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Bio-Linux 6 ~ Bioinformatics made Simple

Bio-Linux 6 ~ Bioinformatics made Simple | Complex Insight  - Understanding our world | Scoop.it
Bio-Linux is an operating system set up for bioinformatics with a vast number of programs pre-installed. It can be obtained for free from the NERC Environmental Bioinformatics Centre. You can obtain a USB drive from NERC and boot from that ...

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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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bioinformatics-databases

bioinformatics-databases | Complex Insight  - Understanding our world | Scoop.it
Bioinformatics - Databases
ComplexInsight's insight:

Dr.Stefan Gruenwalds scoop-it list of bioinformatics databases is an essential resource for anyone looking to discover which datasets are available and accessible. Awesome.

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Rescooped by ComplexInsight from Information, Complexity, Computation
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Polar Swarms

Polar Swarms | Complex Insight  - Understanding our world | Scoop.it
A new theory can explain the formation of swarming patterns observed in ensembles of self-propelled polar particles.

Via Eugene Ch'ng
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Eugene Ch'ng's curator insight, April 13, 5:27 AM

How do individual animals form swarms, schools, and flocks? In the 1990s, physicists modeled collections of self-propelled particles (so-called “active matter”) and could simulate the ordering that occurs in animal flocks.  Theoretical models have reproduced many aspects of this collective behavior, but a number of questions have persisted. One concerns the observation that in polar, active matter—think of a collection of small, mutually interacting swimming arrows—the particles organize themselves into three possible pattern classes: density waves, solitary waves (solitons), and traveling “droplets.”

No single theory has been able to explain the formation and diversity of these patterns. However, in a paper in Physical Review Letters, Jean-Baptiste Caussin and collaborators from institutes in France, Germany, and the Netherlands, have solved a hydrodynamic model of polar active particles and have accounted for the origin and variety of these propagating swarm structures...

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The Surprising Gut Microbes of African Hunter-Gatherers | Science | WIRED

The Surprising Gut Microbes of African Hunter-Gatherers | Science | WIRED | Complex Insight  - Understanding our world | Scoop.it
In Western Tanzania tribes of wandering foragers called Hadza eat a diet of roots, berries, and game. According to a new study, their guts are home to a microbial community unlike anything that's been seen before in a modern human population -- providing, perhaps, a snapshot of what the human gut microbiome looked like before our ancestors figured out how to farm about 12,000 years ago.
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The race to contain West Africa's Ebola outbreak (Wired UK)

The race to contain West Africa's Ebola outbreak (Wired UK) | Complex Insight  - Understanding our world | Scoop.it
Digital volunteers are racing to map regions in West Africa where the Ebola virus, which has a 90 percent fatality rate, continues to spread
ComplexInsight's insight:

The use of OpenStreetMap (OSM) as an unifying geodata system is increasing in humanitarian aid. The current Ebola outbreak in West Africa is a challenge at multiple levels for teams trying to coordinate a response. Due to years of war there are few up to date maps in the region and multiple boundaries mean different groups are collecting data. Digital volunteers creating new OSM entries will be a key asset in enabling health officials to manage the outbreak and hopefully bring things under control.

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The world’s most endangered food

The world’s most endangered food | Complex Insight  - Understanding our world | Scoop.it
Many varieties of fruit, meat and vegetable are disappearing from our plates, says Rachel Nuwer. Why is this happening, and can we stop the rot?
ComplexInsight's insight:

 Its probably not often we stop to think of the impacts of agriculture on the evolution of foodstuffs and what varieties of plants are being lost, along with their distinct tastes, benefits and properties. Compared to pre 1900 agriculture an estimated 75% of global farmed plant diversity is now gone and lost. Diversity is key to sustainable agriculture over the long term, so the points made in the article are particularly worrying. Thought provoking article from the BBC / worth reading.

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Researchers warn against the rise of “big data hubris”

Researchers warn against the rise of “big data hubris” | Complex Insight  - Understanding our world | Scoop.it
Use Google Flu Trends as an example of how things go wrong.
ComplexInsight's insight:

Good article on risks of interpreting large scale data mining using google flu trends as an example. The conclusion that often data indications are a first point of a process that then requires scientific grunt work to identify if a given correlation is actually relevant or not and that reality is sometimes the grunt work wont be done because its hard, requires funding and takes time. Worth reading.

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Three Impediments to the Internet of Things | VentureFizz

Three Impediments to the Internet of Things | VentureFizz | Complex Insight  - Understanding our world | Scoop.it
Three Impediments to the Internet of Things - blog post by Walter Dick of Ascent Venture Partners
ComplexInsight's insight:

 Walter Dick believes the major impediments  for IoT are:

 

1. Networks are not up to Par..

2. Security needs to improve

3. Batteries need innovating

 

Not sure I agree 100% on his top 3 but they are certainly contributing factors. Companies like Blackberry and Nokia Oyj (the parent company of the phone manufacturer recently purchased by Microsoft) are incredibly well placed to deliver IoT in terms of network and security and have expertise for power management. Unfortunately  Blackberry is not focused on IoT much at all and is beset with its own problems. I am more hopeful on Nokia Oyj / now they have hived off the phone business they retained the networking infrastructure and mapping divisions along with the expertise in power electronics. It would be interesting to see them pioneer in the IoT area as they once did with mobile phones...  

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The Best Science and Engineering Visualizations of 2013 - Wired Science

The Best Science and Engineering Visualizations of 2013 - Wired Science | Complex Insight  - Understanding our world | Scoop.it
Science and art don't intersect nearly as often as they should, but when they do, the results can be an astonishing blend of expression and fact. These are the best science and engineering visualizations from 2013.
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Multiple sclerosis link to food bug

Multiple sclerosis link to food bug | Complex Insight  - Understanding our world | Scoop.it

A food poisoning bacterium may be implicated in MS, say US researchers.

ComplexInsight's insight:

Lab tests in mice by the team from Weill Cornell Medical College revealed a toxin made by a rare strain of Clostridium perfringens caused MS-like damage in the brain. And earlier work by the same team, published in PLoS ONE, identified the toxin-producing strain of C. perfringens in a young woman with MS. However experts urge caution, saying more work is needed to explore the link. Click on title or image to go the story.

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Researchers develop a longer, stronger cotton fiber - Texas A&M Univ (2014)

Researchers develop a longer, stronger cotton fiber - Texas A&M Univ (2014) | Complex Insight  - Understanding our world | Scoop.it

An international collaboration... has figured out how to make a longer cotton fiber... could potentially have a multi-billion-dollar impact on the global cotton industry and help cotton farmers fend off increasing competition from synthetic fibers... 

 

"This technology allows improvement of fiber quality in upland cotton, which is widely grown everywhere," said Alan Pepper, an associate professor in the Texas A&M Department of Biology... "This will increase the competitiveness of natural cotton fibers versus synthetic fibers, which have been snagging an increasing amount of the market share every year."

 

The overwhelming majority of cotton harvested in the U.S. and worldwide is upland cotton, or Gossypium hirsutum, with more than 6.5 million acres planted in 2012 in Texas alone... A higher-end cotton called Gossypium barbadense is more desirable because of greater fiber length and strength but is late-maturing, low-yielding and more difficult to grow because it requires dry climates with significant irrigation and is less resistant to pathogens and pests.

 

"For a long time cotton breeders have been trying to develop upland cotton with the fiber qualities ofbarbadense cotton... Globally, everybody's trying to do it. Economically, it's a huge deal, because every millimeter you add to fiber length adds that much to the price of cotton when the farmer sells it." The researchers' method increased the length of the fiber by at least 5 millimeters, or 17 percent, compared to the control plants in their experiment... 

 

The cotton plants developed in the project technically are genetically modified organisms (GMOs)... "What we're doing is a little different," Pepper said. "We're not actually adding in a gene from another species. Rather, we're knocking down the effect of one of the genes that's already in the plant... This was pure basic science, seeking to understand the biological function of a gene... And sure enough, the phytochrome 'knock-down' plants had all these phenotypic changes associated with it [phytochrome], and one of them was longer fiber."

 

The discovery was especially important to Ibrokhim Abdurakhmonov, the lead author of the study who received his master's degree in plant breeding from Texas A&M in 2001 and is now a professor in his native Uzbekistan. The landlocked agricultural nation that borders Afghanistan historically has relied heavily on cotton... Uzbekistan currently accounts for around 10 percent of world cotton fiber exports.

 

"Sustainability and biosecurity of cotton production is pivotal for the Uzbekistan economy because agriculture accounts for 24-to-28 percent of the country's gross domestic product... The increased value of longer and stronger lint, at 10 cents per pound, would be at least $100 per acre more income from the lint for each new cultivar using this technology. New markets for longer, finer, stronger and more uniform cotton lint fiber, as well as early maturity and increased yield potential could further increase estimated economic value. Our anticipation of possible improvement of resistance to abiotic stresses via phytochrome RNA interference further adds to its commercial potential." ... 

 

Press release:  http://www.science.tamu.edu/articles/1157/

Original article:  http://dx.doi.org/10.1038/ncomms4062

 


Via Alexander J. Stein
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Telecommunications data show civic dividing lines in major countries

Telecommunications data show civic dividing lines in major countries | Complex Insight  - Understanding our world | Scoop.it

Many residents of Britain, Italy, and Belgium imagine there to be a kind of north-south divide in their countries, marking a barrier between different social groups and regional characteristics. Now a new study by MIT researchers reveals that such divides can be seen in the patterns of communication in those countries and others.

 


Via Claudia Mihai, Complexity Institute
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4th Student Conference on Complexity Science

4th Student Conference on Complexity Science | Complex Insight  - Understanding our world | Scoop.it

The Student Conference on Complexity Science (SCCS) is the largest UK conference for early-career researchers working under the interdisciplinary framework of Complex Systems, with a particular focus on computational modelling, simulation and network analysis. Since 2010, this conference series has brought together PhD students and early career researchers from both the UK and overseas, whose interests span areas as diverse as quantum physics, ecological food webs or the economics of happiness. This interdisciplinary nature of the conference is reflected by the diversity of keynote speakers as well as practical, hands-on workshops.


The 4th Student Conference on Complexity Science will be held 19-22 August 2014 at the University of Sussex, Brighton, UK.

http://sccs2014.soton.ac.uk


Via Complexity Digest
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Tiny Robot Flies Like a Jellyfish

Tiny Robot Flies Like a Jellyfish | Complex Insight  - Understanding our world | Scoop.it
A new, naturally stable flying robot moves through the air like a jellyfish swims through the water. The robot could be useful for tasks such as air quality monitoring and surveillance.

Via The Robot Launch Pad
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FANTOM

FANTOM | Complex Insight  - Understanding our world | Scoop.it
ComplexInsight's insight:

In our bodies every cell contains the same genetic code, however the active or expressed genes determine cell function.  Which genes are expressed is controlled by tiny bits of the genome called promoters and enhancers and different cell types are determined by different combinations of promoters and enhancers. Now an international consortium of researchers known as FANTOM, led by the RIKEN institute in Japan have created the  clearest map yet of how genes control cells to make our bodies function. The map is already challenging ideas about what our genes do and how they interact and may accelerate the development of gene-based therapies. The team examined more than 800 human tissue samples, covering nearly all cell types, and  found 44,000 enhancers and 180,000 promoters that control gene expression.

 

 

 

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Rescooped by ComplexInsight from Papers
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Towards a Methodology for Validation of Centrality Measures in Complex Networks

Towards a Methodology for Validation of Centrality Measures in Complex Networks | Complex Insight  - Understanding our world | Scoop.it

Our empirical analysis demonstrates that in the chosen network data sets, nodes which had a high Closeness Centrality also had a high Eccentricity Centrality. Likewise high Degree Centrality also correlated closely with a high Eigenvector Centrality. Whereas Betweenness Centrality varied according to network topology and did not demonstrate any noticeable pattern. In terms of identification of key nodes, we discovered that as compared with other centrality measures, Eigenvector and Eccentricity Centralities were better able to identify important nodes.

 

Batool K, Niazi MA (2014) Towards a Methodology for Validation of Centrality Measures in Complex Networks. PLoS ONE 9(4): e90283. http://dx.doi.org/10.1371/journal.pone.0090283


Via Complexity Digest
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Liz Rykert's curator insight, April 15, 7:50 PM

Love this stuff.

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Twins’ immune systems look like those of complete strangers

Twins’ immune systems look like those of complete strangers | Complex Insight  - Understanding our world | Scoop.it
When it comes to our immune response, genetics takes a back seat to pathogens.
ComplexInsight's insight:

Our adaptive immune system, the one that responds to specific pathogens, relies on T cells and B cells. These cells make proteins that have a key job: distinguish between the harmless proteins in all of our cells and foreign proteins that may be harmful. In T cells, these molecules are creatively called T cell receptors (TCRs), and in B cells they are antibodies.

 
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DNA-based logic gates operate inside cockroach cells

DNA-based logic gates operate inside cockroach cells | Complex Insight  - Understanding our world | Scoop.it
The logic units are driven by molecular collisions, not voltage.
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Black death was not spread by rat fleas, say researchers

Black death was not spread by rat fleas, say researchers | Complex Insight  - Understanding our world | Scoop.it
Evidence from skulls in east London shows plague had to have been airborne to spread so quickly
ComplexInsight's insight:

With the exhumation of 25 skeletons, originally buried in the  mid 14th Century scientists in London are discovering new clues which indicate the black death was an pulmonary airborne disease. Good article in the Guardian on the initial findings.

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Big Data & HPC: The Modern Crystal Ball for 2014

Big Data & HPC: The Modern Crystal Ball for 2014 | Complex Insight  - Understanding our world | Scoop.it
ComplexInsight's insight:

Jorge Titinger, CEO of SGI has a good  article on applications of HPC to Big Data including:

 

Graphing and mapping: HPC-powered data mapping and graphing will lead to greater accuracy in business forecastingPattern visualizations: HPC-powered tools will emerge that can provide an intuitive view of complex data sets, enabling rapid identification of relationships for simple analysisScaling in-memory databases: HPC will allow enterprise in-memory systems to handle larger data workloads — allowing closer to complete data sets (over partial sets) to benefit from real-time analytics while in motionMeta-data: The importance of meta-data will jump dramatically — we’ll see enterprises realize leveraging meta-data analytics for virtualization and relational mapping can yield enhanced accuracy, new business insights and even reveal security threats

 

With the advent of on demand compute and cloud based processing it will be interesting to see how the HPC companies continue to differentiate from on demand suppliers such as amazon and microsoft. Jorge's 2014 outlook is interesting and more sane than many big data predictions - certainly worth reading.

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Self-Assembling Molecules Like These May Have Sparked Life on Earth - Wired Science

Self-Assembling Molecules Like These May Have Sparked Life on Earth - Wired Science | Complex Insight  - Understanding our world | Scoop.it
Scientists have discovered building blocks similar to those in modern RNA that can effortlessly assemble when mixed in water and heated.
ComplexInsight's insight:

Easily accessible article on the research of Nicholas Hud and team at Georgia Institute of Technology. Hud's research group are searching for the evolutionary precursor to RNA and after 20 years of research are finding promising results.

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Smallpox: Last refuge of an ultimate killer

Smallpox: Last refuge of an ultimate killer | Complex Insight  - Understanding our world | Scoop.it
If a virus killed millions, why keep it alive? Two places on Earth guard the last vials of smallpox, but Rachel Nuwer finds that they may not be there for long
ComplexInsight's insight:

Good article from the BBC on Smallpox before the World Health Assembly debate destroying the remaining stores at CDC and Vector.

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This Simulation Of The Known Universe Does Not Disappoint

This Simulation Of The Known Universe Does Not Disappoint | Complex Insight  - Understanding our world | Scoop.it
There's the Earth. Annnnnd it's gone. (This simulation of the known universe does not disappoint http://t.co/YuS96HSc2N)
ComplexInsight's insight:

Awesome video that shows our place in the universe as we curently know it. 

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Viruses affect an African flamingo population by killing their bacterial food source

Viruses affect an African flamingo population by killing their bacterial food source | Complex Insight  - Understanding our world | Scoop.it

Trophic cascade effects occur when a food web is disrupted by loss or significant reduction of one or more of its members. In East African Rift Valley lakes, the Lesser Flamingo is on top of a short food chain. At irregular intervals, the dominance of their most important food source, the cyanobacterium Arthrospira fusiformis, is interrupted. Bacteriophages are known as potentially controlling photoautotrophic bacterioplankton. In Lake Nakuru (Kenya), we found the highest abundance of suspended viruses ever recorded in a natural aquatic system. We document that cyanophage infection and the related breakdown of A. fusiformis biomass led to a dramatic reduction in flamingo abundance. This documents that virus infection at the very base of a food chain can affect, in a bottom-up cascade, the distribution of end consumers. We anticipate this as an important example for virus-mediated cascading effects, potentially occurring also in various other aquatic food webs.


Via Chris Upton + helpers, Ed Rybicki
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Rescooped by ComplexInsight from Networks and Big Data
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Mathematical Formulation of Multilayer Networks

Mathematical Formulation of Multilayer Networks | Complex Insight  - Understanding our world | Scoop.it

Describing a social network based on a particular type of human social interaction, say, Facebook, is conceptually simple: a set of nodes representing the people involved in such a network, linked by their Facebook connections. But, what kind of network structure would one have if all modes of social interactions between the same people are taken into account and if one mode of interaction can influence another? Here, the notion of a “multiplex” network becomes necessary. Indeed, the scientific interest in multiplex networks has recently seen a surge. However, a fundamental scientific language that can be used consistently and broadly across the many disciplines that are involved in complex systems research was still missing. This absence is a major obstacle to further progress in this topical area of current interest. In this paper, we develop such a language, employing the concept of tensors that is widely used to describe a multitude of degrees of freedom associated with a single entity.

Our tensorial formalism provides a unified framework that makes it possible to describe both traditional “monoplex” (i.e., single-type links) and multiplex networks. Each type of interaction between the nodes is described by a single-layer network. The different modes of interaction are then described by different layers of networks. But, a node from one layer can be linked to another node in any other layer, leading to “cross talks” between the layers. High-dimensional tensors naturally capture such multidimensional patterns of connectivity. Having first developed a rigorous tensorial definition of such multilayer structures, we have also used it to generalize the many important diagnostic concepts previously known only to traditional monoplex networks, including degree centrality, clustering coefficients, and modularity.

We think that the conceptual simplicity and the fundamental rigor of our formalism will power the further development of our understanding of multiplex networks.

 


Via Claudia Mihai, Complexity Institute
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ECCS'14 European Conference on Complex Systems

ECCS'14 European Conference on Complex Systems | Complex Insight  - Understanding our world | Scoop.it

ECCS’14 will be a major international conference and event in the area of complex systems and interdisciplinary science in general. It will offer unique opportunities to study novel scientific approaches in a multitude of application areas. Two days of the conference, 24 and 25 of September, are reserved for satellite meetings, which will cover a broad range of subjects on all aspects of Complex Systems, as reflected by the conference tracks.

 

ECCS'14 European Conference on Complex Systems

Lucca, Italy

2014-09-22:26

http://www.eccs14.eu


Via Complexity Digest
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António F Fonseca's curator insight, January 16, 9:02 AM

The major conference in Complex Systems this year will be held in Lucca.