

Gigantic Ocean Vortices Seen From Space Could Change Climate Models | Science | WIRED | Complex Insight  - Understanding our world | Scoop.it
Enormous vortices of water, measuring 60 miles across, spin their way across the sea at a deliberate pace---3 miles per day.
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The role of the oceans is often misrepresented in climate discussions. The discovery of large scale migrating eddies and their potential impact on transportation of nutriends, dissolved carbon dioxide and heat may change our understanding of ocean health and weather. Awesome science article on Wired Science explaining how the phenomenon was discovered and some of the questions it raises - worth reading.

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Quantitative Temporal Viromics: An Approach to Investigate Host-Pathogen Interaction: Cell

Quantitative Temporal Viromics: An Approach to Investigate Host-Pathogen Interaction: Cell | Complex Insight  - Understanding our world | Scoop.it

A systematic quantitative analysis of temporal changes in host and viral proteins throughout the course of a productive infection could provide dynamic insights into virus-host interaction. We developed a proteomic technique called “quantitative temporal viromics” (QTV), which employs multiplexed tandem-mass-tag-based mass spectrometry. Human cytomegalovirus (HCMV) is not only an important pathogen but a paradigm of viral immune evasion. QTV detailed how HCMV orchestrates the expression of >8,000 cellular proteins, including 1,200 cell-surface proteins to manipulate signaling pathways and counterintrinsic, innate, and adaptive immune defenses. QTV predicted natural killer and T cell ligands, as well as 29 viral proteins present at the cell surface, potential therapeutic targets. Temporal profiles of >80% of HCMV canonical genes and 14 noncanonical HCMV open reading frames were defined. QTV is a powerful method that can yield important insights into viral infection and is applicable to any virus with a robust in vitro model.


Via burkesquires
ComplexInsight's insight:

Understanding protein change during virus-host interaction offers opportunities for new diagnostics, treatments and clear understanding of how specific viruses interact and manipulate signalling pathways and immune defenses. QTV offers a lot of promise for researchers and practitioners.

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Machined Learnings: Stranger in a Strange Land

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Good article on the differences between big data processing and HPC simulations. Worth reading to see where the two communities focus, worry about and can learn from one another.

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Imagining the Post-Antibiotics Future — Editor’s Picks — Medium

Imagining the Post-Antibiotics Future — Editor’s Picks — Medium | Complex Insight  - Understanding our world | Scoop.it
A few years ago, I started looking online to fill in chapters of my family history that no one had ever spoken of.
ComplexInsight's insight:

Maryn McKenna has consistenly written about the threat of increasing antibiotic resistance for some time and her articles in Wired and other media are worth finding and reading. This is her long form essay on medium, it covers some of the same ground as her other articles it is still very much but its worth reading and reflecting on. 

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Eli Levine's curator insight, April 30, 5:41 PM

It seems that we are about to get closer to death, as our antibiotics, pesticides, herbicides and all other methods of cheating death, disease and crop failure fail.

 

This is before we get into conversations about the looming international and intranational conflicts that are simmering beneath the surface.  At least these can be dealt with with sensible policy changes and changes in attitude, perspective and disposition, if not out right content in our leadership cadres.

 

But alas, I don't see that happening in the foreseeable future.

 

Time is ticking away.

 

And we too will go through an indiscriminate die off phase where friends and family will die off, along with enemies and pestilential people as well.

 

I'd like to think that we'd come off better than before.

 

But, that's the thing about these indiscriminate methods of killing large swaths of the population.  It very rarely yields anything other than what was already present.

 

At least wages should be better, due to the new shortage of laborers (assuming that robots haven't taken over our labor force in the meantime).

 

I'd like to think that our lot is constantly improving, even during these negative phases.

 

But, I know that it's not going to be easy, especially for most of our Western and American population who don't have experience handling these kinds of things.

 

Ah well.

 

Think about it.

 

 

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What Comes After Antibiotics? 5 Alternatives to Stop Superbugs

What Comes After Antibiotics? 5 Alternatives to Stop Superbugs | Complex Insight  - Understanding our world | Scoop.it
"Superbug" bacterial infections that are resistant to common antibiotics are increasing at an alarming rate. But traditional antibiotics aren't the only way to battle dangerous germs. Biomedical scientists are investigating new additions to their arsenal.
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Given the WHO announcement that antibacterial resistance is now a global threat - article on popular mechanic outlines some of the alternate treatments to antibiotics.

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Oracle Cranks Up The Cores To 32 With Sparc M7 Chip

Oracle Cranks Up The Cores To 32 With Sparc M7 Chip | Complex Insight  - Understanding our world | Scoop.it
Say what you will about Oracle co-founder and CEO Larry Ellison, but when the software giant bought Sun Microsystems more than four years ago, for $7.4 bil
ComplexInsight's insight:

It has often been easy to forget following the acquisition of Sun by Oracle - Oracle have continued investing in hardware. The new M7 chip line with 64 sparc cores and Numa interconnect options not only continues to promise speed increases for existing oracle customers but also shows benefits over off the shelf clusters of highly integrated large core systems using optimised connection architectures. Good in depth article - worth reading.

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How CDC Uses Antibiotic Resistance Data - Food Safety News

How CDC Uses Antibiotic Resistance Data - Food Safety News | Complex Insight  - Understanding our world | Scoop.it
Food Safety News How CDC Uses Antibiotic Resistance Data Food Safety News Over the past year, you may have noticed that antimicrobial resistance information has been incorporated in the outbreak reports put out by the Centers for Disease Control...
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CDC are one fo the organisations leading information release on antimicrobial resistance. This article explaines where to find out more info from CDC on this area. Worth reading.

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Do-It-Yourself Biology? Messing Around with DNA Increasingly a Garage-Band Venture

Do-It-Yourself Biology? Messing Around with DNA Increasingly a Garage-Band Venture | Complex Insight  - Understanding our world | Scoop.it

Via Socrates Logos
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Socrates Logos's curator insight, August 13, 12:15 PM

by

Glen Martin
"Silicon is so passé. Those who are truly au courant in the coding world are working with carbon—specifically DNA, that most ancient and elegant of codes. Such biohacking is central to the rapidly expanding field of synthetic biology, a term that somehow seems a little threatening to many of us who are the products of the old fashioned kind of biology that’s been around since the planet first managed to gin up a few primitive prokaryotes 3.5 billion years ago.
That’s especially because messing around with DNA is increasingly a garage band kind of venture. The basic techniques and technology are now sufficiently disseminated so that any reasonably bright and inquisitive person can do all kinds of interesting things in a home or community lab. And—gulp—might that not include weaponizing Ebola or involve some other highly anti-social endeavor?
Relax (really). Those fears are overblown, opines Nina DiPrimio, the editor of BioCoder, a quarterly published by and for the DIYbio (as in, Do It Yourself biology) community.
 In the first place, says DiPrimio, endowing viruses with new and ever-more-lethal characteristics requires the kind of equipment and skill sets usually found only in large government or corporate labs. Second, if anyone wants to attempt it, the mischief-maker wouldn’t need to figure out how to manipulate Ebola or HIV. Relatively simple procedures already are known for weaponizing basic old anthrax, or manufacturing and distributing astoundingly powerful poisons such as ricin, or—well, you get the idea.
“It takes a lot of skill and equipment to do bad things” with gene-spliced microbes says DiPrimio, until recently a postdoctoral researcher at UC Berkeley and the co-organizer of the university’s Synthetic Biology Super Group. “A DNA cloning class won’t teach you how to create something pathogenic. That isn’t to say potential dangers should be ignored. At a certain point, regulation (of homegrown biohacking) is likely. We don’t know what that will look like, but the community is aware of it and discussing it.”
DiPrimio is also deeply concerned about safety within these do-it-yourself operations. BioCoder’s articles include pointers to ensure one’s lab is legal, and emphasize basic protocols so tyro researchers don’t burn, blow up or electrocute themselves. But first and foremost, the publication serves as an agora for the biohacking community...."
http://bit.ly/1ywJmX7

BTW have a look to the paper about the Leukippos  - a SynBio Lab in the cloud  in BioCoder:
http://bit.ly/1skwvZu
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First ever biological amplifier created by Imperial scientists

First ever biological amplifier created by Imperial scientists | Complex Insight  - Understanding our world | Scoop.it

cientists have made an amplifier to boost biological signals, using DNA and harmless E. coli bacteria.

 Conventional amplifiers, such as those that are combined with loudspeakers to boost the volume of electric guitars and other instruments, are used to increase the amplitude of electrical signals. Now scientists from Imperial College London have used the same engineering principles to create a biological amplifier, by re-coding the DNA in the harmless gut bacteria Escherichia coli bacteria (E. coli). 
Via Socrates Logos
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Socrates Logos's curator insight, August 14, 3:08 PM

by Gail Wilson

"Scientists have made an amplifier to boost biological signals, using DNA and harmless E. coli bacteria.

Conventional amplifiers, such as those that are combined with loudspeakers to boost the volume of electric guitars and other instruments, are used to increase the amplitude of electrical signals.
Now scientists from Imperial College London have used the same engineering principles to create a biological amplifier, by re-coding the DNA in the harmless gut bacteria Escherichia coli bacteria (E. coli). 

The team say this ‘bio-amplifier’ might be used in microscopic cellular sensors , which scientists have already developed, that could detect minute traces of chemicals and toxins, to make them more sensitive. Ultimately, this could lead to new types of sensors to detect harmful toxins or diseases in our bodies and in the environment before they do any damage.
In laboratory tests, the team’s bio-amplifier was able to significantly boost the detection limit and sensitivity of a sensor designed to detect the toxin arsenic. The device is also modular, which means that the devices can be easily introduced in different genetic networks, and can potentially be used to increase the sensitivity and accuracy of a broad range of other genetic sensors to detect pathogens and toxins.
The results of the study are published in the journal Nucleic Acids Research. 
Dr Baojun Wang, who is now based at the University of Edinburgh, but carried out the study while in the Division of Cell and Molecular Biology at Imperial, said: “One potential use of this technology would be to deploy microscopic sensors equipped with our bio-amplifier component into a water network. Swarms of the sensors could then detect harmful or dangerous toxins that might be hazardous to our health. The bio-amplifiers in the sensors enable us to detect even minute amounts of dangerous toxins, which would be of huge benefit to water quality controllers.”
Scientists have previously known that cells have their own inbuilt amplifiers to first detect and then boost biological signals, which are crucial for survival and reproduction. They have been attempting to understand how they work in more detail so as to remodel them for other applications. However the challenge for scientists has been engineering a device that can predictably amplify signals without distortion or feedback.
In the study, scientists first re-engineered genes involved in a special cell network called hrp (hypersensitive response and pathogenicity), which have naturally occurring amplifying proteins that function just like an electronic amplifier. They then cloned these amplifying components and inserted them into the harmless gut bacteria E. coli, fitting it with a synthetic arsenic input sensor and a fluorescent green protein gene as the output.  ..."


http://bit.ly/Yadvkb

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Transcriptic Aims to Make the Biology Lab Programmable - Bio-IT World

Transcriptic Aims to Make the Biology Lab Programmable - Bio-IT World | Complex Insight  - Understanding our world | Scoop.it
Bio-IT World
Transcriptic Aims to Make the Biology Lab Programmable
Bio-IT World
At a time when monkeys are exerting telepathic control over mechanical limbs, most biologists still don't have access to robotics for even the simplest procedures.
ComplexInsight's insight:

Transcriptic is an awesomely promising start up - that aims to provide automated execution of different lab protocols.  Intersting article at Bio-IT World. If you are interested in the future of weblab work and how it connects to synthetic biology and bio discovery - well worth reading.

 

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Canada to give WHO Ebola vaccine

Canada to give WHO Ebola vaccine | Complex Insight  - Understanding our world | Scoop.it

Following the WHO decision that it was ethical to use untested drugs on Ebola patients if it gave them a possibility of recovery, Canada says it will donate up to 1,000 doses of an experimental Ebola vaccine to help battle the disease's outbreak in West Africa.

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Dinosaurs shrank for 50 million years to become birds - life - 31 July 2014 - New Scientist

Dinosaurs shrank for 50 million years to become birds - life - 31 July 2014 - New Scientist | Complex Insight  - Understanding our world | Scoop.it
The meat-eating theropod dinosaurs shrank 12 times in a row, going from over 200 kilograms to less than a kilogram, until they were small enough to fly
ComplexInsight's insight:

Evidence in a study by  Mike Lee of the South Australian Museum in Adelaide and colleagues has shown that a gradual wave of evolution led theropods to evolve into modern birds. Great article from New Scientist on Mike Lee's research work.

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A World Cup Visitor: Polio from Africa in Brazil | Science Blogs | WIRED

A World Cup Visitor: Polio from Africa in Brazil | Science Blogs | WIRED | Complex Insight  - Understanding our world | Scoop.it
The World Health Organization announced on Monday that a polio sample was collected in March at Viracopos International Airport in Campinas, which is about 60 miles outside Sao Paulo, and is where many of the World Cup teams have been landing. The agency said no cases of polio have been identified and there is no evidence the disease has been transmitted.
ComplexInsight's insight:

Another awesome article by Maryn Mckenna, highlighting the interconnectedness of our health ecossystem as polio virus from Afric is found in a Brazilian sewer. The possible vector - visitors for the world cup. Article very worth reading.

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Cellular traffic control system mapped for the first time

Cellular traffic control system mapped for the first time | Complex Insight  - Understanding our world | Scoop.it

Cells regulate the uptake of nutrients and messenger cargos and their transport within the cell. This process is known as endocytosis and membrane traffic. Different cargos dock onto substrate specific receptors on the cell membrane. Special proteins such as kinases, GTPases and coats, activate specific entry routes and trigger the uptake of the receptors into the cell. For their uptake, the receptors and docked cargos become enclosed by the cell membrane. In the next steps, the membrane invaginates and becomes constricted. The resulting vesicle is guided via several distinct stations, cellular organelles, to its final destination in the cell.

 

For her study, Dr. Prisca Liberali, senior scientist in the team of Professor Lucas Pelkmans, sequentially switched off 1200 human genes. Using automated high-throughput light microscopy and computer vision, she could monitor and compare 13 distinct transport paths involving distinct receptors and cellular organelles. Precise quantifications of thousands of single cells identified the genes required for the different transport routes. Surprisingly, sets of transport routes are co-regulated and coordinated in specific ways by different programs of regulatory control.

 

Subsequently, Dr. Liberali calculated the hierarchical order within the genetic network and thereby identified the regulatory topology of cellular transport. "The transport into the cell and within the cells proceeds analogously to the cargo transport within a city" describes the scientist. "Like in a city, the traffic on the routes within a cell and their intersections is tightly regulated by traffic lights and signs to guide the cargo flow."

 

Thanks to this unique quantitative map, the fine regulatory details of transport paths and processes within a cells could be mapped for the first time. Particularly the genes that encode for these traffic lights and switches are often de-regulated in disease. With this map, it is now possible to predict how this leads to traffic jams in the cells, causing the disease phenotype. Alternatively, since many drugs have been developed to target these traffic lights and switches, the map can be used to come up with possible drug combinations to target unwanted traffic, such as viruses, to the waste disposal system of the cell.


Via Dr. Stefan Gruenwald, burkesquires
ComplexInsight's insight:

Mapping the fine regulatory details of transport paths and processes within cells is key to understanding gene and protein functions, cancer, viral interactions and potential treatments.  Interesting read.

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VIZBIplus - Visualizing the Future of Biomedicine

VIZBIplus - Visualizing the Future of Biomedicine | Complex Insight  - Understanding our world | Scoop.it
Community Resource for the VIZBI conference series on computer methods for visualizing biological data, including genomes, protein sequences, phylogenies, macromolecular structures, systems biology, microscopy, and magnetic resonance imaging.
ComplexInsight's insight:

If you are fortunate enough to be in Sidney on the 29th of May this is a must not miss event. David Goodsells illustrations have inspired a generation of scientists and artists, His watercoloured biological illustrations directly influenced some of the leading biomedical animators including Drew Berry and team and helped fire imaginations and understanding of molecular machinery. Really hoping VIVID sydney record this and make the recording available at a later date. Pure Awesome.

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The Gigaom interview: Why synthetic biology and the Netflix model are the future of medicine

The Gigaom interview: Why synthetic biology and the Netflix model are the future of medicine | Complex Insight  - Understanding our world | Scoop.it
Life is a programming language, and molecular biologist Andrew Hessel thinks that it will be increasingly available to anyone interested in designing with the building blocks of life.
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Good article on Autodesk's Project Cyborg and update from some of the research coming out of Autodesk's Bio/Nano research group.

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WHO | WHO’s first global report on antibiotic resistance reveals serious, worldwide threat to public health

New WHO report provides the most comprehensive picture of antibiotic resistance to date, with data from 114 countries
ComplexInsight's insight:

Resistance to antibiotics poses a "major global threat" to public health, says a new report by the World Health Organization (WHO).

The WHO team analysed data from 114 countries and said resistance was happening now "in every region of the world". The report describes a "post-antibiotic era", where people die from simple infections that have been treatable for decades.

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