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Comment: I'd actually like to get one of these watches... (Score 1) 129

by aussie.virologist (#47402799) Attached to: Android Wear Is Here

...wait, wait, wait hear me out.

I work in a BSL2+ lab where obviously I can't take my phone out and answer calls etc. But what I've always wanted is a notification band that is relatively low profile, that I can wear on the inside of my wrist. I just need it to let me know who is calling and scroll SMS messages so that I can tell if it is an emergency that needs to be addressed immediately. It takes a bit of time to de-gown and decontaminate before leaving the lab to deal with missed calls and I tend to waste a bit of time during the day replying to calls and SMS messages that were just not that urgent. It's only a matter of time before it'll be possible to get a 5-day working week out of the battery life and hopefully the construction will handle decontamination with mild disinfectants. I'm very close to giving the Galaxy Gear Fit a try as it seems to be close what I'm looking for, but I'm not so sure about battery life. It doesn't seem to be getting good reviews either. I'll be getting something eventually, but I think it's going to take a little longer for manufacturers to iron out the kinks. Cheers.

Comment: Re:There are other applications (Score 2) 291

by aussie.virologist (#45295279) Attached to: GPUs Keep Getting Faster, But Your Eyes Can't Tell

Aren't there are other areas of science that a faster GPU benefits namely structural biology and the modeling proteins?

Absolutely, I run complete atomistic molecular dynamics simulations of viruses that cause disease in humans (enterovirus simulations around the 3-4 million atom mark). Five years ago I had to use a supercomputer to model 1/12 of a virus particle which barely scraped into the nanosecond range. I'm now able to run complete virus simulations on my desktop computer (Tesla C2070 and Quadro 5000) and I get 0.1ns/day or on my 2U rack (4x Tesla M2090) with 2 viruses running simultaneously at almost 0.2ns/day. That's using the last generation of nVidia cards (Fermi), I should in theory be able to almost double that with the new Kepler cards. I will be VERY interested to see how the next ?Maxwell architecture pans out in the future. I can see a time in the not to distant future when I can model multiple instances of virus-drug interactions on-site here in the lab and get results overnight that I can compare with our "wet lab" results. I use NAMD for the simulations which works well with the CUDA cards.

Comment: This has been suspected for some time... (Score 5, Interesting) 202

by aussie.virologist (#45197929) Attached to: Finnish Team Makes Diabetes Vaccine Breakthrough

There is a significant body of literature attempting to associate the onset of type 1 diabetes with infection by members of the species B enteroviruses, specifically CVB's (Coxsackieviruses B1 to B6) , if you search pubmed you will find hundreds of manuscripts. The problem has been nailing down a definitive causal relationship, from my understanding it is thought that there may be an element of molecular mimicry involved in the disease (or something similar). Essentially the virus infects the host and damages specific parts of the pancreas, the host's immune system mounts a response to the insult, but in the process creates antibodies that target the hosts own islet cells, resulting in the autoimmune disease that is type 1 diabetes. The problem of definitively implicating CVB's for type 1 diabetes is similar in some ways to that of other enterovirus infections like Polio. Basically there are other host mediated issues at play but with Polio you are able to detect the virus around the time of infection, with diabetes the disease presents after the infection has been cleared, complicating matters. To this day we still don't understand why only about 1% of people infected with Polio will develop paralysis, whilst the majority of people ~95% will show no significant signs of illness. Host factors are really important and not fully understood, there may even be a role for certain bacteria in the gut assisting the infection!
As a side note there has been some recent rumblings about the possibility of viral infections triggering transient type 2 diabetes, I can't link to any papers at the moment (too busy at work) but if anyone is interested I can have a dig around later.
Hopefully the vaccine is able to account for the amount of drift in the enterovirus genome that occurs at up to ~1% per annum, a similar problem exists with the new enterovirus 71 vaccine, an emerging bug similar in presentation to Polio.

Comment: This would be awesome with curved screens... (Score 1) 125

by aussie.virologist (#44505371) Attached to: John Carmack Joins Oculus VR As CTO
...That way you could cover your peripheral vision. Imagine being in a darkened VR room with "something else" somewhere in the building and you keep seeing movement out the corner of your eye. I remember playing Doom 3 for the first time in a pitch black room with the surround sound cranked,it was the first game that made my arm hairs stand on end, VR would be awesome. I'd love to explore my 3D atomic virus models with this as well, it would make measuring and observing subtle changes so much easier. Awesome work guys, bring it on.

Comment: Re:This could be good... (Score 2) 79

by aussie.virologist (#43618555) Attached to: LLNL/RPI Supercomputer Smashes Simulation Speed Record

Hey thanks "ratbag" for your kind words. The work that Barnes et al. are doing is so important for researchers like us. It opens the door for us to answer questions in a manner that even 5 years ago was considered "ambitious" to say the least. I am very lucky to be in a position where I have access to resources that allow me to explore new ways of answering some very old questions about how viruses behave, with the added bonus that we may hopefully be able to contribute to making the world just a little bit better. Fingers-crossed.

"jkflying" I started off by working in electronics engineering when I left school, funnily enough I was running a company with some friends designing and building robotics systems, mainly focusing in animatronics. I wanted to start using my robotics background to work in the development of prosthetic limbs, but ended up changing the focus of my undergrad from anatomy and physiology to pathology, specifically microbiology with a lot of biochemistry thrown in. My post-grad was in computational biology. I actually started doing the simulation work after playing around with the tutorials on the VMD/NAMD website at the University of Illinois. I would recommend doing them, it's great nerdy fun and it gets you thinking about the different ways that you apply the techniques.

Have a great day:)

Comment: Re:This could be good... (Score 2) 79

by aussie.virologist (#43617305) Attached to: LLNL/RPI Supercomputer Smashes Simulation Speed Record
Agreed, at this point we are looking at virus dynamics in response to drug binding events and gross alterations in conformational structure in response to significant changes in temperature and ionic content. So for these simulations, the longer the better. I dream of a day when we can model complex host cell interactions and hopefully I will a grey bearded old man still full of enthusiasm when these sort of simulations are considered "run of the mill". Your work helps to keep me excited about the future of HPC and how it can benefit not only my research, but humanity's understanding of the world as a whole. Cheers.

Comment: This could be good... (Score 4, Interesting) 79

by aussie.virologist (#43615527) Attached to: LLNL/RPI Supercomputer Smashes Simulation Speed Record
I'd be interested in seeing if this system could run our full Poliovirus simulations (consisting of around 3.5 million atoms). I've run our simulations on the BlueGene/Q at VLSCI using 32,768 cores (65,536 threads) and have been getting a very respectable 11.2 nanoseconds per day of simulation data using NAMD. Some data on our full virus simulations can be found here... (VIDRL supercomputer simulation page). Hey Lank, maybe you can help me figure out a way to crack the millisecond mark for our full-virus sims??? Great work and cheers from down under :-)

Comment: Re:Meteorite composition? (Score 1) 111

by aussie.virologist (#43255819) Attached to: Meteor Streaks Over American East Coast
Cool, thanks SternisheFan, good ol' wiki :) I wonder if it would be possible to record the spectra of light being emitted and then match other meteors with the same spectral pattern. If the fragments that have been hitting lately all have the same colour pattern it may imply that they came from a single source. It's probably already being done, I'm a virologist not an astronomer so I don't know about these things. Surely we have enough high quality "scopes" recording what is going on in the upper atmosphere to compare data. Cheers.

Comment: Meteorite composition? (Score 1) 111

by aussie.virologist (#43255655) Attached to: Meteor Streaks Over American East Coast
I noticed a lot of the comments saying that the tail was blue/green with a white/ yellow explosion. Is there anyone in the know who can comment if this gives an indication of the meteorites' composition. Green maybe indicating copper content, yellow maybe Sulfur? If so can you use the colour of tail upon entry to identify meteorites that have the same colour as being of the same origin? Just thinkin'

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