On 25 Sep 2012, at 18:01, Jesse Becker wrote:
> The .2bit FASTA[1] format specifically compresses the ACGT data into
> 2 bits (T:00, C:01, A:10, G:11), plus some header/metada information.
> Other formats such as 'VCF' specifically store variants against known
> references[2]. The current *hum
That is something I am more then happy to setup and host for this
community. A blog would be perfect to write articles or link to articles
and have a summary on the page and others can post comments to discuss the
topic or otherwise.
On Tue, Sep 25, 2012 at 11:00 PM, Andrew Holway wrote:
> Hello
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On 17/09/12 07:52, Jeffrey Rossiter wrote:
> I am getting started on a cluster building project at my
> university. We just replaced all of our lab machines so I am going
> to be using the old machines to rebuild our cluster.
I'd suggest that you als
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On 23/09/12 00:25, Vincent Diepeveen wrote:
> Oh comeon i've been over there myself
Please do not send replies to private emails back to the Beowulf list.
- --
Christopher SamuelSenior Systems Administrator
VLSCI - Victorian Life Sciences
> assuming or projecting any background in bio. I stand by my claim that even
> 2TB is absurd to expect a tiny, 6 hour long-living device to push via USB,
not to be argumenative, but 93 MB/s is feasible with USB3 ;)
___
Beowulf mailing list, Beowulf@be
On 09/25/2012 10:01 PM, Mark Hahn wrote:
>> you're talking about around 90MB/s to process, and at 30TB now we're
>> talking about near to 1.4GB/s to process.
>
> I think you're mixing up the two (radically different) approaches.
> the old short-read systems are definitely more data (and reassembly)
>> According to this article, raw sequence can take up between 2-30 TB,
>> and a processed one 1.5 GB. (Disclaimer: I only read the executive summary)
>
> At 2TB and a 6 hour lifespan for this thing to pull in the genome,
512 pores, each 15 bp/second, totalling "about" 7500 bp/sec
or 1875 bytes/s
>> not particularly large (say .5G raw data from the device lifespan.)
>>
> Where did you get that data-point from? I've been told a single genome
> sequence takes up about 6 GB of data, and I think that's after it's been
> processed.
I took it from the referenced article. yes, various organisms
Jim Lux
-Original Message-
From: Robert G. Brown [mailto:r...@phy.duke.edu]
Sent: Tuesday, September 25, 2012 1:44 PM
To: Lux, Jim (337C)
Cc: Per Jessen; beowulf@beowulf.org
Subject: Re: [Beowulf] electricity prices
On Tue, 25 Sep 2012, Lux, Jim (337C) wrote:
> I'm going to assume tha
Am 25.09.2012 um 12:19 schrieb Andrew Holway:
>
> Im pretty sure faulty hardware is the root cause of out fault
> tolerance problems :). In any case the main issue seems to be the loss
> of a chunk of your application memory when the node fail not so much
> the retransmission of messages. MPI has
Jim,
Without wanting this to become an energy forum.
Price is way higher than industry gets it for here - seems it's
variable prices - most producing industry uses a constant amount
of energy with their machines however, so doesn't need to pay the
high variable price quoted there.
Next to Be
On Tue, 25 Sep 2012, Lux, Jim (337C) wrote:
> I'm going to assume that the data is some sort of bulk average over
> all industrial consumers.. And the prices are remarkably low (are they
> subsidized?)
>
> Does it include "distribution costs"..
>
> For instance, here in Southern California, my all
-Original Message-
From: beowulf-boun...@beowulf.org [mailto:beowulf-boun...@beowulf.org] On
Behalf Of Igor Kozin
Sent: Tuesday, September 25, 2012 8:16 AM
To: Bogdan Costescu; Beowulf Mailing List
Subject: Re: [Beowulf] value of parallel programming experience (was:
Checkpointing using
I'm going to assume that the data is some sort of bulk average over all
industrial consumers.. And the prices are remarkably low (are they subsidized?)
Does it include "distribution costs"..
For instance, here in Southern California, my all-in price for the next kWh is
anywhere from $0.11 to $0
Hi Ellis,
if we are to believe the video on the page John pointed to then the
membrane indeed processes both DNA strands. You will probably want to
have a second read anyway in order to improve reliability. We can only
guess what's their signal to noise ratio is.
Igor
> I do wonder however if the
On Sep 25, 2012, at 5:44 PM, Hearns, John wrote:
>
> It is not so much about parallel programming experience but about
> scientific software development career path. Quite often parallel
> skills are needed anyway. A former colleague and a good friend of mine
> explains it quite nicely here:
>
>
On Tue, Sep 25, 2012 at 12:33:49PM -0400, Igor Kozin wrote:
>stored as characters (1 byte per char) the genome is ~ 3 GB. you could
>use two bits to represent the four letter alphabet but probably nobody
>does that. better yet, you can store only the difference against a
>known reference genome or
On 09/25/2012 12:33 PM, Igor Kozin wrote:
> "this thing" does only ~ 1/20 of the genome. you have to pay quite a
> bit more for your full genome which makes it comparable (price-wise)
> with other technologies. hopefully in a few years time it'll get
> cheaper.
> stored as characters (1 byte per ch
"this thing" does only ~ 1/20 of the genome. you have to pay quite a
bit more for your full genome which makes it comparable (price-wise)
with other technologies. hopefully in a few years time it'll get
cheaper.
stored as characters (1 byte per char) the genome is ~ 3 GB. you could
use two bits to
It is not so much about parallel programming experience but about
scientific software development career path. Quite often parallel
skills are needed anyway. A former colleague and a good friend of mine
explains it quite nicely here:
http://software.ac.uk/blog/2012-04-23-work-scientific-software-
Forgive me for posting yet another article.
I think it is relevant, as after all Beowulf is all about putting COTS
components to work doing HPC.
http://www.zdnet.com/inside-facebooks-lab-a-mission-to-make-hardware-open-source-704557/
John Hearns | CFD Hardware Specialist | McLaren Racing Lim
On 09/25/2012 11:17 AM, Prentice Bisbal wrote:
> Where did you get that data-point from? I've been told a single genome
> sequence takes up about 6 GB of data, and I think that's after it's been
> processed.
>
> According to this article, raw sequence can take up between 2-30 TB,
> and a processed
On 09/25/2012 10:02 AM, Mark Hahn wrote:
>> Talking about Raspberry Pi, I saw this mentioned on a Pi forum:
>>
>> http://www.gizmag.com/minion-disposable-dna-sequencer/21513/
> talk about non-sequitur!
>
>> Woudl anyone want to comment? What impact wlll a $900 sequencer have?
> I'm not sure price
It is not so much about parallel programming experience but about
scientific software development career path. Quite often parallel
skills are needed anyway. A former colleague and a good friend of mine
explains it quite nicely here:
http://software.ac.uk/blog/2012-04-23-work-scientific-software-e
On 09/25/2012 08:19 AM, Ellis H. Wilson III wrote:
>
> On a related note (I assume a majority of your users are scientists),
> regarding your or somebody else's post a bit back about how poor
> scientists are at coding -- I've witnessed the exact opposite. Now,
> this is going on limited experien
> Talking about Raspberry Pi, I saw this mentioned on a Pi forum:
>
> http://www.gizmag.com/minion-disposable-dna-sequencer/21513/
talk about non-sequitur!
> Woudl anyone want to comment? What impact wlll a $900 sequencer have?
I'm not sure price or accessibility is what holds back DNA today.
yo
On 09/24/2012 12:57 PM, Andrew Holway wrote:
>> Haha, I doubt it -- probably the opposite in terms of development cost.
>>Which is why I question the original statement on the grounds that
>> "cost" isn't well defined. Maybe the costs just performance-wise, but
>> that's not even clear to me w
Talking about Raspberry Pi, I saw this mentioned on a Pi forum:
http://www.gizmag.com/minion-disposable-dna-sequencer/21513/
Woudl anyone want to comment? What impact wlll a $900 sequencer have?
The contents of this email are confidential and for the exclusive use of the
intended recipient.
2012/9/24 Justin YUAN SHI :
> I think the Redundant Memory paper was really mis-configured. It uses
> a storage solution, trying to solve a volatle memory problem but
> insisting on eliminating volatility. It looks very much messed up.
http://thebrainhouse.ch/gse/silvio/74.GSE/Silvio's%20Corner%20
I'm aware of this website. I don't know their intentions. They are
one of the first you can find with google.
For households this website lists 22.08 cents for Netherlands. Yet i
pay 4.4 cents here above 10k kWh usage. How's that possible?
If you don't know how to negotiate you lose your mone
Vincent Diepeveen wrote:
> Oh comeon i've been over there myself - everyone knows that this
> bunker has a max of a couple of hundreds of kilowatt of very expensive
> electricity. 4.3 cents the article quotes. That's what i pay in this
> office as well.
According to this table, a kilowatthour is
On Thu, 20 Sep 2012, Prentice Bisbal wrote:
I have a good one: generate a mandelbrot fractal. It's interesting
because you can see it move through iterations faster as you add more
processors to it. Of course, this means you need to ssh into the head
node from a system with X-windows, and be abl
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