Wait a year. I’ll be cheaper.

diskdrive by AlexWitherspoon
The $4400 Genome:
[Via ScienceNOW]

The cost of sequencing an entire human genome continues to plummet. Complete Genomics, a Mountain View, California-based biotechnology company last year claimed it would soon be able to sell full human genome sequences for as little as $5000 apiece. That now appears within reach. In tomorrow’s Science, the company will report that it sequenced three human genomes for about $4400 each, at least in the cost of reagents. Such cheap sequencing could vastly accelerate studies designed to pinpoint genes underlying complex diseases.
[More]

And they claim to be able to do it in a day! I’d like to see how accurate the data is but it does represent a huge decrease in time and money:


The rapid fall in sequencing prices may give genomics an equivalent of Moore’s Law, which describes how the number of transistors on computer chips doubles every 18 months, steadily driving down the cost of computing power. In 2003, the cost of sequencing a human genome was an estimated $300 million. That was down to $1 million in 2007 and $60,000 last year.


It is now dropping about an order of magnitude every 18 months or so. So by the end of next year, we could be looking at $500 genomes. As i said below,
buy stock in hard drive makers.

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Who are they empowering?

They kept the Asian dude but lost the Black guy. And they actually look like they obviously put a White guy’s head on top since the hands are still black!

What a bad Photoshop job. And let’s not even talk about the color scheme. MS marketing needs some real help.

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Weird Internet today

The internet has not been it reliable self recently. I was without Internet service on Friday due to a fire in a datacenter in downtown Seattle. Of course, trying to find out what was going on WITHOUT internet service was quite a chore.

I mean first I had to check my system, since the Verison modem was all green, indicating that it was connected fine. Everything checked out fine on my end.

I tried accessing Verizon via my iPhone. That worked but there was nothing at the Verizon site to explain the service outage, not even at the page called System Service.

So, after digging out an old bill, I found a number for the DSL service. After a fun phone tree, I got a recorded message that service in my area code was out and was expected back online in a few hours.

Which it was, saving me the worry of a July 4th weekend without internet.

Then today, accessing pages using several different browsers was really slow. Some sites would load fine (such as Amazon). Others would load very slowly or timeout before they were loaded. But email worked just fine. And my newsreader (NewsNetWire) was able to get the news feeds from sites that I could not get to directly from my browser!

I figured that perhaps email, using a different protocol, might be able to access the 4 different mail servers I use for different accounts but doesn’t the newsreader was using the same HTTP protocol that the browsers do. Well I’m self-educated so I might be missing something. (I tried playing around with changing DNS servers in case Verizon’s had been hosed but this did not help).

I was able to get Goggle News and see that there were a lot of government servers under a DDOS attack so I made the leap that that might be having some effect. Call it Internet magic.

So, with no real explanation, things have returned to normal. But I hate not knowing why.

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Not good

zune by Joe Attardi
Every 30GB Zune In The World Froze At 2am This Morning [Microsoft]:
[Via Consumerist]

If you’re Steve Jobs, you probably dream of stories like this: Zunes all over the world foze up at around 2am this morning and won’t reboot, and nobody knows why.

ArsTechnica says it seems to have affected all owners of the 30 gig model, and hit no matter what you were doing at the moment:

[More]

This is an epic fail. Not only does something screw up, but it causes the player to crash and just became a brick. And all MS has said is:


Customers with 30gb Zune devices may experience issues when booting their Zune hardware. We’re aware of the problem and are working to correct it. The Zune Social might be slow or inaccessible. Sorry for the inconvenience, and thanks for your patience!


I figure to be zuned will appearon the Urban Dictionary soon.

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Let’s vote on a slot machine

Greater Transparency for Slots Than Voting (Priorities Folks!):
[Via Concurring Opinions]

120px-Slot_machine.jpg
News from Underground has a priceless posting comparing the steps states take to ensure the accuracy and security of slot machines and e-voting machines. Here are some highlights. Nevada requires vendors of slot machines to provide it access to the machines’ software. By contrast, for most states, the source code for e-voting machines remains safely in the hands of vendors with no right of access provided to election officials or the public. A Nevada agency certifies slot machines, and the public has an opportunity to comment on that certification process. Depressingly, a select number of private companies certify e-voting machines at the vendor’s expense and the certification process is deemed a trade secret. Yes, even the certification process is hidden from public view.

The bottom line: the gaming business is subject to greater transparency and accountability than our voting process. It seems wrong, and a bit shameful, to associate a greater sense of responsibility and accuracy to gambling than voting. We care more about money earned through somewhat licentious means than our fundamental right to pick our elected officials in an accurate and secure manner. That seems to be where we are right now, but I have my hopes for the future. More to come on that in 2009. For now, happy holidays CoOp readers!

Maybe we should let the slot machine manufacturers produce out e-voting machines. Sounds like they could bring some valuable experience. I like the irony that the source code from the slot machines has to be open while the makers of voting machines are able to keep their code private for proprietary reasons.

Which one do you think is designed to make cheating more likely?

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Whither SGI?

SGI by blakespot
Industry watching: Is this the end?:
[Via business|bytes|genes|molecules]

One wouldn’t have been able to tell looking at the huge Supercomputing booth, but SGI has been struggling for years. The company, whose machines were the mainstay of computational science, especially life science back in the day, and got this blogger through grad school, might just be on its final legs. Today, they received a delisting notice from the Nasdaq. Now, this is not the first time they’ve been in trouble, having filed for Chapter 11 in the past following delisting from the NYSE, so it’s entirely possible they will come out of it, but with the economy the way it is, and no real market for what they offer, I am not so sure. If it is the beginning of the end, it will be the end of a proud company that was once the epitome of visualization technology and built some of THE best computers ever made.

This is a shame. I go back to when Evans and Sutherland were the big computers used for visualizing all sorts of things. An old LDS-1 was the first ‘graphics’ computer I ever used, although the ‘pictures’ it showed were made up of many vector lines, not the smooth color-filled shapes we have today.

The Silicon Graphics came along, with its raster-based graphics and really fine looking representation of protein structure. While there was some competition with E&S systems, SGI was always the coolest. Great programs for representing biological structures and nice looking machines (colored plastics long before Apple). At one point in my career, I had a Mac as my regular computer and an old Indigo2 that the protein structure people gave me as a hand-me-down.

It was really sweet to have both computers working on structural problems at the same time.

Now it may be gone. E&S long ago left biological market, now making digital theaters and such.

Memories. E&S and SGI back when structural programs had great names like FRODO (I learned about this while at Rice from Jim Pflugrath who helped port it to an E&S PS300 while in Flo Quicho’s lab) and mice all had 3 buttons. #-D representations using blinking goggles synched to the monitor.

Now it can all be done by desktops. I do feel old.

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Great maps

Where Wars Kill People:
[Via Cosmic Variance]

The World’s Fair links to a great site at Telegraph.co.uk: the Atlas of the Real World. It’s a set of world maps (really cartograms), with the area of countries proportional to something more interesting than the mere land area – number of nuclear weapons, wealth in the year 1, and so on. Here is one to chew over: number of war deaths in the years since WWII.

Africa, the Middle East, and Asia. Latin America shows up just a bit. The big orange country in Asia is China, not Russia.

There are 18 maps and some of them are really interesting. NIce to have software that can help visualize data for us.

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My first paid app

App Store Pick of the Week: Grocery IQ:
[Via Apple Hot News]

Thanks to Grocery iQ ($4.99), you may never have to write another shopping list. Now you can tap to quickly build a comprehensive and highly legible list on iPhone or iPod touch, arrange your list by aisle to match the layout of your grocery store, check off items as you add them to your cart, build a purchase history and a list of favorites. Grocery IQ even lets you email your list to a designated shopper.

Really nice execution.

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Secret flash drive

Create a Secret Data Stash with a Fake Phonejack [Weekend Project]:
[Via Lifehacker]

This is very cool. Waiting to see it in a TV show soon.

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Helpful

Apple’s bid to change (browser) history:
[Via Buzzworthy]

Apple recently filed for a patent on a radically different way of organizing and navigating your browser history.
[More]

This could really be useful. A more graphically oriented view of history. But I wonder how you get a patent for something like this? Probably why I am not a patent attorney.

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Microsoft trademarked windows, so…

clouds by Nicholas_T
Can Dell Trademark “Cloud Computing”?:
[Via Enterprise 2.0 Blog]

This PC World article reports that Dell has applied to the U.S. Patent and Trademark Office to trademark the term “Cloud Computing.” Uh, I’m no expert on trademarks but can they do that? Any why are the other big cloud computing vendors not up in arms over this? Can any one company own a name so general as “Cloud Computing?” Back in 2006 the company I work for and their business partner attempted to trademark “Web 2.0″ in association with the Web 2.0 Summit conference and met with a huge backlash from the community. Will we see a similar response on Cloud Computing? According to the document on file with the US Patent and Trademark office, the status on this request is report as “Opposition period completed, a Notice of Allowance has been issued”

I never understood how MS could trademark Word or Windows until someone told me that the trademark was actually Microsoft Word, so perhaps this will be Dell Cloud Computing. Otherwise are they going to sue everyone who discusses computing in the cloud?

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Site update

Just wanted to do another introduction. I have been doing biotech research for 30 years, worked in industry at Immunex for 16 and at a small startup for the last four.

Besides working at the bench, I have always been very interested in the border between biology and high tech, which has developed into the field of bioinformatics. But I was really interested in another, less specialzed aspect – how these tools increased information dispersal, resulting in huge impacts on a community’s ability to innovate and create.

For example, I created the first intranet pages at Immunex and managed the internal website for over two years, while still doing research in the lab. From 18 pages I created over Christmas to several thousand.

I saw first hand what worked and what did not in a research setting. Many of the problems could not be easily solved then because the tools were not mature enough. Even so, I created, for internal use, what we would call a blog before the name was common.

Yep, back in those old days, I had to do the coding by hand, while walking uphill to and from work in the snow ;-)

Towards the end of my time at Immunex, I used this knowledge and the ideas I had developed to write two blogs back in the early part of this century. The first, my personal one, was called A Man with a Ph.D. – Richard Gayle’s Blog. The other called, Living Code, was more science-driven and was one of the top five medical blogs selected by Forbes in 2003.

But after joining a small biotech as Vice-President of Science, I had little time to keep the blogs going and both feel into disarray. However, I have recently left the small company and now have the opportunity to try to make some of my ideas concrete.

So I have decided to focus my efforts on getting Web 2.0 tools into the hands of researchers. The tools are mature enough that people can rapidly begin using them.

The scientists just have to be shown why it is worth their time to learn these tools. I expect than in a few years, these tools will be ubiquitous but for now, there is a large activation energy present before use.

Like an enzyme, I’m working to reduce that activation energy, and to make a living.

Thus this blog and also one at the site for the company I started, SpreadingScience.

There will be some overlap in but this site will be a little more personal while the business one will focus more on creating Science 2.0. I hope they will complement oner another.

The synthetic organization, part 2

pencils 2 by Paul Worthington
[Crossposted at SpreadingScience]

{See
The Synthetic Organization, Part 1 }

Pixar is different from every other movie studio. Why?

One aspect is mentioned in the article – a leader at Pixar for one movie becomes a follower and supporter for the next. They remain engaged in each other’s projects. The success of one helps the success of all.

But I also believe that there is a little more than this. Because each Pixar movie is more than just telling a story; it is adding to the tool box being used by all the innovators at Pixar. The impact of each movie to this continually enlarging storehouse of knowledge engages these innovators who work at the leading edge of technology.

There are other computer animated movies that are quite good. Kung Fu Panda , for instance. But many of these are really no different at their basis than regular 2-D animation. That is, the movie would not have been much different using classic cel-based animation. The gags would have been the same and just as funny.

On the other hand, each Pixar movie, besides the obvious need to create an enjoyable experience, seems to have another motive for being created. Each actually seems to be an exercise in solving a difficult technical question, one that can only be examined using computer animation.

Toy Story proved that a compelling story told by computer generated animation could actually be accomplished. A Bug’s Life examined the problem of opening up the world, from the relatively claustrophobic, medium shot world of Toy Story to an almost Cinerama widescreen not seen since How the West Was Won .

Toy Story 2 brought increased pathos and emotionality from animated characters, indicating that these completely virtual creations could twist our emotions like regular actors. Monsters, Inc. stretched the reality of the computer animated world, taking it into fantastical directions impossible in any other medium, while using increases in technology to address things like animated hair. Finding Nemo added the problematical world of water, something always very difficult to do with any animated approach.

The Incredibles began an examination of an effective animated caricature of the human form, something that had just looked too weird in previous movies (even Monster, Inc. covered up Boo in a costume for large periods of time) and was thus often avoided.

Cars demonstrated an increasing sophistication by creating normally inanimate objects that could actually act. That is, they only had eyes and mouths to convey emotion. No arms or legs to help demonstrate emotionality. It is as if an entire movie was made with only head shots.

Ratatouille now combined all the lessons previously learned into human characters that could emote. While the human figures in The Incredibles often acted in grand gestures and seemed larger than life (well, they were superheroes), the people who inhabited Ratatouille looked and acted much smaller, like regular people.

The characters did not have to ’shout’ to convey action but could tell us what they were thinking by a subtle change in facial expression. Ratatouille was the first computer animated movie that seemed to have actual human beings occupying the screen.

And WALL-E is the solution to a dandy problem. Can a computer animated character be created that is emotionally engaging but has no human eyes or mouth, who does not speak? Essentially, could an animated movie be created combining a robotic Buster Keaton with the first 20 minutes of 2001:A Space Odyssey ?

Now illustrating a great story has been done with computers before and they can make enjoyable movies. But each Pixar movie has been on the path to creating singular movie characters that can emote on the same complex level as human actors. Pixar has put together a tool chest that no one else has.

So part of the way Pixar has kept its creative people engaged is to provide them opportunities to succeed at solving very difficult questions using tools no one else has. Recreating all of this elsewhere would be difficult.

Each of these very difficult questions (realistic animated characters, realistic surroundings, emotional connections, toolbox of techniques) had to not only be answered but had to be done inside a commercially successful creation. Simply solving these problems, as if they were some sort of Labors of Hercules, was not enough. Pixar movies also had to be have narrative that was worth the price of admission. Simply pushing the envelope would not be successful.

Pixar set itself up to attack very complex problems that required solutions at many different levels in order to achieve success, with the added problem that success would be measured by box office response. Success at just one of these levels only would result in failure.

Pixar has been able to do this because it seems to be designed along different lines than many multinational or MBA-driven companies. It is synthesizing the knowledge it learns to create something not seen before, and developing methods of organization to sustain this synthesis.

As discussed in the Harvard article , Pixar’s innovators lead some times and provide support at others. I’ll talk more soon but check out The Unplanned Organization by Margaret Wheatley to get a hint of where I am going…

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I’ve been saving my money

phone by aussiegall
Apple introduces the new iPhone 3G:
[Via Apple Hot News]

The new iPhone 3G combines all the revolutionary features of iPhone with 3G networking, built-in GPS, and iPhone 2.0 software that supports Microsoft Exchange ActiveSync and runs hundreds of third party applications built with the iPhone SDK. Available in 22 countries on July 11, iPhone 3G comes in two models: an 8GB model priced at $199 (US) and a 16GB model priced at $299 (US).

Now I just have to see what ATT will charge. Wish they had it as a pay as you go phone.

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No wonder

trs-80 by blakespot
Why is the FEC Using TRS-80’s?:
[Via Balloon Juice]

Am I not understanding this:

The record-shattering fundraising by Democratic presidential candidates Barack Obama and Hillary Clinton has reshaped the financing of presidential elections and generated breathless coverage and analysis of the otherwise arcane area of campaign finance.

Yet it’s had another consequence that has gone all but unnoticed. The campaign finance reports filed by Obama and Clinton have grown so massive that they’ve strained the capacity of the Federal Election Commission, good government groups, the media and even software applications to process and make sense of the data.

A milestone of sorts was reached earlier this year, when Obama, the Illinois senator whose revolutionary online fundraising has overwhelmed Clinton, filed an electronic fundraising report so large it could not be processed by popular basic spreadsheet applications like Microsoft Excel 2003 and Lotus 1-2-3.

Those programs can’t download data files with more than 65,536 rows or 256 columns.

***

If you want to comb through Obama or Clinton’s cash, you either need to divide and import their reports section-by-section (a time-consuming and mind-numbing process) or purchase a more powerful database application, such as Microsoft Access or Microsoft Excel 2007, both of which retail for $229.

The FEC can’t afford a copy of Excel 2007? I can lend them my laptop if they need, but they better not talk while I am watching BSG, and they should be warned that Tunch loves company and will probably pester them when they come over.

It is not clear that from the article that the SEC has any problem with the data. It is simple stating that the files from Clinton and Obama are so big that you could not use Excel 2003 for them. It does not state that the SEC does not have Excel 2007.

So it is pretty much a filler article trying to look more important than it is. The main bit of real information – the campaigns now have so many donors that they overwhelm old software. Whoopi.

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