castanyes blaves

Random ramblings about some random stuff, and things; but more stuff than things -- all in a mesmerizing and kaleidoscopic soapbox-like flow of words.



Latitude ON Reader and Ready

Latitude ON Reader... - Page 3 - Notebook Forums and Laptop Discussion
Reader = Software (Linux) booting from HDD where you can access contacts and email stored in outlook. NO internet connectivity.... but includes the internal antenna wiring required for internet connectivity if you upgrade to the latitudeON hardware.

LatitudeON = Additional hardware used to run the Linux environment. Can connect to the internet via wifi / WWAN / Ethernet ... can connect to more email account than just outlook... Includes web-browser.

Ready = The motherboard in your machine has a socket to support the latitudeON hardware.


GPU closer to general-purpose computing

AMD unleashes open-source 3D code • The Register
AMD has released "the fundamental Linux code" needed to develop open-source 3D-acceleration drivers for its R600 and R700 ATI graphic-processors series.
OpenCL - Wikipedia, the free encyclopedia
AMD has decided to back OpenCL (and DirectX 11) instead of its now deprecated Close to Metal (aka Stream) framework.[5][6] RapidMind announced their adoption of OpenCL underneath their development platform, in order to support GPUs from multiple vendors with one interface.[7] Nvidia announced on December 9, 2008 to add full support for the OpenCL 1.0 specification to its GPU Computing Toolkit.[8]

If there is one characteristic about the computing world it would be that there are so many idle hands in bedrooms in front of cheap PCs nowadays that, no matter how imaginative you are about new developments, somebody has already put such idle hands to work on it. But these idle hands need foundations, tools to use in their tweaking and hacking. This is why the GCC toolchain and Linux kernel were of such importance a decade ago for the Googles, Yahooes and Facebooks of today. In another turn of the crank, the SETI@home and related "@home" projects took advantage of all those juicy idle CPUs from all those cheap PCs to enable new developments never imagined before. And now there is another opportunity: juicy *G*PUs in combination with juicy CPUs. Why is the announcement by AMD so important? Well, when you release the full 3D documentation for these mighty GPUs, you are providing all those bedrooms with a lot of new tools to play around with. And it seems OpenCL may have been approved in time to lay down a spec that everybody builds on. Will see. Interesting...


The mighty power of *escaped* beaver...

BBC NEWS | England | Escaped beaver fells river trees
Escaped beaver fells river trees



Git for Emacs

Magit - I Still Know What You Learned Last Summer
Magit is a spectacular Emacs add-on for interacting with git. Magit was designed with git in mind (unlike VC mode, which is a more generic utility), so git commands map quite straightforwardly onto Magit commands. M-x magit-status tells you about the current state of your repo and gives you one-key access to many common git commands. However, what really sold me on Magit was its patch editor, which completely obsoletes my use of git add, git add --interactive, and git add --patch. If Magit had this patch editor and nothing else, I would still use it. That's how great this is



Linux versus Mac vs Windows graphics

Slashdot | Linux 2.6.28 Promises Year-End Presents
Maybe I'm misunderstanding your assertion, but hasn't MacOS X had universal GPU RAM management for many years? I don't think MS has any monopoly on this... it was my impression that it was just Linux that was on Microsoft's heels playing catch-up.

Yes you are misunderstanding, and NO the Mac has not...

OS X uses the 3D GPU as a bitmap composer for the display, and that is it.

OS X's composer is years behind most Linux desktop composers as well as Vista's DWM/Aero. Vista's DWM for example is Vector/Bitmap based, and works with the WDDM of Vista that gives it a lot of power. (WDDM is the new driver model in Vista)

Here are some of the things Apple needs to add to catch up to even Vista.

- GPU RAM Virtualization/sharing (something kind of like what they are trying do with the Intel chipsets and Linux in this article - except Vista does this over the AGP/PCI bus with any Video card and works with or without dedicated GPU VRAM.

- GPU Scheduler - In Vista, the OS, not the applications controls the GPU, and Vista brings pre-emptive multi-tasking to the GPU. (And no this is not like OpenGL applicaiton yielding/cooperative multitasking, as DirectX also does what OpenGL does. This is an OS level management system that opens up a new way of thinking beyond one 3D application on screen at a time concepts that don't depend on applications yielding the GPU. Kind of like the move to the 32bit era where the Intel CPUs offered a pre-emptive scheduler.

(Example: several games on screen at once in Vista, set transparent with a HD video waterfall playing in the background and losing very few FPS in each game and Aero also using the 3D GPU to do its things, like compose the Game Windows with a transparent waterfall behind them and do a shared texture combine write to the video card.) - This is not something you want to try on a Geforce 5200, but it will work, and on newer video cards, even the 7900 series from Geforce, you can do some really amazing things when running multiple games 'viewable' on the screen at once.

- Legacy application 3D acceleration. Apple tried to get this going with 10.4 as an optional switch, but it was too buggy and scrapped as a feature for 10.5. This means that OS X still renders content using good old fashion legacy 2D GPU features or SSE Intel extensions. On Vista, even Windows 3.1 applications get a performance boost as GDI drawing, Font Rendering, and even internal bitmap APIs are shoved through the 3D GPU because it is significantly faster than older 2D GPU rendering methods.

- Vector composer. On Vista when it is running newer WPF applications, instead of the DWM getting a bitmap that is composed to the final render of the screen, the WPF applications tell the DWM/Aero what changes are made, usually vector based (XAML), and the Vista composer makes the changes at the composer level instead of the application having to redraw the application and send a new bitmap of the Window to the composer to assemble. (This is also why RDP (Remote Desktop) on Vista is faster and more featured than XP, as it works at the DWM level and a lot of the operations sent over the network to render the screen are vector based and lightweight, leaving the client to do the heavy rendering instead of passing bitmaps all the time. This is why you can do Aero Glass and WPF 3D over a slow RDP connection remotely.

Ok, I am going to stop here, as I am writing this off the top of my head and it would better if you would just visit technet at and lookup the Vista WDDM and DWM and WPF technologies.

The whole driver and video changes in Vista were dramatic and borrowed ideas from the XBox 360 development team and do some really impressive things, even though MS didn't put much into the 'cute' uses of it in the UI like they are doing with Windows7.


Linux/*nix also has some good composer technologies that make OS X's composer pretty sad in comparison.

With Linux there are still some major driver and kernel level hurdles


1000 Genomes project, or more?

It turns out that the Solexa machines are getting better at such a pace that the calculations that the 1000 Genomes Project made are no longer true. Under the assumption that the read length and throughput of these NextGen machines would increase in 2008 and 2009, the project was funded enough money to fully sequence 1000 genomes from a panel of diverse ethnicities. The production capacity is currently led by the Sanger Institute, the Beijing Genomics Institute and the Broad Institute, then Baylor and WashU. The MaxPlanck offered to do some production in mid 2008, and Illumina, Roche and ABI are also contributing. Now the machines are better which means that the project is going to aim at even more than 1000 genomes. Where does the money come from? Well, it comes from biomedical research funding, as the aim of the project is to create a deep catalog of human genetic variation that will represent all rare shared variants in our species. This catalog will facilitate biomedical research by enabling the prospection of phenotypes on all the sampled genotypes, and link both to identify the causes of human diseases and traits. Beyond this obvious goal, such a deep sampling of population genomics data will give us great clues on the evolutionary processes that took place in our genome in the last hundreds of thousands of years. Particularly, one will be able to see what are the polymorphism patterns in the chromosomes, and how these correlate with all the genetic features we are getting from another big project, the scale-up ENCODE project. Add to that the comparative genomics information to closely related monkeys to compare divergence vs polymorphism levels, and you have a winner!

Now that we even have a browser for the 1000 genomes project, you can get a snippet of the kind of data the project will produce:;gene=ENSG00000128573;context=200;transcript=ENST00000393489;context=200

Notice the "context=200" argument in GeneSNPView and TranscriptSnpView URLs: some people may mistakenly think that the intronic sequences are depleted of variation when one would expect to have most of the SNPs there: well, they are there, but the context in Gene and Transcript SNP Views restricts intronic SNPs to 100bp left and right to the exon by default. This allows for a more coding-centric view of variations, which according to the Ensembl HelpDesk tickets, is what people working in hospitals around the world really like about this view.

I remember when I joined the Ensembl project three years ago that these new machines were only a rumour, something that was secretly happening in a small science park in Great Chesterford, something that people at that time was dismissing simply as an undelivered promise: "Oh, but I've heard that they can only sequence 25bp pairs...", etc, etc. It's been like that for a lot of other scientific and technological promises:

- like production plug-in electric/hybrid cars -- "Oh, but I've heard that they only have an autonomy of a few miles..."
- inexpensive solar energy on the roof of your house --  "Oh, but I've heard that they only pay after 25 years..."
- your very own robotic butler -- "Oh, but I've heard that it doesn't even know how to make a good latte..."



System notifications

Mark Shuttleworth on system notifications. Interesting read.


BBC iPlayer for Linux

I've tried the BBC iPlayer for Linux this afternoon, and started downloading stuff into my Ubuntu laptop for my Christmas journey.

Word of caution: the player will complain that you have reached the download limit very soon,

unless you go to Settings and define a bigger "Hard disk space allocated".

I haven't found any glitches or problems so far, apart from the fact that one cannot download stuff that is

older than a given date. I wanted to get the full collection of "Stephen Fry in America" but I can only

download the latest one. Ugggh!

Thanks British Broadcasting Corporation for this Christmas gift!

Update: I've been pointed to the wonderful alternative called, which provides even more functionality than the Windows and Mac official players...



The G1 reviewed on the BBC News

BBC NEWS | Programmes | Click | Gadgets to keep you entertained
The G1 is one one of my favourite phones of 2008. OK, it is not the best looking, but the full qwerty keyboard is a joy to use and the trackerball is responsive enough to keep Blackberry fans happy. It allows scrolling without having to put your finger over what you are reading!

Add a smooth responsive touchscreen for all those who wanted an iPhone but just could not bring themselves to jump on Apple's bandwagon and this phone just bleeds control options. It offers speedy connectivity via 3G and wi-fi.

Google maps works a treat with GPS, and satnav is free with no subscriptions or need to buy extra maps that you sometimes find when you go with other suppliers.

Marketplace - the G1's "App Store" - is a mine of free whizzy gadgety apps that are added to on a daily basis.

I downloaded the latest Opera Mini browser (4.2) - a speedy internet browser for mobiles and now I do not miss the pinching action I was able to do with my iPhone to zoom in and out.

When I zoom in on my G1 the text on each page automatically reformats to fit the screen. Nice! The G1 is all about choice.

Whilst Apple's iPhone does things with more style and more glamour, the G1 is a more than capable and fun alternative which will only get more useful each day.



Wrong way to go

Spain proposes tougher laws for immigrants - Yahoo! News
Grappling with rising unemployment and a moribund economy, the Spanish government proposed new immigration rules Friday to limit the influx of immigrants.

The measures, which need Parliamentary approval, would let police hold undocumented aliens longer pending expulsion and make it harder for foreign-born residents to bring relatives over. They are yet another reflection of the dramatic turnabout in Spain's economy

If one discourages immigration, the end result is a worsening economy. Albania, from the de-Stalinization until the end of Enver Hoxha's ruling (1960-1985) is an example of a country where influx of people was null for 25 years, and that didn't work quite well for them...



Merry Christmas!

BBC NEWS | Technology | BBC iPlayer now available on Mac
The BBC has created a version of the iPlayer that works with both Mac and Linux computers.


Production Plug-in Hybrid

BYD F3DM - Wikipedia, the free encyclopedia
The BYD F3DM is a production plug-in hybrid compact sedan for sale December 15th, 2008 in China[1] and 2010 in Europe.[2] The F3DM was introduced at the 2008 Geneva Motor Show. The automaker expects to boost total sales to 350,000 cars next year from an expected 180,000 this year, founder and Chairman Wang Chuanfu told reporters in Shenzhen Dec 15th, 2008. U.S. sales of the F3 DM will likely start in 2011, Wang said.


MySQL landscape

The New MySQL Landscape (by Jeremy Zawodny)
Interesting things are afoot in the MySQL world. You see, it used to be that the MySQL world consisted of about 20-40 employees of MySQL AB (this funny distributed Swedish company that built and supported the open source MySQL database server), a tiny handful of MySQL mailing lists, and large databases were counted in gigabytes not terabytes. A Pentium III was still a decent server. Replication was a new feature!

Hey, anyone remember the Gemini storage engine? :-)

How times have changed...

Nowadays MySQL is sort of a universe onto itself. There are multiple storage engines (though MyISAM and InnoDB are still the popular ones), version 5.1 is out (finally), and the whole company made it over 400 employees before it was gobbled up by Sun Microsystems (a smart move, IMHO, though history will judge that) a while back.

If I had to guess 5 years or so ago what would be interesting to me today about MySQL, I'd have been really, really wrong. The future rarely turns out like we think. Just ask Hillary Clinton.

Here's a little of what's rattling around in the MySQL part of my little brain these days...
Outside Support, Patches, and Forks

The single most interesting and surprising thing to me is both the number and necessity of third-party patches for enhancing various aspects of MySQL and InnoDB. Companies like Percona, Google, Proven Scaling, Prime Base Technologies, and Open Query are all doing so in one way or another.

On the one hand, it's excellent validation of the Open Source model. Thanks to reasonable licensing, companies other than Sun/MySQL are able to enhance and fix the software and give their changes back to the world.

Some organizations are providing just patches. Others, like Percona are providing their own binaries--effectively forks of MySQL/InnoDB. Taking things a step further, the OurDelta project aims to aggregate these third party patches and provide source and binaries for various platforms. In essences, you can get a "better" MySQL than the one Sun/MySQL gives you today. For free.

Meanwhile, development on InnoDB continues. Oh, did I mention the part where they were bought by Oracle (yes, *that* Oracle) a while back? Crazy shit, I tell you. But it makes sense if you squint right.

Anyway, the vibe I'm getting is that folks are frustrated because there's not a lot of communication coming out of the InnoDB development team these days. I can't personally verify that. It's been years since I corresponded with Heikki Tuuri (the creator of InnoDB). So folks like Mark Callaghan of Google have been busy analyzing and patching it to scale better for their needs.

And we all benefit.

Taking things a step further yet, the Drizzle project is a re-making of MySQL started primarily by Brian Aker, who worked as MySQL's Director of Architecture for years. Brian is now at Sun and, along with a handful of others at Sun and elsewhere, is ripping out a lot of the stuff in a fork of MySQL that doesn't get used much, needlessly complicated the code, or is simply no longer needed.

In essence, they're taking a hard look at MySQL and asking what it really needs to provide for a lot of it's uses today: Web and "cloud" stuff. He visited us at Craigslist a few months ago to talk about the project a bit and get our input and feedback. I believe it was that day I joined one of the mailing list and started following what's going on. Heck, I even build Drizzle on an Atom-powered MSI Wind PC regularly.

It's great to see a re-think of MySQL going on... keeping the good, getting rid of the bad, and modularizing the stuff that people often want to do differently (authentication, for example).

It's even better to see the group that's hacking on it. They really have their heads on straight.
Unanswered Questions

Why is all this even necessary? Are the "enterprise" customers and their demands taking focus away from what used to be the core use and users of MySQL? Is Sun hard to work with?

It's clear that both the MySQL and InnoDB teams could be doing more to help. But having worked at a large company for long enough, I realize that things are rarely as simple as they should be.

Will this stuff get integrated back into mainline MySQL? Will Linux distributions like Ubuntu, Debian, and Red Hat pick up OurDelta builds? What about Drizzle?

Will Drizzle hit its target and be the sleek and lean database kernel that MySQL once could have been?

Hard to say.

It's hard to guess what the future holds and too easy to play armchair quarterback about the work of others. But these are question worth wondering about a bit.
What's it all mean?

Nowadays MySQL has a much slower release cycle that it used to. It's still available in "commecial" and free ("community") releases. There's still a company behind it--a much larger one in fact. But one that also has a vested interest in showing how it works better on their storage appliances or 256 "core" computers and whatnot.

Clustering is still very niche. Transactions are not.

Meanwhile, all the cutting edge stuff (at least from the point of view of scaling) is happening outside Sun/MySQL and being integrated by OurDelta and even Drizzle. The OutDelta builds are gaining steam quickly and Drizzle is shaping up.

Heck, I'm hoping to get an OurDelta box or two on-line at work sometime soon. And I'd like to put a Drizzle node up too. I want to see how the InnoDB patches help and also play with the InnoDB plug-in (and its page compression).

The next few years are proving to be far more interesting than I might have expected from a project and technology that looked like was on a track straight for Open Source maturity.

And you know what? I like it.



12.8% and rising

Economic crisis means brisk business for Spanish pawnshops - Yahoo! News
Pawnshops and second-hand stores are doing a brisk business in Spain where the end of a decade-long property boom has pushed the country's unemployment rate to 12.8 percent in October, according to Eurostat, its highest level in over four years and the highest rate in the 27-nation European Union.


Advise which obviously is going to be ignored

BBC NEWS | Technology | Internet Explorer security alert
Users of the world's most common web browser have been advised to switch to another browser until a serious security flaw has been fixed.



Installation Guide

Compiling and Installing GPU-HMMER for Linux

Prerequisites : You will need to have a C++ compiler (assumes g++), a C compiler, and the NVIDIA nvcc compiler in your path. Also take note of where you have installed the CUDA SDK. GPU-HMMER assumes that the CUDA SDK is in the default location (normally ${HOME}/NVIDIA_CUDA_SDK), but if it's not, you'll need to make a couple of changes, described later. GPU-HMMER was designed to support version 2 of the CUDA SDK.

Installation Steps:

1) Download and untar GPU-HMMER from the source archive.

* Get GPU-HMMER from our downloads section.

* tar xvzf GPU-HMMER-0.9.tar.gz

2) Configure and compile GPU-HMMER.

* run configure as you normally would :


* At this point, if you have any non-standard install options you need to apply those to the Makefile in the src directory. In particular, if you need to change the location of the CUDA SDK, you should change src/Makefile to point CUDAINCDIR to your custom location. Also, you can change the number of active sequences by changing CUDADEFS in src/Makefile. If you're using the 8800 GTX Ultra, you shouldn't need to make any changes. Otherwise, you can raise or lower the thread size and block size as your architecture allows. When you're done, build GPU-HMMER from the toplevel directory by executing:


* Make should complete without errors

3) Installing GPU-HMMER.

* You are not required to install the GPU-HMMER binaries in the typical system locations. Instead, GPU-HMMER can be left in-place and will run without errors. For users wishing to perform a true installation, please execute:

make install



NYTProf and mod_perl

'A great new profiler which works with mod_perl - Devel::NYTProf' - MARC
Using it in mod_perl is as easy as adding this to your httpd.conf (before you load any other Perl modules): PerlModule Devel::NYTProf::Apache It is worth starting apache in single process mode otherwise it writes to multiple log files: apachectl -X Once you've finished using your code (in order to generate stats), you can generate the reports with: nytprofhtml -f /tmp/nytprof.$PID.out If you've got your Perl modules in some directory other than the compiled in @INC, you can use:  nytprofhtml -f /tmp/nytprof.$PID.out -lib /path/to/libs I use a framework which autogenerates a number of classes, so I had to edit nytprofhtml to add a few lines in order to initialise my framework before running the report. Try this out - it is super easy, and very very useful


The Economist on netbooks

How to choose a netbook | Small is beautiful | The Economist
STEVE JOBS says Apple does not know how to make a $500 computer “that’s not a piece of junk”.[...]

The most basic model of the Acer Aspire One can be found for £179 in Britain and around $300 in America. It simply switches on and runs with the minimum of fuss. It has 8 gigabytes (GB) of flash storage and 512 megabytes of RAM, which is a bit puny. But that is perfectly adequate to run the customised version of Linux that comes pre-installed on it, along with a suite of software, including Open Office. With no hard drive, and a switch to turn off the wireless connection (not the fastest in the world), power can be conserved. So a bigger, bulkier battery may not be necessary either, unless you want to use the computer untethered for long periods. Because it boots up in a few seconds, rather than thinking of the Acer as a mini laptop it might make more sense to view it as a beefed-up personal digital assistant, such as an old PalmPilot or Psion, but with a better screen and a proper keyboard.



Well-earned victory

FCB demonstrated that they are the new updated Johan Cruiff's team, playing fast with great rhythm and very confident. Well done and all the luck!



Efforts for war vs efforts for peace

Wind, water and sun beat other energy alternatives, study finds
Because the wind turbines would require a modest amount of spacing between them to allow room for the blades to spin, wind farms would occupy about 0.5 percent of all U.S. land, but this amount is more than 30 times less than that required for growing corn or grasses for ethanol. Land between turbines on wind farms would be simultaneously available as farmland or pasture or could be left as open space.

Indeed, a battery-powered U.S. vehicle fleet could be charged by 73,000 to 144,000 5-megawatt wind turbines, fewer than the 300,000 airplanes the U.S. produced during World War II and far easier to build. Additional turbines could provide electricity for other energy needs.



Stephen Fry's gPhone versus iPhone

The New Adventures of Mr Stephen Fry
Without most or all of these requests being implemented Apple will find itself in danger of falling behind. But hell, they know that better than me, and I’m sure they will surprise us with capabilities I haven’t begun to think of. I believe that not only can they now afford to open up but also that they cannot afford not to. Google’s Android is the reason they have to redouble their efforts as we shall see later on.

I disagree with Stephen Fry's comment on Apple's need to open up. I think they cannot afford to open up because their code is what currently makes the iPhone sleeker than the gPhone or other phones. This may not be true at some point, if enough people pick up on the Open Handset Alliance, but right now, Apple simply has better code on a hardware that is not special in any way. This latest statement is also true in some aspects for Apple's laptops and desktop computers. They shifted to Intel processors a few years ago, so now any comparison at the hardware level is trivial, leaving only the smoother corners and slicker mice and keyboards as an excuse. For casual users of personal computers, I agree that Apple has a smoother user experience in today's computers, solely on the basis of their proprietary code. Their hardware is overpriced, to the extend that a 250GBP netbook with a hacked version of OSX Leopard seems pretty functional to me!



If this is a prank, it's a very good one...

Blog of helios: Linux - Stop holding our kids back
This blog is momentarily interrupted to bring you a snippet of recently received email.

"...observed one of my students with a group of other children gathered around his laptop. Upon looking at his computer, I saw he was giving a demonstration of some sort. The student was showing the ability of the laptop and handing out Linux disks. After confiscating the disks I called a confrence with the student and that is how I came to discover you and your organization. Mr. Starks, I am sure you strongly believe in what you are doing but I cannot either support your efforts or allow them to happen in my classroom. At this point, I am not sure what you are doing is legal. No software is free and spreading that misconception is harmful. These children look up to adults for guidance and discipline. I will research this as time allows and I want to assure you, if you are doing anything illegal, I will pursue charges as the law allows. Mr. Starks, I along with many others tried Linux during college and I assure you, the claims you make are grossly over-stated and hinge on falsehoods. I admire your attempts in getting computers in the hands of disadvantaged people but putting linux on these machines is holding our kids back.

This is a world where Windows runs on virtually every computer and putting on a carnival show for an operating system is not helping these children at all. I am sure if you contacted Microsoft, they would be more than happy to supply you with copies of an older verison of Windows and that way, your computers would actually be of service to those receiving them..."

Karen xxxxxxxxx
xxxxxxxxx Middle School



Light concentrator for solar devices

Efficiency records claimed for solar devices : Nature News
Light concentrator promises higher power output.

Katharine Sanderson

A transparent polymer plate has set a new record for concentrating the Sun's light on to a solar cell, boosting the promise of a technology that could lead to vastly improved solar-power capabilities at much cheaper cost.



Performance tools in Linux

[Phoronix] Linux Kernel Performance Counter Subsystem
Thomas Gleixner has proposed a series of patches to the Linux kernel that would (finally) introduced a performance counter sub-system. This sub-system would make it possible to read performance-oriented data off special registers on modern processors such as the number of CPU instructions executed, cache misses, branches mis-predicted, etc.

Thomas describes this proposed performance counter subsystem as being very simple (it only takes a few lines of user-space code to read the counters) but still an extensible design that can implement a full range of features. Also posted on the Linux Kernel Mailing List was a simple monitoring demo. Thomas believes that the design of this subsystem is superior to that of some of the other recent patch sets that add similar functionality. However, there still is quite a bit of work left to be accomplished for this performance counter subsystem. Right now Intel Core 2 and newer CPUs are supported with their performance counting registers, but beyond that there isn't any non-Intel CPU support.


Mountaintop removal for coal

BBC NEWS | Science & Environment | Barack Obama's coal conundrum
The first sight of the impact of US hunger for coal takes the breath away, here at Kayford in West Virginia, there's a yawning chasm where a mountain used to stand.
Open cast sites in Virginia
The coal is accessed by blasting the open cast site

And stretching a dozen barren miles to the horizon there's a series of hills with unnaturally flat tops - their peaks have been blasted off in a type of mining known as "mountaintop removal"

On a flight organised by the conservation charity SouthWings, pilot Susan Lapis tells me she's "horrified" to see how the quest for coal has devastated great tracts of landscape, some estimates suggest that more than 400 tops have been demolished so far.



Engineering and Physical Sciences in Cambridge, UK

BBC NEWS | England | Cambridgeshire | University secures new £6m centre
The University of Cambridge has won £6m funding for a centre aimed at helping create a new generation of scientists.

The Engineering and Physical Sciences Research Council has awarded the funding to the university to set up a new Doctoral Training Centre.

The centre will train students to tackle some of the biggest problems the world faces, the university said.

It will support more than 50 PhD students over the next five years and train them in a range of disciplines.

The centre will be one of 44 training facilities across the UK which will train more than 2,000 PhD students.


PolITiGenomics » Next-Generation Sequencing Informatics
Next-Generation Sequencing Informatics

Below is a table with informatics and IT statistics for the major next-generation/massively parallel sequencing platforms. The information in the table is approximate and should only be used for general, informational purposes.
Next-Generation Sequencing Informatics Statistics
Vendor: Roche Illumina ABI
Technology: 454 Solexa SOLiD
Platform: GS 20 FLX Ti GA GA II 1 2
Reads: 500 k 500 k 1 M 28 M 80 M 40 M 115 M
Read length: 100 200 350 35 50 75 25 35
Run time: 6 hr 7 hr 9 hr 3 d 3 d 4 d 6 d 5 d
Yield: 50 Mb 100 Mb 400 Mb 1 Gb 4 Gb 6 Gb 1 Gb 4 Gb
Images: 11 GB 13 GB 27 GB 500 GB 700 GB 900 GB 1.8 TB 2.5 TB
PA Disk: 3 GB 3 GB 15 GB 175 GB 300 GB 350 GB 300 GB 750 GB
PA CPU: 10 hr 140 hr 220 hr 100 hr 70 hr 100 hr NA NA
SRA: 1 GB 4 GB 30 GB 50 GB 75 GB 100 GB
Read length: 200 2×35 2×50 2×75 2×25 2×35
Insert: 3.5 kb 200 b 200 b 200 b 3 kb 3 kb
Run time: 7 hr 6 d 6 d 8 d 12 d 10 d
Yield: 100 Mb 2 Gb 8 Gb 11 Gb 2 Gb 8 Gb
Images: 13 GB 1 TB 1.3 TB 1.8 TB 3.6 TB 5 TB
PA Disk: 3 GB 350 GB 500 GB 600 GB 600 GB 1.5 TB
PA CPU: 140 hr 160 hr 120 hr 170 hr NA NA
SRA: 1 GB 60 GB 100 GB 150 GB 200 GB

* Units: B - bytes, b - bases
* PA is primary analysis (includes image feature extraction and base calling)
* PA CPU is calculated as the wall clock multiplied by the number of CPU cores
* ABI SOLiD data are representative of a single slide
* ABI SOLiD primary analysis is done on the instrument cluster
* SRA is the size of the files (SFF or SRF) that are submitted to the NCBI Short Read Archive


Perl and property information

I've been playing around with Nestoria, which is a site for property information in the UK and a few other european countries. Nestoria sponsored this years London Perl Mongers Workshop and use Perl and other open source projects as the building blocks for their service. It's all googly-mappy and clean, but most of all, it shows how good visualization makes information a lot useful...



More on partitioning

Whatever....: mysql partitioning
LINEAR HASH partitioning -> This is almost similar to hash partitioning except for the fact that the algorithm used to divide data is different. The syntax is also almost same. We use PARTITION BY LINEAR HASH instead of PARTITION BY HASH.

The algorithm used is :

Given an expression expr, the partition in which the record is stored when linear hashing is used is partition number N from among num partitions, where N is derived according to the following algorithm:

* Find the next power of 2 greater than num. We call this value V; it can be calculated as:
V = POWER(2, CEILING(LOG(2, num)))

* Set N = F(column_list) & (V - 1).

* While N >= num
Set V = CEIL(V / 2)
Set N = N & (V - 1)

The advantage in partitioning by linear hash is that the adding, dropping, merging, and splitting of partitions is made much faster, which can be beneficial when dealing with tables containing extremely large amounts of data. The disadvantage is that data is less likely to be evenly distributed between partitions as compared with the distribution obtained using regular hash partitioning.

KEY partitioning ->
Partitioning by key is similar to partitioning by hash, except that where hash partitioning employs a user-defined expression, the hashing function for key partitioning is supplied by the MySQL server. The syntax used is PARTITION BY KEY instead of PARTITION BY HASH.

In most of the cases either a primary key or an unique key is used to create partitions.

Mysql also supports sub partitioning whereby a partition can be divided into further sub partitions of similar type.



Reboot circadian rhythm

BBC NEWS | Health | 'Time-bending drug' for jet lag
A new cure for jet lag could be on the market in the next few years after trials show a pill can reset the body's natural sleep rhythms.

Tasimelteon works by shifting the natural ebb and flow of the body's sleep hormone melatonin.

In trials, published in The Lancet, the drug helped troubled sleepers nod off quicker and stay asleep for longer.

Experts said the drug would be a welcome alternative to addictive sedatives like benzodiazepines.

Commenting on the work, Dr Daniel Cardinali from the University of Buenos Aires said the findings would be welcomed by millions of people - "shift-workers, airline crew, tourists, football teams, and many others."


Oh Lord!

BBC NEWS | Technology | Apple pushes anti-virus for Macs
Apple has urged Mac owners to use anti-virus software.

In a note posted on its support site in late November, Apple said it wanted to "encourage" people to use anti-virus to stay safe online.

The move is widely seen as a response to the growing trend among cyber criminals of booby-trapping webpages that can catch out Mac users.

Before now Mac users have been largely free of the security problems that plague Microsoft's Windows.



Interesting blog entry

Dual systems « Chris’ Big Bond Blog
Iv’e started to notice a cool tendency in the computer market. It seems like we are moving towards an age of dual systems. One system for mobility and one system for performance.

ASUS and Dell Latitude ON are delivering motherboards with a Linux OS burned into a chip on the motherboard. This way you don’t have to boot into windows if you just want to do some easy surfing or listen to some music. It saves power and increases mobility for laptops.

Lenovo also incorporates this into their Ideapad machine. You get a serious graphics card, wich you can turn on or off as you need it or not. Thereby, you can decide if you want performance or mobility.

This is a very interesting line of thought. I like to be able to have performance only when I need it. I wonder how far this will go. Will you eventually end up having a computer that is actually two computers?


Waiting time for MySQL 5.1

5.1 was released but it looks like it's worth waiting a bit for production ready...


Proudly born and raised in Igualada, or not so much sometimes...

Born and raised in Igualada, in the centre of Catalonia, one of the richest regions in Spain. Although catalans are often associated to wealthy lives, expensive summer holidays and sports cars, at least in Igualada, we have the highest rate of unemployment around, currently above 15%.

Crisi industrial a l'Anoia - Televisió de Catalunya
Crisi industrial a l'Anoia

La comarca de l'Anoia no aixeca el cap i registra una de les taxes d'atur més altes a Catalunya. Sobrepassa el 15% de la població, arriba a 7.500 parats. Actualment, hi ha en marxa molts expedients temporals i indefinits que afecten prop de 900 persones més. La preocupació s'ha traduït avui en manifestació als carrers d'Igualada.


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