I am a firmware engineer in Applied Biosystems (formerly PE Biosystems). I was one of the people who developed the 3700 DNA analyzer, as well as a a couple of other instruments before this one.
Mike Hunkapiller is my boss's boss's boss's boss. Four levels. Compare to HP, Microsoft, or even Sun, and you will find that this is a very flat structure.
Hunkapiller sits in 2nd floor on one of the "Bay Towers" (the first two buildings you see on your right as you come west across the San Mateo bridge). In the floors above him are the software development and software product test teams. He sits in a cubicle, along with everyone else. He eats lunch in the cafeteria.
Those groups are going to move out of those buildings and onto the main campus (next to it), yielding more space for our neighbour, Inktomi. Instead, Applied Biosystems has just bought some property in Pleasanton. Mike Hunkapiller is currently lobbying for, and seeing if it is possible, for those people who live in the East Bay and want to work there to move to Pleasanton, and the remainder to stay on the main campus in Foster City.
You get the point. He has fostered a very informal, casual, and respectful culture in this company. People are allowed to enjoy themselves and to be Nice.:-) I.e. trusting, creative, personable. (Except IT, of course). The last employee survey showed that we had one of the highest motivated work force anywhere.
If he was Bill Gates, or Larry Ellison, or even Craig Venter (of Celera), he would be a lot more ego-driven. The company would be made into an image of his mind. We would have a lot more procedures, "employee agreements", and a lot less fun.
I have friends working both in Microsoft, Oracle, and Celera. I know what I'm saying here.
Sorry if I sound a bit exaggerative here. I do really like people like Hunkapillar, and there are plenty of them here. Even if they are a dying breed in corporate America at large.
Yes, Applied Biosystems dominates the market for DNA analyzers. It always has. That has nothing to do with "monopolistic practices" or such rubbish. Mike Hunkapiller, Leroy Hood, and a couple of others, invented electrophoresis scanning. The company has always had the edge, and always made the best equipment. People here want to do a good job. And it certainly has the best field support apparatus.
So, sorry JonKatz, but your sensationalist huff-puff upsettedness about the world (and anything that sounds like a suitable target for your "corporate America" label) is probably best applied to your own pidestal.
And iff you haff doubts about our genuine motifation to help mannkind, vee haff very effektif mezods off deelink witz you. Ve vill just allter your genes to make you look like ze monkey you are.
What I would like to see, is a lawsuit against porn sites who grab the 100 most searched words and put them in their meta tags for search engines to find
What actually happens is extortion. There are mafia-like organizations that jump on any "legitimate" domain name that is let expire (maybe because the original owner did not pay the registration fee in time) or domain names that have a familiar ring to it. They then add a site under this domain name, filled with porn or other "inflammable" material. Often, real companies do not want to be associated with the filth, and then pay money to get hold of the domain name.
For instance, my company had a product line named "Amplitaq Gold", and a website 'amplitaqgold.com'. Not exactly the kind of domain name you would come up with out of the blue. The domain was let expire after we didn't need it any more; the day after it was filled with pointers to a porn site in Russia.
To make matters worse, searches on Altavista for terms related to our company, our product lines etc would invariably turn up pointers to this stuff.
We got the domain name back through legal action. However, not everybody would go through that hazzle, and would rather buy the domain name back even if it meant giving in to the Russian mafia.
Only part of the DNA is actual genes. Genes look 99% or more similar from one animal to another, and the major difference between e.g. a human and a mouse is in the other "garbage", outside of the genes.
Also, not all genes are necessarily in use. One key to understanding which ones are "turned on" and which ones are not, might lie to understand that "garbage" outside of the genes.Compare to a software application; the genes are the data, while the stuff outside is the actual instructions which tell how to read that data.
Celera is now about 1/3 on the way to sequencing the mouse genome. Being able to compare genomes from different animals might give us some further clues to understanding ourselves./P.
The installation screen (nice btw) lists under system requirements: RedHat 6.0 or above. Sure enough, I just tried installing on my Debian "Woody" system, and got a segmentation fault while it was copying files.
Probably a glibc incompatability or somesuch (I'll investigate further), but this starts looking like corporate proprietary stuff already. Just a thought.
The hi-tech industry, automakers etc need to sell their products to the same people over and over again in order to have a sustained source of income. Thus, there is a perpetual "upgrade" cycle in such products. In order to stay ahead, you cannot hang on to something for too long. Thus, there is no point in owning it.
<P>This lack of reference is also a catch 22; the more fluid your lifestyle, the less likely you are to take care of your environment and property. The less likely you are to take care of your property, the less likely you are to be willing to own it for life.</P>
As you said, the issue is incompatability between QPL and GPL, not that one of these is non-free
In other words, it is an internal KDE/Qt problem, which would prevent anyone from distributing compiled versions of KDE if they were adhering to the license.
Also, this was not an insightful post because it says to go to the KDE FTP site and manually grab.deb's if you want KDE on your Debian system. The "Debian way" is to have automatic retreival and updating through APT, by adding the following lines to/etc/apt/sources.list:
deb http://kde.tdyc.com potato kde kde2 contrib rkrusty
deb-src http://kde.tdyc.com potato kde kde2 contrib rkrusty
Sounds like Madonna still is in the shock-to-promote game, and plays that "sue-Napster" as advertisement for her CD. She leaked the song out in the first place. And, it is available from numerous sources just as easily as from Napster.
Too bad such airheads do not realize that their silly little promotion scheme has such large ramifications for freedom of speech - or basic freedoms in general.
I, too, had Covad as a line provider a couple of years back (Epoch was the ISP, PacBell was the ones that actually owned the physical lines into my house).
Not only do they have an unfair advantage when competing with PacBell (in price, as well as complexity); they also appear as the "Bad Guys" in front of the customers.
In this regard, they are not that much different from long distance companies. Various charges that are levied against them from local telephone Co's are showing up in your long distance bill.
The moral of this story is that monopolies are evil and they should be destroyed. Penguins are OK.
Such a system exists commercially - it is basically a marketplace for IT support. You can provide tech support for a fee, to users who are asked to direct their questions into major and minor "groups" (e.g. Linux -> Networking).
First, realize that the biotech world is full of pissing contests. Thus can a slow-moving government-funded sequencing effort suddenly speed up, in a (albeit futile) attempt to beat new competition from the the private sector. As a matter of fact, from the same company that brought them DNA sequencing (i.e. the electrophoresis method of analyzing DNA) in the first place.
PE Biosystems (formerly Applied Biosystems, started by Leroy Hood of the article in question) has since before these events been the one player that has brought DNA technologies to the commercial world. Two years ago, the company launched the 3700 sequencer, for the first time providing throughput that would enable the sequencing of the human genome at the speed we have been witnessing lately. Initially, as part of the marketing campaign for this new instrument, we also started Celera Genomics, to actually do the sequencing and later sell the access tools to read the data.
This has undoubtedly stirred up the sequencing world. The HGP suddenly realized that they needed to produce something, and now even Sun Microsystems has entered the race for the human genome. Hence, the pissing contest.
Nevertheless, the technology which makes this possible (electrophoresis) was conceived, deployed, and commercialized by Applied Biosystems and Leroy Hood. We'll have to see what the courts say about the funding parts of this, but patents are normally awarded to the inventor, not the funder, in either case.
Thus, although the sudden outbreak of this "news" undoubtedly is performed by those entities who want to "get back" at Celera (and in this world, there are quite a few of them, and yes, they are quite childish), it should have little or no impact as far as the awarding of the elecrophoresis patents etc. goes.
I myself has received one patent in this area: A method for velocity-based normalization of readouts from the elecrophoresis process. Sure, some of the customers who fund our company are from the public sectory, but they are buying the machines, and not the rights to these patents.
And no, neither I, PE Biosystems, or Celera are interested in patenting human DNA. These companies are <i>not</i> lobbying for it. As usual, the common belief that Celera is out to patent Human Genomic Data is just due to the slashdot effect (i.e. sensationalizing, gossip-mongering, etc).
There may be companies that are out to do this, but they also realize it is a lost cause.
So, all-fired-up-slashdotters - relax. Have a drink. Watch the show, and please reduce the noise level around here.
Ok, I took a good look over the patent. It appears that the patent is for a software package management system that operates over the internet specifically. Well, there's a good chance that was never patented.
Actually, if you look closer at the patent description, it references some other patents related to updating software components over the internet
This patent is a bit more specific, and relates to providing a remote server with information about installed software, then have the server return with a list of needed updates.
This is a tiny little bit different from Debian's "dselect" and APT tools, in that these latter ones receive a list of available software from the server, and locally determine which software can/should be upgraded or which software is newly available/obsolete.
The cynical part of us all (and we are probably right, given Microsoft's history) will conclude that this is done on the server in Microsoft's case only to provide some information back to them about how their customer's computers look - i.e. do do a little bit of surveying, policing and the like.
In either case, it will be very hard for Microsoft to hold up this patent in court, given that there is prior art (patented as well as non-patented) in this area.
Our problem is that this still means litigation; and even if we may be right, Debian/SPI do not have the same economical resources at their disposal as does Microsoft. If Microsoft sues the organization, or any U.S.-based member of it, for patent violations, chances are that this will be a major obstacle for Debian's packaging method.
Unless, of course, Corel or Storm Linux (both derived from Debian) would be willing to assist.
Celera may be able to circumvent that clause temporarily.
You (as so many others in this forum) misunderstand the business model of Celera - they are not there to patent stuff. They are not even there to "own" information, or hold on to it.
Celera was created by my own company, PE Biosystems, in order to sequence the human genome (using our 3700 DNA Analyzer), and then sell the tools that people could access this data with.
a failed revenue model for the open source software industry.
Overhyped, not failed. Most newcomers to the Linux world measure its success by its ability to generate revenue, which is not the reason Linux (or free software in general) was created in the first place.
It is so far relatively unimportant for the penetration of Linux that it be able to make some company money. If only technical support, userfriendlyness, etc can continue to be finessed and standardized without a particular corporate agenda, we are going to remain immune to the rise or fall of particular companies.
Celera will provide data from its own databases, via tools it sells for the job.
Other companies can then patent particular sequences as they apply to a particular discovery. For instance, Incyte could patent the knowledge that a given sequence causes colon cancer, or AIDS.
Nobody can (yet) patent a sequence itself - nobody is even lobbying for this.
Incyte is, OTOH, still going ahead with their own sequencing of the human genome, AFAIK.
Somebody said that if you compare the Genomic mining with the goldrush from the 1850s, Celera is the company selling the maps. Their sister/mother company, PE Biosystems (where I work) is selling the picks and shovels (the sequencers, PCR tools, chemcials & consumables, etc).
Having mapped the Human Genome will be the platform for about 100 years worth of research, even taken into account the accellerating pace of such research based on technological advances.
During this time, more and more products will come to market, some of which are human drugs, some of which are tailored treatments (e.g. body tissue), some of which are more informational in nature. For this reason, it is very important that politicians such as Clinton and Blair concentrate on these bigger issues at stake - get debates started on what the boundraries are and what we want to do with this information - rather than trying to score populist points by portraying incorrect/ignorant viewpoints about the private sector's intentions in this race. (I guess, they can't make themselves saviors without enemies, but still...)
Actually the sequencing part was completed earlier this year (giving tremendous subsequent rise to Celera stock). What they now did was the mapping - i.e. piecing the small fragments together.
Moreover, Celera have also completed more than 90% of the human genome within the last year or so. Once complete, this is an indication that the time before the human genome (more than 200 trillion base pairs) are mapped will be shorter than originally anticipated. To compare, the government-funded Human Genome Project has so far spent over 10 years on the same job.
Celera is doing a 4x oversampling on the human genome, unlike the HGP, which does 10x oversampling. This is possible because Celera is sequencing DNA from one single individual (most likely Craig Venter?), thus avoiding the uncertainty of wheter differences are due to sequencing artifacts or personal variations.
Plus, Celera is using our (PE Biosystems) 3700 DNA Analyzer (fully automated, unattended operation 24 hours per day), whereas the Human Genome Project mostly use our older 377 DNA Sequencer, which requires manual reloading of samples after each run (every 2-3 hours).
As originally stated when Celera was created two years ago, the data is going to be publicly available - a point that has gotten lost among very opinionated but not so informed readers of Slashdot. There will be a 3-month lag period, to ensure accuracy of the data, and to see if there is any information that could be used for patentable drugs & applications.
(Mostly, Celera's business model is based on providing the tools that will give access to this database).
Sometimes (more than other times) I am a bit amazed at the level of opinionated bigotry combined with ignorance that the Slashdot readers manage to spew out. Obviously this is a very, very young crowd.
First off, there is no conflict - as far as the availability of genomic data is concerned. The International Human Genome Project is making available to the public all sequences as they discover them. Celera is too, albeit in a lump after they have sequenced the whole thing.
Second off, Celera is <B>not</B> building their business on patents. In fact, Celera is not even lobbying for the possibility of patenting sequences per se. (Unlike, for instance, Incyte - who are more or less building their business on the sale of rights to partiuclar sequences).
On the other hand, if someone in Celera (as result of their genomic knowledge) come up with promotors &al that help manufacture seqences inside the human body - that is an actual product that is already patentable alongside any other drug.
So - guys - forget this "open source" militia stance. Celera is as much "open source" as the government - actually much more (being mostly based on Linux, anyway). That is a non-issue.
As far as Bill goes, he only says what sounds good in populist ears. The fact that he said HGP data will be publicly available, and that he urges the private sector to make their data available as well - all that is already the case. So even though he is a personal friend of Craig Venter, he has obviously not studied this matter too deeply.
Celera aren't mapping as such. They're trying to sequence most of the genome, by picking random fragments.
<P>Not correct, I am afraid. <UL> <LI>Celera <b>are</b> doing mapping after they have sequenced data. In fact, they have one of the world's largest computing facilities, in order to do this. <LI>They <b>are</b> sequencing 100% of the genome, with about 4x oversampling. The difference is that they are using the "Shotgun" approach to extract fragments. Earlier this year, they announced that they already had sequenced 90% of the human genome. Later the same week, they had also completed mapping of some type of a firefly (one of the simpler genomes). <LI>They are doing 4x oversampling, but all from the same individual (possibly Craig Venter). This eliminates gene expressions from coming into effect - and any differences will be known to be due to sequencing artifacts. They can then later take any sequences that were in question and redo them, and also get more individuals sequenced at a later time. </UL> </P>
<P><I>WIW, the public consortium have done about twice as much sequencing on the human genome as Celera, and are still sequencing (AFAICT) at almost twice the rate.</I> </P> <P>It is true that the HGP has (still) more raw data sequenced, mostly because they perform a larger oversampling (they have to, since they involve several individuals).</P>
<P>However, you are wrong about the speed. Celera has 230 ABI3700 sequencers, each working 24 hours, in full, unattended operation. In comparison, most of the HGP participants use the older ABI377 to do their work; where manual intervention is required between each run. That is why Celera has in 1 year collected about 50% as much raw data as the HGP has done over the last 10 years.</p>
Give it to opinionated teenagers, religious zealots, and ignorant mass media to screw up the intentions of the parties involved.
Celera is a company that was formed by my own company, PE Biosystems, 2 years ago -- in order to sequence the human genome using our 3700 DNA Analyzer. While the sequencing itself is important, the main motive for creating the company was to promote this new instrument, and give the BioTech community a glimpse of its capacity compared to previous instruments. (The Human Genome Project had setup a timeframe based on our older 377 sequencer, which they for the most part are using).
The squabble mostly arises from the fact that Celera thus are able to accomplish in 2-3 years what the HGP had setup a 13-year time frame to do.
And oh sure, Celera is planning to review the mapped sequences (for accuracy, and to find out if there is stuff that can give them an edge over their competitors in terms of coming up with drugs etc), before releasing the information to the public; however they have committed to no more than a 3-month lag time from the time when they have mapped the genome (basically, put the puzzle together after having sequenced each piece) before the information is made public.
This, too, would mean that they would provide public data before the HGP. HGP, having received billions of dollars in government funding, are obviously a bit upset.
Now, there is of course a tendency among SlashDot readers to be somewhat militant with regards to anything that smells of a corporation, especially if it involves money. After all, the stock price of Celera (and PE Biosystems) have gained much more the last half year or so than has RedHat or VA Linux. Thing is though, there are still people (often with the same concerns for opennes) working inside companies like these, as there are outside. I, for one, can probably argue better than most people here why it is important that standards, platforms, and formats remain public, not subject to any one company's tyrannies. Thus, I think it is a bit far-fetched, and perhaps alienating, to put on the religious zeal and apply it against Celera, before even knowing what they are all about.
Have you noticed that nowadays hardly anyone mispronounces linux?
Actually, they almost all still do - though in a better way than before. In Finnish, the "i" in Linu[xs] is a long one. So "Leenux", not "Linn-ux", would be the correct phonetic spelling in English.
KDE was taken out between Hamm and Slink, and will not go back in again until it is built entirely on free Software. In this case, until it uses only Qt 2.0.
By referring to revenue, MacOS is larger than Linux; Apple may still be larger than Microsoft (?).
Especially in the Brave GNU World of Linux, that is garbage. If you are so obsessed about size of your distribution, you should count number of users.
RedHat still has the most users; according to a copule of slashdot polls earlier Debian is next, far more than SuSE and Slackware. (Granted, this is among net.addicts; the picture may be different overall).
If you count number of packages, and amount of pre-packaged software available, Debian wins hands down. It has by far the largest number of developers as well. Too, if you count automation, sophistication, number of slick concepts (window manager menu registry, package diversions, auto-update features, conflict/dependency resolution, bug tracking, hierarctical control, etc. etc.) it wins, wins, and wins again.
Sure there are a lot of raging teenage hormones out there, hormones that should have been used fro dating, but actually get applied to OS holy wars. Sure, a large portion of these sit with Linux users. (The 3rd wave of them, anyway - after the developers, and the technically adventurous).
That's true for people who have discovered any new religion, be it MacOS, BeOS, OS/2, and - yes - Windows. These tend to get ignored by the mainstream press nowadays. They are supposed to do this, being of a technically less savvy demographic composition. But somehow it makes stories every time such 'rage' appears in a new arena, like the "new" world of Linux.
In either case - relax. OS/2, MacOS, etc. failed for other reasons. They did not fail because of overzealous advocates. Even if they did, it would be for factors not relevant to Linux and Open Source(TM).
To me, this whole Mincraft deal just stinks more and more. Why are they so obsessed with proving that Windows is the way to go, that Windows users are of a genetically superior breed, etc. - even if it costs them so much PR? It sounds kindof like Robert Cringely's description of Bill Gates in his book - he just has to prove himself to the world - prove that he really, really can do something. Mincraft now are at a stage where they just want to say "We were right" long after facts slap them in their face over and over and over again..
Slashdot Mirror
I am a firmware engineer in Applied Biosystems (formerly PE Biosystems). I was one of the people who developed the 3700 DNA analyzer, as well as a a couple of other instruments before this one.
Mike Hunkapiller is my boss's boss's boss's boss. Four levels. Compare to HP, Microsoft, or even Sun, and you will find that this is a very flat structure.
Hunkapiller sits in 2nd floor on one of the "Bay Towers" (the first two buildings you see on your right as you come west across the San Mateo bridge). In the floors above him are the software development and software product test teams. He sits in a cubicle, along with everyone else. He eats lunch in the cafeteria.
Those groups are going to move out of those buildings and onto the main campus (next to it), yielding more space for our neighbour, Inktomi. Instead, Applied Biosystems has just bought some property in Pleasanton. Mike Hunkapiller is currently lobbying for, and seeing if it is possible, for those people who live in the East Bay and want to work there to move to Pleasanton, and the remainder to stay on the main campus in Foster City.
You get the point. He has fostered a very informal, casual, and respectful culture in this company. People are allowed to enjoy themselves and to be Nice. :-) I.e. trusting, creative, personable. (Except IT, of course). The last employee survey showed that we had one of the highest motivated work force anywhere.
If he was Bill Gates, or Larry Ellison, or even Craig Venter (of Celera), he would be a lot more ego-driven. The company would be made into an image of his mind. We would have a lot more procedures, "employee agreements", and a lot less fun.
I have friends working both in Microsoft, Oracle, and Celera. I know what I'm saying here.
Sorry if I sound a bit exaggerative here. I do really like people like Hunkapillar, and there are plenty of them here. Even if they are a dying breed in corporate America at large.
Yes, Applied Biosystems dominates the market for DNA analyzers. It always has. That has nothing to do with "monopolistic practices" or such rubbish. Mike Hunkapiller, Leroy Hood, and a couple of others, invented electrophoresis scanning. The company has always had the edge, and always made the best equipment. People here want to do a good job. And it certainly has the best field support apparatus.
So, sorry JonKatz, but your sensationalist huff-puff upsettedness about the world (and anything that sounds like a suitable target for your "corporate America" label) is probably best applied to your own pidestal.
And iff you haff doubts about our genuine motifation to help mannkind, vee haff very effektif mezods off deelink witz you. Ve vill just allter your genes to make you look like ze monkey you are.
What I would like to see, is a lawsuit against porn sites who grab the 100 most searched words and put them in their meta tags for search engines to find
What actually happens is extortion. There are mafia-like organizations that jump on any "legitimate" domain name that is let expire (maybe because the original owner did not pay the registration fee in time) or domain names that have a familiar ring to it. They then add a site under this domain name, filled with porn or other "inflammable" material. Often, real companies do not want to be associated with the filth, and then pay money to get hold of the domain name.
For instance, my company had a product line named "Amplitaq Gold", and a website 'amplitaqgold.com'. Not exactly the kind of domain name you would come up with out of the blue. The domain was let expire after we didn't need it any more; the day after it was filled with pointers to a porn site in Russia.
To make matters worse, searches on Altavista for terms related to our company, our product lines etc would invariably turn up pointers to this stuff.
We got the domain name back through legal action. However, not everybody would go through that hazzle, and would rather buy the domain name back even if it meant giving in to the Russian mafia.
Only part of the DNA is actual genes. Genes look 99% or more similar from one animal to another, and the major difference between e.g. a human and a mouse is in the other "garbage", outside of the genes.
Also, not all genes are necessarily in use. One key to understanding which ones are "turned on" and which ones are not, might lie to understand that "garbage" outside of the genes.Compare to a software application; the genes are the data, while the stuff outside is the actual instructions which tell how to read that data.
Celera is now about 1/3 on the way to sequencing the mouse genome. Being able to compare genomes from different animals might give us some further clues to understanding ourselves./P.
The installation screen (nice btw) lists under system requirements: RedHat 6.0 or above. Sure enough, I just tried installing on my Debian "Woody" system, and got a segmentation fault while it was copying files.
Probably a glibc incompatability or somesuch (I'll investigate further), but this starts looking like corporate proprietary stuff already. Just a thought.
While IE has some clutter, it does not have the annoying pane (that takes up a lot of room) that Netscape does
Actually, it does; it just is not turned on by default in the web browser. (It is in Outlook Express, though).
Needless to say, you can also get rid of this pane by a single mouse click in Mozilla.
The hi-tech industry, automakers etc need to sell their products to the same people over and over again in order to have a sustained source of income. Thus, there is a perpetual "upgrade" cycle in such products. In order to stay ahead, you cannot hang on to something for too long. Thus, there is no point in owning it.
<P>This lack of reference is also a catch 22; the more fluid your lifestyle, the less likely you are to take care of your environment and property. The less likely you are to take care of your property, the less likely you are to be willing to own it for life.</P>
<P>In a word: <i>affluenza</i></P>
As you said, the issue is incompatability between QPL and GPL, not that one of these is non-free
In other words, it is an internal KDE/Qt problem, which would prevent anyone from distributing compiled versions of KDE if they were adhering to the license.
Also, this was not an insightful post because it says to go to the KDE FTP site and manually grab .deb's if you want KDE on your Debian system. The "Debian way" is to have automatic retreival and updating through APT, by adding the following lines to /etc/apt/sources.list:
Sounds like Madonna still is in the shock-to-promote game, and plays that "sue-Napster" as advertisement for her CD. She leaked the song out in the first place. And, it is available from numerous sources just as easily as from Napster.
Too bad such airheads do not realize that their silly little promotion scheme has such large ramifications for freedom of speech - or basic freedoms in general.
I, too, had Covad as a line provider a couple of years back (Epoch was the ISP, PacBell was the ones that actually owned the physical lines into my house).
Not only do they have an unfair advantage when competing with PacBell (in price, as well as complexity); they also appear as the "Bad Guys" in front of the customers.
In this regard, they are not that much different from long distance companies. Various charges that are levied against them from local telephone Co's are showing up in your long distance bill.
The moral of this story is that monopolies are evil and they should be destroyed. Penguins are OK.
Such a system exists commercially - it is basically a marketplace for IT support. You can provide tech support for a fee, to users who are asked to direct their questions into major and minor "groups" (e.g. Linux -> Networking).
http://www.nowonder.com
First, realize that the biotech world is full of pissing contests. Thus can a slow-moving government-funded sequencing effort suddenly speed up, in a (albeit futile) attempt to beat new competition from the the private sector. As a matter of fact, from the same company that brought them DNA sequencing (i.e. the electrophoresis method of analyzing DNA) in the first place.
PE Biosystems (formerly Applied Biosystems, started by Leroy Hood of the article in question) has since before these events been the one player that has brought DNA technologies to the commercial world. Two years ago, the company launched the 3700 sequencer, for the first time providing throughput that would enable the sequencing of the human genome at the speed we have been witnessing lately. Initially, as part of the marketing campaign for this new instrument, we also started Celera Genomics, to actually do the sequencing and later sell the access tools to read the data.
This has undoubtedly stirred up the sequencing world. The HGP suddenly realized that they needed to produce something, and now even Sun Microsystems has entered the race for the human genome. Hence, the pissing contest.
Nevertheless, the technology which makes this possible (electrophoresis) was conceived, deployed, and commercialized by Applied Biosystems and Leroy Hood. We'll have to see what the courts say about the funding parts of this, but patents are normally awarded to the inventor, not the funder, in either case.
Thus, although the sudden outbreak of this "news" undoubtedly is performed by those entities who want to "get back" at Celera (and in this world, there are quite a few of them, and yes, they are quite childish), it should have little or no impact as far as the awarding of the elecrophoresis patents etc. goes.
I myself has received one patent in this area: A method for velocity-based normalization of readouts from the elecrophoresis process. Sure, some of the customers who fund our company are from the public sectory, but they are buying the machines, and not the rights to these patents.
And no, neither I, PE Biosystems, or Celera are interested in patenting human DNA. These companies are <i>not</i> lobbying for it. As usual, the common belief that Celera is out to patent Human Genomic Data is just due to the slashdot effect (i.e. sensationalizing, gossip-mongering, etc).
There may be companies that are out to do this, but they also realize it is a lost cause.
So, all-fired-up-slashdotters - relax. Have a drink. Watch the show, and please reduce the noise level around here.
-tor
Ok, I took a good look over the patent. It appears that the patent is for a software package management system that operates over the internet specifically. Well, there's a good chance that was never patented.
Actually, if you look closer at the patent description, it references some other patents related to updating software components over the internet
This patent is a bit more specific, and relates to providing a remote server with information about installed software, then have the server return with a list of needed updates.
This is a tiny little bit different from Debian's "dselect" and APT tools, in that these latter ones receive a list of available software from the server, and locally determine which software can/should be upgraded or which software is newly available/obsolete.
The cynical part of us all (and we are probably right, given Microsoft's history) will conclude that this is done on the server in Microsoft's case only to provide some information back to them about how their customer's computers look - i.e. do do a little bit of surveying, policing and the like.
In either case, it will be very hard for Microsoft to hold up this patent in court, given that there is prior art (patented as well as non-patented) in this area.
Our problem is that this still means litigation; and even if we may be right, Debian/SPI do not have the same economical resources at their disposal as does Microsoft. If Microsoft sues the organization, or any U.S.-based member of it, for patent violations, chances are that this will be a major obstacle for Debian's packaging method.
Unless, of course, Corel or Storm Linux (both derived from Debian) would be willing to assist.
-torCelera may be able to circumvent that clause temporarily.
You (as so many others in this forum) misunderstand the business model of Celera - they are not there to patent stuff. They are not even there to "own" information, or hold on to it.
Celera was created by my own company, PE Biosystems, in order to sequence the human genome (using our 3700 DNA Analyzer), and then sell the tools that people could access this data with.
-tor
a failed revenue model for the open source software industry.
Overhyped, not failed. Most newcomers to the Linux world measure its success by its ability to generate revenue, which is not the reason Linux (or free software in general) was created in the first place.
It is so far relatively unimportant for the penetration of Linux that it be able to make some company money. If only technical support, userfriendlyness, etc can continue to be finessed and standardized without a particular corporate agenda, we are going to remain immune to the rise or fall of particular companies.
Celera will provide data from its own databases, via tools it sells for the job.
Other companies can then patent particular sequences as they apply to a particular discovery. For instance, Incyte could patent the knowledge that a given sequence causes colon cancer, or AIDS.
Nobody can (yet) patent a sequence itself - nobody is even lobbying for this.
Incyte is, OTOH, still going ahead with their own sequencing of the human genome, AFAIK.
Somebody said that if you compare the Genomic mining with the goldrush from the 1850s, Celera is the company selling the maps. Their sister/mother company, PE Biosystems (where I work) is selling the picks and shovels (the sequencers, PCR tools, chemcials & consumables, etc).
:-)
Having mapped the Human Genome will be the platform for about 100 years worth of research, even taken into account the accellerating pace of such research based on technological advances.
During this time, more and more products will come to market, some of which are human drugs, some of which are tailored treatments (e.g. body tissue), some of which are more informational in nature. For this reason, it is very important that politicians such as Clinton and Blair concentrate on these bigger issues at stake - get debates started on what the boundraries are and what we want to do with this information - rather than trying to score populist points by portraying incorrect/ignorant viewpoints about the private sector's intentions in this race. (I guess, they can't make themselves saviors without enemies, but still...)
Anyway - glad the bottle is out of the genie.
Actually the sequencing part was completed earlier this year (giving tremendous subsequent rise to Celera stock). What they now did was the mapping - i.e. piecing the small fragments together.
:-)
Moreover, Celera have also completed more than 90% of the human genome within the last year or so. Once complete, this is an indication that the time before the human genome (more than 200 trillion base pairs) are mapped will be shorter than originally anticipated. To compare, the government-funded Human Genome Project has so far spent over 10 years on the same job.
Celera is doing a 4x oversampling on the human genome, unlike the HGP, which does 10x oversampling. This is possible because Celera is sequencing DNA from one single individual (most likely Craig Venter?), thus avoiding the uncertainty of wheter differences are due to sequencing artifacts or personal variations.
Plus, Celera is using our (PE Biosystems) 3700 DNA Analyzer (fully automated, unattended operation 24 hours per day), whereas the Human Genome Project mostly use our older 377 DNA Sequencer, which requires manual reloading of samples after each run (every 2-3 hours).
As originally stated when Celera was created two years ago, the data is going to be publicly available - a point that has gotten lost among very opinionated but not so informed readers of Slashdot. There will be a 3-month lag period, to ensure accuracy of the data, and to see if there is any information that could be used for patentable drugs & applications.
(Mostly, Celera's business model is based on providing the tools that will give access to this database).
And I have stock options!
-tor
Guys,
Sometimes (more than other times) I am a bit amazed at the level of opinionated bigotry combined with ignorance that the Slashdot readers manage to spew out. Obviously this is a very, very young crowd.
First off, there is no conflict - as far as the availability of genomic data is concerned. The International Human Genome Project is making available to the public all sequences as they discover them. Celera is too, albeit in a lump after they have sequenced the whole thing.
Second off, Celera is <B>not</B> building their business on patents. In fact, Celera is not even lobbying for the possibility of patenting sequences per se. (Unlike, for instance, Incyte - who are more or less building their business on the sale of rights to partiuclar sequences).
On the other hand, if someone in Celera (as result of their genomic knowledge) come up with promotors &al that help manufacture seqences inside the human body - that is an actual product that is already patentable alongside any other drug.
So - guys - forget this "open source" militia stance. Celera is as much "open source" as the government - actually much more (being mostly based on Linux, anyway). That is a non-issue.
As far as Bill goes, he only says what sounds good in populist ears. The fact that he said HGP data will be publicly available, and that he urges the private sector to make their data available as well - all that is already the case. So even though he is a personal friend of Craig Venter, he has obviously not studied this matter too deeply.
There.
-tor
Celera aren't mapping as such. They're trying to sequence most of the genome, by picking random fragments.
<P>Not correct, I am afraid.
<UL>
<LI>Celera <b>are</b> doing mapping after they have sequenced data. In fact, they have one of the world's largest computing facilities, in order to do this.
<LI>They <b>are</b> sequencing 100% of the genome, with about 4x oversampling. The difference is that they are using the "Shotgun" approach to extract fragments. Earlier this year, they announced that they already had sequenced 90% of the human genome. Later the same week, they had also completed mapping of some type of a firefly (one of the simpler genomes).
<LI>They are doing 4x oversampling, but all from the same individual (possibly Craig Venter). This eliminates gene expressions from coming into effect - and any differences will be known to be due to sequencing artifacts. They can then later take any sequences that were in question and redo them, and also get more individuals sequenced at a later time.
</UL>
</P>
<P><I>WIW, the public consortium have done about twice as much sequencing on the human genome as Celera, and are still sequencing (AFAICT) at almost twice the rate.</I>
</P>
<P>It is true that the HGP has (still) more raw data sequenced, mostly because they perform a larger oversampling (they have to, since they involve several individuals).</P>
<P>However, you are wrong about the speed. Celera has 230 ABI3700 sequencers, each working 24 hours, in full, unattended operation. In comparison, most of the HGP participants use the older ABI377 to do their work; where manual intervention is required between each run. That is why Celera has in 1 year collected about 50% as much raw data as the HGP has done over the last 10 years.</p>
Give it to opinionated teenagers, religious zealots, and ignorant mass media to screw up the intentions of the parties involved.
Celera is a company that was formed by my own company, PE Biosystems, 2 years ago -- in order to sequence the human genome using our 3700 DNA Analyzer. While the sequencing itself is important, the main motive for creating the company was to promote this new instrument, and give the BioTech community a glimpse of its capacity compared to previous instruments. (The Human Genome Project had setup a timeframe based on our older 377 sequencer, which they for the most part are using).
The squabble mostly arises from the fact that Celera thus are able to accomplish in 2-3 years what the HGP had setup a 13-year time frame to do.
And oh sure, Celera is planning to review the mapped sequences (for accuracy, and to find out if there is stuff that can give them an edge over their competitors in terms of coming up with drugs etc), before releasing the information to the public; however they have committed to no more than a 3-month lag time from the time when they have mapped the genome (basically, put the puzzle together after having sequenced each piece) before the information is made public.
This, too, would mean that they would provide public data before the HGP. HGP, having received billions of dollars in government funding, are obviously a bit upset.
Now, there is of course a tendency among SlashDot readers to be somewhat militant with regards to anything that smells of a corporation, especially if it involves money. After all, the stock price of Celera (and PE Biosystems) have gained much more the last half year or so than has RedHat or VA Linux. Thing is though, there are still people (often with the same concerns for opennes) working inside companies like these, as there are outside. I, for one, can probably argue better than most people here why it is important that standards, platforms, and formats remain public, not subject to any one company's tyrannies. Thus, I think it is a bit far-fetched, and perhaps alienating, to put on the religious zeal and apply it against Celera, before even knowing what they are all about.
So there.
-tor
--
Får i ulveklær.
Not to worry - his English was not that good either. ("Here, here.")
-tor
Have you noticed that nowadays hardly anyone mispronounces linux?
Actually, they almost all still do - though in a better way than before. In Finnish, the "i" in Linu[xs] is a long one. So "Leenux", not "Linn-ux", would be the correct phonetic spelling in English.
KDE was taken out between Hamm and Slink, and will not go back in again until it is built entirely on free Software. In this case, until it uses only Qt 2.0.
By referring to revenue, MacOS is larger than Linux; Apple may still be larger than Microsoft (?).
:-/
Especially in the Brave GNU World of Linux, that is garbage. If you are so obsessed about size of your distribution, you should count number of users.
RedHat still has the most users; according to a copule of slashdot polls earlier Debian is next, far more than SuSE and Slackware. (Granted, this is among net.addicts; the picture may be different overall).
If you count number of packages, and amount of pre-packaged software available, Debian wins hands down. It has by far the largest number of developers as well. Too, if you count automation, sophistication, number of slick concepts (window manager menu registry, package diversions, auto-update features, conflict/dependency resolution, bug tracking, hierarctical control, etc. etc.) it wins, wins, and wins again.
Want revenue? Go work for Microsoft.
Sure there are a lot of raging teenage hormones out there, hormones that should have been used fro dating, but actually get applied to OS holy wars. Sure, a large portion of these sit with Linux users. (The 3rd wave of them, anyway - after the developers, and the technically adventurous).
That's true for people who have discovered any new religion, be it MacOS, BeOS, OS/2, and - yes - Windows. These tend to get ignored by the mainstream press nowadays. They are supposed to do this, being of a technically less savvy demographic composition. But somehow it makes stories every time such 'rage' appears in a new arena, like the "new" world of Linux.
In either case - relax. OS/2, MacOS, etc. failed for other reasons. They did not fail because of overzealous advocates. Even if they did, it would be for factors not relevant to Linux and Open Source(TM).
To me, this whole Mincraft deal just stinks more and more. Why are they so obsessed with proving that Windows is the way to go, that Windows users are of a genetically superior breed, etc. - even if it costs them so much PR? It sounds kindof like Robert Cringely's description of Bill Gates in his book - he just has to prove himself to the world - prove that he really, really can do something. Mincraft now are at a stage where they just want to say "We were right" long after facts slap them in their face over and over and over again..