Daily Archives: May 17, 2017

FREMONT, Calif., May 15, 2017 Penguin Computing, provider of high performance computing, enterprise data center and cloud solutions, today announced support for Singularity containers on its Penguin Computing On-Demand (POD) HPC Cloud and Scyld ClusterWare HPC management software.

Our researchers are excited about using Singularity on POD, said Jon McNally, Chief HPC Architect at ASU Research Computing. Portability and the ability to reproduce an environment is key to peer reviewed research. Unlike other container technologies, Singularity allows them to run at speed and scale.

Weve long desired to support containers in our public HPC cloud, but the most adopted technology of our users was Docker, said Will Cottay, Director of Cloud Solutions at Penguin Computing. For loosely coupled applications in a virtual or private environment Docker is great, but it doesnt scale up to supercomputers. Singularity provides the flexibility of containers with the security and scalability needed for tightly coupled HPC workflows. Were very grateful to Greg Kurtzer with the High Performance Computing Services group at Lawrence Berkeley National Laboratory for inventing and developing Singularity.

Penguin Computing customers are able to build and run Singularity containers on their in-house HPC resources and run the same container on POD, ensuring the same application and OS environment. Entire workflows can be built into a container enabling both bursting and replication for disaster recovery.

Since Singularity supports the import or direct execution of Docker images, users can use their existing Docker assets, or leverage others work. A single command will download and run an image from a Docker Hub repository.

Penguins POD team is maintaining a public GitHub repository of specification files to make it easy for users to build containers tuned for HPC clusters.

Penguin Computing also now ships Singularity with Scyld ClusterWare 7 HPC management software. Earlier this year Penguin Computing announced Scyld ClusterWare 7 as the companys latest version of its HPC provisioning software, enabling support of large scale clusters with enhanced functionality for clusters ranging to thousands of nodes.

Visit https://pod.penguincomputing.com/documentation/Singularity for information and documentation about Singularity on POD.

Visit http://singularity.lbl.gov for more information about Singularity.

About Penguin Computing

Penguin Computing is one of the largest private suppliers of enterprise and high performance computing solutions in North America and has built and operates the leading specialized public HPC cloud service Penguin Computing On-Demand (POD). Penguin Computing pioneers the design, engineering, integration and delivery of solutions that are based on open architectures and comprise non-proprietary components from a variety of vendors. Penguin Computing is also one of a limited number of authorized Open Compute Project (OCP) solution providers leveraging this Facebook-led initiative to bring the most efficient open data center solutions to a broader market, and has announced the Tundra product line which applies the benefits of OCP to high performance computing. Penguin Computing has systems installed with more than 2,500 customers in 40 countries across eight major vertical markets. Visit http://www.penguincomputing.com to learn more about the company and follow @PenguinHPC on Twitter.

Source: Penguin Computing

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Penguin Computing Announces Support for Singularity Containers on POD HPC Cloud and Scyld ClusterWare - HPCwire

Brain balls sound like something straight out of a Tim Burton movie: starting as stem cells harvested from patients, they eventually develop into masses of living neurons, jumbled together in misshapen blobs.

Just like the developing brain, these neurons stretch and grow, reaching out skinny branches that grab onto others to form synapsesjunctions where one neuron talks with the next.

And they do talk: previous attempts at growing these brain organoids found that they spark with electrical activity, much like the webs of neurons inside our heads that lead to thoughts and memories.

Theyre creepy. Theyre fascinating. And they may be neuroscientists best bet at modeling developmental disorders like autism in a dish.

Last week, two studies published in the prestigious journal Nature argued for brain balls as a reductionist model for broken brains. In one study, scientists took skin cells from patients with Timothy syndrome, a devastating neurodevelopmental disorder that often ends with childhood death, and grew them into brain balls to study where and how the developing brain veered off track.

In a separate paper, researchers used cutting-edge technology to profile the inhabitants of brain balls as they matured for eight months in a dish. Heres a creepy teaser: some blobs contained retinal neurons that normally allow us to see. Brain balls with eyes?!

As bizarre as that sounds, the fact that brain balls can develop a variety of neuron types with densely packed synapses is a win. Because theyre made from human cells, brain balls may eventually mimic diseases like schizophrenia, autism, or Alzheimers better than mouse models, revealing what went wrong and offering ample test grounds for potential treatments.

Weve never been able to recapitulate these human-brain developmental events in a dish before, says Dr. Sergiu Pasca at Stanford, who led the Timothy syndrome study. Our method lets us see the entire movie, not just snapshots.

Brain balls, better known by their scientific name cerebral organoids, first came onto the neurodevelopmental scene in 2013.

They often begin their short life as run-of-the-mill skin cells. Scientists first transform them back into stem cells. Then, using a chemical concoction of nutrients and signaling molecules, the stem cells are pushed to spontaneously assemble into little Frankenstein blobs of brain tissue.

But the process isnt just random bursts of division and growth. Rather, the way the brain balls mature roughly echoes how a fetuss cortex develops in the womb: the outer edges curl inward, forming outer and deeper layers.

What really sparked scientists interest was this: almost 90 percent of the neurons within a brain ball had active synapses, often spontaneously shooting electrical pulses to others in their network. While scientists believe brain balls arent capable of thinkingthe high-level cognitive processes constantly churning in our headstheyre definitely doing something.

To begin getting some answers, Dr. Paola Arlotta and team at Harvard followed a number of brain balls for nine months as they gradually maturedroughly the amount of time for human gestation, and much longer than any previous attempts.

Periodically, the researchers harvested more than 80,000 brain balls and ran sophisticated genetic tests to figure out their gene expression profile. Like law enforcement using DNA to match a perpetrators identity, this allowed researchers to profile the inhabitants of the organoids.

It was a cellular bonanza: as expected, excitatory neurons and non-neuronal cells called glia both made an appearance. More surprising were inhibitory neurons that dampen network activity, and cells that normally form the corpus callosum, a highway that connects the brains two hemispheres.

But creepiest by far, every single type of retinal cell also made an appearance. Although they couldnt really see in the normal sense, when bathed under light they did fire off electrical signals.

Just like a developing brain, the older they got the more complex the brain balls became. At eight months old, they contained roughly the same density of synapses as a human fetus cortex.

The cells connect witheach other, forming circuits, and once theyre connected, they can synchronize their activity, potentially mimicking higher-order functions of the human brain, says Arlotta.

Thats great, because it means mini brains could be used to study how different types of neurons connect with each other, and how disrupting the process leads to developmental problems.

Thats the direction the second study took. Rather than letting the mini brains grow wild, Pasca and team at Stanford tweaked the protocol to force them into different identities.

As a fetus brain grows, it gradually separates into an outer layer chock full of excitatory neurons, and an inner sanctum where inhibitory neurons reside. A big part of brain wiring is inhibitory neurons reaching out towards the surface and hooking up with their respective partners.

Starting from skin cells collected from patients with Timothy disease, the scientists used distinct chemical concoctions to form two batches of brain balls, each roughly 1/16 of an inch across and containing one million cells. One batch contained mostly inhibitory neurons, mimicking deeper brain regions, whereas the other modeled the cortex.

The spheroid cells were remarkably similar to those from corresponding regions of the human fetal brain, says Dr. J. Gray Camp and Dr. Barbara Treutlein at the Max Planck Institute in Germany, who were not involved in the studies.

The team then stuck the two types of brain blobs together into the same dish, and as expected, the inhibitory ball started nudging its way into the cortical one, until the two fused together.

As it turns out, the inhibitory neurons from Timothy patients were terrible migrants. Rather than smoothly slithering their way into the mesh of excitatory partners, they stuttered, stopped, but somehow ended up much further than theyre supposed to go, as if making up for their inefficiency.

The problem seemed to be the faulty neurons themselves, rather than defective signals from the environment. When researchers fused a Timothy inhibitory ball with a healthy excitatory one, they still fumbled without heads or tails.

But surprisingly, when treated with a chemical normally used for high blood pressure, the Timothy balls calmed down and migrated normally.

Spheroids are opening up new windows through which we can view the normal development of the fetal human brain, says Pasca. More importantly, it will help us see how this goes awry in individual patients.

While the scientists dont know whether the same drug could help babies with Timothy after theyre bornand their basic brain wiring already establishedPasca hopes that there may be a window of opportunity later on in life to correct the misguided migration.

All said, brain balls are an extremely reductionist model of the human brain. Although its hard to say whether the root of Timothy disease is faulty inhibitory neuron migration, its a great place to start looking for answers.

Pasca is rushing to speed up the process of growing spheroids, hoping to develop a giant depository harvested from many patients to screen for drugs that steers them towards a normal developmental path.

Others are a bit more cautious. These new studies show that brain balls whipped up from the same patient or patients with the same disease can express very different genes, warned Camp and Treutlein. The problem is likely more prominent in neurodevelopmental disorders like autism, in which the cause is a lot more heterogeneous.

But the fact that brain organoids behave like actual brains on several fundamental functionsmaking connections, spontaneously firing, responsive to external cuesis promising, so much so that theyre sparking intense ethical debates. Can they eventually see or think? Do they feel? Will consciousness spontaneously emerge without us detecting it?

For now, the mini brains are simply too tiny for higher-level thinking. Only time will tell what theyll eventually become, and how much information these mini brains can provide, says Camp and Treutlein.

Image Credit:PascaLab

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Bizarre Mini Brains Offer a Fascinating New Look at the Brain - Singularity Hub

Uber has shaken up the taxi industry and is trying to put driverless cars on our roads. Now the company aims to have flying ride-sharing vehicles in our skies by 2020.

Uber is not alone in working towards flying cars. But is this realistic, or just marketing hype?

To many of us, the concept of flying cars is synonymous with the future, just like silver jumpsuits and gourmet food in the form of a pill. Those dreams have not yet materialized, so what about flying cars?

The classic idea of a flying car was just that: a car that could somehow fly.

In fiction, the author Ian Fleming was a fan of flying cars, writing his novel Chitty Chitty Bang Bang around the concept in 1963. He also included a flying car in his James Bond novel (1964) and subsequent film, The Man with The Golden Gun. These concepts are based on a car with wheels that can drive on the road but is also capable of flying when required.

Science fiction writers and directors have often dispensed with the need to have future vehicles ever drive on the road. Instead, the cars are simply small aircraft such as the one Anakin Skywalker used in the Star Wars film Attack of the Clones.

The recent flying car announcements vary in type from single-seat, multi-copter drone-type aircraft, to road-style cars that turn into light aircraft and small flying boats that hover above the water.

It would appear that almost any small flying vehicle capable of transporting a person is now referred to as a flying car. But clearly, they are really just a kind of small aircraft.

Any potential passenger will want to know: How safe is this contraption?

The likely answer right now is not very safe," as with all early-stage technology. Companies are working feverishly to make their aircraft safe enough in the hope of convincing regulators and governments that the vehicles can be entrusted with human lives.

But there are incredible safety challenges. One of the biggest is what to do when things go badly wrong.

With a normal car, you can often just slow to a halt and stop. But a flying car might fall out of the sky, killing not only its occupants but potentially bystanders too.

The Chinese company Ehang is proposing to equip its flying car service in Dubai with a parachute. This service will apparently take a single occupant from the roof of one Dubai skyscraper to the roof of another.

Should the parachute deploy, it is not clear whether the vehicle will have any way to control where it lands, or how safely.

In the existing aviation industry, much of the mechanics of flying is automated. Given the challenges of a person flying compared to driving a car, and the efforts to reduce human error in aviation, there is even more likelihood of flying cars becoming automated so that no human pilot is needed.

But there will be differences between existing aviation practice and flying cars. Passenger jet air travel owes much of its impressive safety record to improvements in aircraft maintenance procedures and our understanding of failures. It is unlikely that the business case for small flying cars will allow for such rigorous practices.

Instead, flying cars will be less complex than modern jets, and the latest demonstrators show exactly that.

The use of large numbers of small electric motors, such as in the Lilium all-electric aircraft, reduces the maintenance complexity drastically. It also provides an inbuilt measure of redundancy in case one motor fails.

Wouldnt it be great to avoid the traffic and public transport congestion of our major cities? We think so.

For example, it currently takes 23 minutes to drive the 19km from our offices in Brisbane to the domestic airport when traffic is freely flowing.

If we could fly from our office roof (and there is a pad on our roof that is ideally suited to deploying a flying car), the trip would only take 8 minutes.

Wed get a double boost, first from flying at an average speed of (say) 100kmh, and second by taking the straightest path, a mere 13km.

This example journey is well within the capabilities of the flying cars being demonstrated today.

Of course, it may be that authorities mandate we stick to flight corridors reserved for flying cars, so a direct route is not always an option. These corridors may be strategically located over low-risk areas of land that have minimal population.

There are lots of things about flying cars that are hard, but some problems may become easier.

There is a lot more space available for cars when you have access to three dimensions for travel, as long as the navigation challenges are solved.

Using the several hundred meters of space above the ground means you can potentially have a lot less traffic congestion. You also dont need to build and maintain expensive road infrastructure.

For self-driving flying cars, moving into the sky actually makes some aspects of planning and traffic control easier.

It is too early to know how the economics of flying cars will work.

Given the huge regulatory hurdles, the safety issues to overcome, and the lack of special infrastructure to support flying cars (such as take-off and landing areas and charging points for the all-electric aircraft), it is difficult to estimate what a trip should cost.

The current non-flying car ride-sharing companies such as Uber appear to be operating at a massive loss.

The price paid by the consumer in an Uber vehicle is reported to be on average less than half the actual cost of the trip, but the company is hoping to recoup some of these costs by implementing driverless cars. Given that theres even more chance that flying cars will be driverless, maybe the economics will be favorable.

What would a consumer be willing to pay to possibly get to their destination in half the time? Theres at least one famous historical example in Concorde that posed that same question, and had safety issues. Sadly, its supersonic passenger flights are not available any more.

There is still so much to do before flying cars can become common. The technology has come a long way, mainly due to the rapid development of drones. But the technology of the flying machine itself is just one part of a very complex system.

Like ground-based self-driving cars, its likely that if they ever happen, flying cars will occur in certain priority areas first.

Imagine a cheaper but still expensive option for high-level executives, such as the Dubai proposal.

For the rest of us, we may already be walking around in silver jumpsuits and eating meals in a pill before we get to ride in a flying car.

This article was originally published on The Conversation. Read the original article.

Image Credit:Shutterstock/Pavel Chagochkin

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The Future of Flying Cars: Science Fact or Science Fiction? - Singularity Hub