How can you possibly charge the person receiving the calls? [...] Which
countries do this? I think Scandinavia does, but didn't think it was widespread.
Nope, caller pays also in Scandinavia. What's more, some subscription schemes (like mine, a phone card actually) even give you a bonus if someone calls you! Yes, people have already started to abuse this by going into someones office, calling your own phone and not hang up.
This line of debate gets silly fast. Is a "computer scientist" a computer scientist if they focus on biology, or
take a biology-centric view of the world? Vice-versa? Yes, you can define people in computational biology
as either computer scientists or biologists, depending on how you like to think of them. I'll agree with you
that the best researchers are highly competent in both realms. But the absolute best are biologists at heart.
I'd say that you should ask the scientist, and I don't think Stephen Altschul, Michael Waterman, Gene Myers, Webb Miller, Anders Krogh, David Haussler, David Sankoff, to name a few, would call themselves biologists. And you do agree that they have made significant contributions to computational biology, don't you?
Please don't go into rating of scientists, because that is silly.
In my experience, this happens more often among CS researchers in computational biology than it does among biologists.
[snip]
Biologists are certainly not innocent--after all, everyone has an ego--but the debates of this variety tend to be
among two or three competing alternatives (i.e. the parsimony vs. likelihood debates in phylogeny) that have
been accepted by a majority of the researchers in a field.
Computer scientists are generally interested in methods, so yes, they more likely to propose their own method than a biologist. New methods are a good thing, although not if they have not biological basis, sure. But most CS people I know actually try to communicate with biologists to try to establish what is relevant or not. It is not easy, especially when biologists are unsure themselves. You mention micro array data; The k-means or hierarchical clustering methods in use to day are to me quite without biological relevance too in my opinion. Go look at some of the examples in the literature and start scrutinizing (sp?) the computed clusters. They can look quite weird.
The parsimony vs. ML is about whether they have biological relevance and are scientifically sound. If a method has to be accepted before you can start deciding whether it should be thrown out or not, nothing will ever happen.
If Biologists were studying NP-complete problems, and not
biology, then they couldn't be excused for not knowing the existing research in that field of computer science.
But they're not. They're studying biology, and they're using whatever computational tools they need to do
their job
If they write papers that actually are more about describing algorithms than applying them, then they should not be excused. What is wrong with walking over to the CS department and discuss methods a little? Why not try to do just a little bit more than the greedy approach to see if you can get an improvement? Using a hammer on a screw is not very impressive when you neighbour might have a screwdriver.
Well, if you're going to make that kind of dispersion, you're going to have to be a lot more specific. Yes,
there's a lot of bad literature on protein folding. A lot of it comes from polymer physicists.
I am thinking of the "beads on a lattice" model, and I actually know molecular biologists who have worked on stuff like that, so I don't think you should blame the polymer physicists...
"Repugnant" might be a bad word, English is not my native tongue, but my opinion is that the logical step needed to make conclusions on real proteins based on the simplistic lattice models is a giant leap that is very hard to defend. CS people have certainly worked on it, but they did not invent the field!
Certainly. But not equal humility. Computer scientists are entering an entirely new discipline where their own
skills are of lesser importance, and they need to understand that. The CS/biology trade-off isn't equal at all,
IMO.
Computer scientists have an interesting field on their own right and they don't need excuse themselves in any way. Some make forays into computational biology that are not the brilliant, but that is no reason to put down all those computer scientists that actually make the effort of learning the biology and even better, talk to the biologists, and make contributions.
The software that has achieved notoriety and widespread use, while
primitive in method (i.e. dynamic programming--boring, but widespread), is often based on very, very solid
statistical theory.
The software packages that comes to my mind when reading this are in fact written by statisticians and/or computer scientists... And if there is a rivalling package by a biologist, you'll see that they have often picked up statistics and methods from their competitors.
Also, as a student in comp bio myself, I can't tell you the number of times I've heard computational "biologists"
stand up and give silly lectures on new algorithms to resolve solved problems (but in slightly faster time), or
worse, completely abstract away the relevant details of a biological system in order to make new applications for
their fancy new methods.
I have numerous examples of biologists contending that their heuristic is much better than all the other heuristics (well at least on their own dataset). There are also excellent examples of biologists promoting their version of a traditional greedy heuristic as a "new algorithm" for solving an NP complete problems. Have you looked at protein folding? That field is a source for the most repugnant oversimplifications ever made in science.
My point is that pointing fingers to either disciplin is ridiculous. There are offenders on both sides. The real path to successful bioinformatics is cooperation and humility. Biologists need to talk to CS, and CS must talk to biology. I think this is generally well understood these days.
The classic example, of course, is Watson and Cricke (sp?) celebrating the error of another Linus, Pauling in this
case, when he announced that the structure of DNA was a triple helix. Pauling had made a simple calculation
mistake, which thanks to Pauling's son they were aware of. Rather than notify Pauling prior to his publishing his
information, they kept quiet and continued on their own researches.
Really? I have never heard this one. Got a reference?
In any case, while a lot of actions and behaviour in science is selfish, it works on the openess principle. If you want people to believe you, you have to tell them how you did it. These methods can then be verified and refined, much like how we want to see open source work. I think the analogy is quite valid.
Uh, yeah, but why not go directly to PubMed? OK, you don't get relative co-occurrence and those nice little charts, but on the other hand, I cannot come up with a research question where you want the relative co-occurence.
Lars
__
As a lot of people here have noticed, the basic technique used in PubGene is quite simple. The novelty of their work is mostly in how to evaluate co-citation of genes, and perhaps also in the quite comprehensive setup. Several other systems have been suggested and setup for discovering protein-protein interactions, gene interaction networks, and also automatic discovery keywords to be associated with genetic conditions.
More elaborate techniques have also been suggested for learning about the interactions. By simple text analysis, you can deduce with fair (but not perfect) certainty if a gene is up or down regulating another gene. Other systems try to find support for hypothesis on interaction networks by doing pubgene-similar analysis. If your experiments support many tentative networks, you can let the vast amounts of knowledge in the published literature dismiss the bad suggestions.
The need for systems like this is huge. More articles than ever are being published, and there is no way a researcher can keep up with the information flow. New technology also admits large scale genome-wide experiments that generates enormous amounts of data. Such data needs to be analysed automatically, and if we can tie in the published knowledge, the value of the data increases.
If you are interested in systems like these, look up the works of Andrade, Valencia, Bork, Ouzounis, and their collaborators!
This technigue, morover, appears only to collate published interactions-- helpful, perhaps, in guiding the conduct
of basic research, and the avoidence of duplicate studies-- but less useful when the goal of a researcher is
determining the function of unknown genes, or putative protein products. In those cases, protein fold databases
or motif databases are much more useful.
Sure structures and motifs are good to have, but there are a lot of structures out there that we don't know much more about. And the issue here is about interactions, beyond simple statements like "this is a catalytic protein" or whatever.
Can one give Pubgene a pdb or fasta file-- and find papers on homolougous genes or structurally similar
proteins-- or must one use BLAST, or a fold recognition algoritm prior to searching Pubgene?
No, you are supposed to have a set of genes names that you are working with. Homology can be asses elsewhere. What you can ask this system is about known and inferred interactions out there.
Maybe I'm missing something here, but isn't the fact that the other genes are being mentioned in the same
article as the first gene already imply a relationship between the two? Why else would the authors mention them
in the same article?
That is the basis for their technique yes. The thing is that they are using this transitively. If gene A is mentioned together with B in one paper, and then B is shown to work together with C in another, then that is evidence for A and C having some sort of relationship.
There are problems with this approach, and I think the authors are aware of it (have not had access to the article yet). For example, if a paper is talking about a certain new technology, it could bring out examples from various systems in the cell, and thus mentioning genes that are quite unrelated.
Another thing to consider is that scientist don't just go around randomly picking a gene and studying it. There are
generally reasons why the gene is interesting, and those genes are studied more than others.
This may be true historically, but we are entering a whole new era in genomics. Industrial science is here. The fashionable experiments today are genomewide, studying for example the workings of a large set (thousands) of genes at the the time. Genes are no longer selected for sociological reasons, but based on predictions on various aspects of the gene. "Are there reasons to believe that this gene encodes a protein sitting in the cell membrane? Let's include it in out experiment because it is then probably doing interesting signalling."
With industrial genomics and a higher publication rate than ever, new tools are needed to sift through the data. These Norwegians provides one attempt at addressing this.
Every other free software project starts off with the intent to get rid of bloat, get better stability, yadda yadda, better color combinations, yadda, XML, yadda. And then I see a feature list which equals or exceeds that competition. In this particular case, we have things such as all-GUI configuration tools and a key combo to highlight the mouse pointer would you have misplaced it on your vast 21" desktop.
Don't get me wrong: I think it is really cool that people try to one-up each other on free software, but should I really believe all these claims of superiority? I have not tried out XFce, but surely there is something that has been sacrificed? Can this beast be both lean and mean? Any data points? IMHO, if you make claims about being slim and bloat-free, you need to provide some evidence in that direction. Otherwise, just be proud over your featue list!
... so that everybody knows that comercial driven open source not works - at least using this way.
Oh come on. With this line of reasoning nothing software-related would work, and certainly not proprietary-software based businesses, given last year's fall-outs.
I have not used or downloaded Nautilus myself, but IMHO they have a sound business plan: Invest in a software that grows popular and people use for free to have them hooked on services you charge for. Not unreasonable. What magical touch does theKompany use to make them so superior?
Should I have to pay if you have activated call forwarding on your landline phone to some other number? No, because it is at your convienence, not mine.
Well, implement it the right way then: If you forward calls to phone 1 to another phone 2, you pay for a call from 1 to 2. This is how it is done in Sweden.
I don't know about Benefon, but Spectronics have been around for a while. I remember reading about them as an interesting challenger of the big guys at the beginning of the GSM revolution a few years back. I presume they have been making a fortune as a supplier/developer for the big corporations during recent years.
It is not so surprising that small independent (have no idea about their indepence actually) company can build a phone since most GSM circuitry are standard components nowadays. The hard part will be to market the gadget. Some say the mobile phone market is more marketing driven that technology driven these days.
Uh, well... some of us don't want to bother tweaking the code in our operating systems. I like to code as much as anyone,
but my own little college projects.
I have several times taken delight in being able to read source code to understand why something is going wrong. One does not need to understand a whole system to detect a misuse of a feature. Remember that we are not only talking about the kernel here, but all the auxiliary libraries as well.
On the same note, there have been occasions when I have not been able to understand why something is going wrong with a proprietary system---and there has been no fast way of looking up why.
EtherNet to the home is being deployed in large scale here in Sweden right now. Best of all, my neighbourhood is scheduled to be done in April. Rumour has it that you will automatically get your own virtual private network over the LAN. So my neighbours will not have an advantage over other 31337 hackers on the Net.
I like the argument of man for quick summaries and something else for manuals. I still say use html for what is currently in info. Then I can use lynx, links, w3m, Netscape, Konqueror, Opera,... whatever I want. Why must I be forced to use info?
Well, you are not really forced to use an Info browser. I just searched using Google and found a site with a info2html tool.
For me, however, the main argument is that there is an excellent info browser in my programming editor and it is very easy to switch from programming to reading. OK, so there is the W3 browser implemented in elisp, but it does not quite cut it for me. The web pretty much need a "real" GUI browser.
And there is no way you will be able to have a ready-to-print typeset manual using an HTML format. If you have a manual in Info, there are sources marked up using texi, and then you have a TeX backend. It is unbeatable for printing quality. To me this is one of the most remarkable aspects of Info. The markup is so carefully chosen that a document is instantly ready for both pleasurable online viewing and printing.
When it comes to collection of citations, I believe you are basically out of luck if you rely on PubMed as your primary source. As others have pointed out, the situation is quite different in CS, math, and other (typically formula-heavy) fields. I have actually considered making a PubMed front-end that searches their database for you (they provide URLs delivering the result as XML) and then reformat for BibTex. Who is interested?
Regarding management of citations however, I don't believe you can get anything better than using (X)Emacs in conjunction with the right modes. For managing your citation file(s), you have the BibTeX mode which is marvellously simple. For writing your paper, you use AUCTeX mode and the RefTeX minor mode. With RefTeX, you can search the citation database without leaving your emacs session and choose among matching citations to get the one you want in at the point. There is also support for managing references to figures and tables. For example, you can list all labels (to equations, figures, and tables) in a buffer, indented after sectioning.
But the inquirer confuses me regarding one thing. It is listed as a feature that EndNote can renumber your citations. In Latex, who cares?! You get all those details for free.
I don't much about Gnome and their help system, but I think it is sad if they are not using the man pages.
However, one should not see the Gnu Info system as a competitor, as they have totally different purposes. The man page should be fairly short and give you a speedy answer. The Info manual should give you access to complete manuals for large systems. For instance, a complete bash manual does not belong in a man page. Yes, I know it is there, but how managable is it? Then on the other hand, I should not have to use an Info browser to get the command line options for 'cat'.
In Info, you get easily navigated sections, hyperlinks, and a good index system. In addition, a manual set in Info can also be beautifully printed on paper since there is an excellent TeX backend. The result is beyond what you can get using HTML!
While not a true GUI solution, (X)Emacs offers the command M-x manual-entry which loads the man-page in a buffer. You may then navigate using scrollbars if you are so inclined and, more importantly, click on references to other man-pages to get those in its own buffer.
Make sure to have keyboard shortcut for that command in your C-mode. It makes for a speedy lookup of the function name you have by the point.
The strength of using man-pages in an emacs buffer become apparent when repeatedly working with very long man-pages.
"Assembly" referred without doubt to the actual problem: assembling the many snippets of DNA to larger fragments.
I don't know what he actually coded in though.
Lars
__
Re:What about the quality of assembly?
on
Genetic Stone Soup
·
· Score: 3
There is a biased comparison available over at the Sanger Center. Summary: The public assembly is much better even though less data is used.
They measure things such as the number of fragments (fewer=better) and their lengths (longer=better) and estimated coverage of the genome.
There is also a less biased comparison over at the Nature website. I don't know if you can get to read it without a paid subscription though. Their findings are less controversial, saying that the statistics are similar for the two assemblies, but that the annotations (i.e. descriptions of what is actually there, comparison: A group photo with note on peoples names and their relationships) are better in the public version.
I agree with you on your thoughts on socialized versus free-market health systems. The idea of non-profit insurance companies is however something I'd recommend not spending any energy on.
Here in Sweden, cooperative non-profit initiatives is an old idea, still with a large trusting following. In particular, we have a large cooperative insurance provider (non-health care, since we have socialized medicine and insurance here) that is basically indistuingishable from other companies. In fact, they have a pretty bad reputation with some people. The only reason they are so big is probably through momentum and people thinking that a cooperative business (I believe it is owned through unions and consumer organisations) must be good. This is not true!
The point is that in an efficient and functioning market, as I believe the insurance industry is in most countries, there is no point in having a non-profit provider. History suggests that they are not more efficient and competative than other companies.
You argument is only against socialized medicine, not universal coverage. This is a common mixup that often confuses issues.
You can have free-market medicine catering to a publicly-funded insurance system. The competition will be there, both on the care side and the insurance side.
To me, the point is that the more insurance companies are able to predict, the more important it becomes for society to step up and help those with unfortunate genetic dispositions. This is a moral responsibility.
Lars
__
As the article mostly discusses scientific literature, I don't see how the AAP can have a case. When I go download an online article from a publisher today, it is not conceptually different from when I go and physically "download" same article from a shelf, only much more efficient. It is speedier for me, and at least in theory it is more efficient for both libraries and publishers as they have to deal with less papercopies. I can do this both in academia and in a corporate environment and they typically have their paper subscriptions "upgraded" to online access.
Where do the publishers loose money here? People rarely hand around PDF files, so I don't think there is much pirating. It is probably less PDF-copying around than papercopying, simply because the PDF files are much more accessible than the paper versions.
In fact, if the publishers keep track of downloading, they have more control on the journal distribution and usage than in the "old paper world" where they would have no idea how many paper copies a library have made from an article.
if the deal can give one a lot of money, be sure that one is going to make it, no matter how much it will cost to the society...
These projects cannot be done without the cooperation of health authorities, simply because they sit on data (not only samples that you could drive around and collect, but medical records) that are essential to the project.
if you don't put rule and laws to regulate the market, don' t expect the market to regulate itself!
Right. And that is why I don't want these health authorities to create monopolies by selling exclusive rights!
What I responded to was the implication that this was possible because "Autogen has cynically found a jurisdiction with a compliant and corrupt ruling clique." (judd). The original pressrelease is too lacking in information to deduce that people's rights has not been defended.
You are also not understanding what they are selling in Iceland and Sweden. It is not your genes or genome that is taken away from you; You can take it to anyone else to sell it or whatever. The deal is about the exlusive cooperation of healt authorities and the access to data and statistics that same authorities have collected.
One controversial issue is of course whether anonymous medical records belong to the originator or not. Representants of the people(s) have decided that is OK, but understanding it is a controversial issue, and very much an issue of trust, they have made it possible for people not to participate. I don't understand what more you can ask for.
What is really debatable is whether a government should be able to sell those publicly owned rights to one single company, shutting out everyone else.
Slashdot Mirror
Nope, caller pays also in Scandinavia. What's more, some subscription schemes (like mine, a phone card actually) even give you a bonus if someone calls you! Yes, people have already started to abuse this by going into someones office, calling your own phone and not hang up.
Lars
__
I'd say that you should ask the scientist, and I don't think Stephen Altschul, Michael Waterman, Gene Myers, Webb Miller, Anders Krogh, David Haussler, David Sankoff, to name a few, would call themselves biologists. And you do agree that they have made significant contributions to computational biology, don't you?
Please don't go into rating of scientists, because that is silly.
In my experience, this happens more often among CS researchers in computational biology than it does among biologists.
[snip]
Biologists are certainly not innocent--after all, everyone has an ego--but the debates of this variety tend to be among two or three competing alternatives (i.e. the parsimony vs. likelihood debates in phylogeny) that have been accepted by a majority of the researchers in a field.
Computer scientists are generally interested in methods, so yes, they more likely to propose their own method than a biologist. New methods are a good thing, although not if they have not biological basis, sure. But most CS people I know actually try to communicate with biologists to try to establish what is relevant or not. It is not easy, especially when biologists are unsure themselves. You mention micro array data; The k-means or hierarchical clustering methods in use to day are to me quite without biological relevance too in my opinion. Go look at some of the examples in the literature and start scrutinizing (sp?) the computed clusters. They can look quite weird.
The parsimony vs. ML is about whether they have biological relevance and are scientifically sound. If a method has to be accepted before you can start deciding whether it should be thrown out or not, nothing will ever happen.
If Biologists were studying NP-complete problems, and not biology, then they couldn't be excused for not knowing the existing research in that field of computer science. But they're not. They're studying biology, and they're using whatever computational tools they need to do their job If they write papers that actually are more about describing algorithms than applying them, then they should not be excused. What is wrong with walking over to the CS department and discuss methods a little? Why not try to do just a little bit more than the greedy approach to see if you can get an improvement? Using a hammer on a screw is not very impressive when you neighbour might have a screwdriver.
Well, if you're going to make that kind of dispersion, you're going to have to be a lot more specific. Yes, there's a lot of bad literature on protein folding. A lot of it comes from polymer physicists.
I am thinking of the "beads on a lattice" model, and I actually know molecular biologists who have worked on stuff like that, so I don't think you should blame the polymer physicists...
"Repugnant" might be a bad word, English is not my native tongue, but my opinion is that the logical step needed to make conclusions on real proteins based on the simplistic lattice models is a giant leap that is very hard to defend. CS people have certainly worked on it, but they did not invent the field!
Certainly. But not equal humility. Computer scientists are entering an entirely new discipline where their own skills are of lesser importance, and they need to understand that. The CS/biology trade-off isn't equal at all, IMO.
Computer scientists have an interesting field on their own right and they don't need excuse themselves in any way. Some make forays into computational biology that are not the brilliant, but that is no reason to put down all those computer scientists that actually make the effort of learning the biology and even better, talk to the biologists, and make contributions.
Lars
__
The software packages that comes to my mind when reading this are in fact written by statisticians and/or computer scientists... And if there is a rivalling package by a biologist, you'll see that they have often picked up statistics and methods from their competitors.
Also, as a student in comp bio myself, I can't tell you the number of times I've heard computational "biologists" stand up and give silly lectures on new algorithms to resolve solved problems (but in slightly faster time), or worse, completely abstract away the relevant details of a biological system in order to make new applications for their fancy new methods.
I have numerous examples of biologists contending that their heuristic is much better than all the other heuristics (well at least on their own dataset). There are also excellent examples of biologists promoting their version of a traditional greedy heuristic as a "new algorithm" for solving an NP complete problems. Have you looked at protein folding? That field is a source for the most repugnant oversimplifications ever made in science.
My point is that pointing fingers to either disciplin is ridiculous. There are offenders on both sides. The real path to successful bioinformatics is cooperation and humility. Biologists need to talk to CS, and CS must talk to biology. I think this is generally well understood these days.
Disclaimer: I am a computer scientist.
Lars
__
Really? I have never heard this one. Got a reference?
In any case, while a lot of actions and behaviour in science is selfish, it works on the openess principle. If you want people to believe you, you have to tell them how you did it. These methods can then be verified and refined, much like how we want to see open source work. I think the analogy is quite valid.
Lars
__
Uh, yeah, but why not go directly to PubMed? OK, you don't get relative co-occurrence and those nice little charts, but on the other hand, I cannot come up with a research question where you want the relative co-occurence.
Lars
__
As a lot of people here have noticed, the basic technique used in PubGene is quite simple. The novelty of their work is mostly in how to evaluate co-citation of genes, and perhaps also in the quite comprehensive setup. Several other systems have been suggested and setup for discovering protein-protein interactions, gene interaction networks, and also automatic discovery keywords to be associated with genetic conditions.
More elaborate techniques have also been suggested for learning about the interactions. By simple text analysis, you can deduce with fair (but not perfect) certainty if a gene is up or down regulating another gene. Other systems try to find support for hypothesis on interaction networks by doing pubgene-similar analysis. If your experiments support many tentative networks, you can let the vast amounts of knowledge in the published literature dismiss the bad suggestions.
The need for systems like this is huge. More articles than ever are being published, and there is no way a researcher can keep up with the information flow. New technology also admits large scale genome-wide experiments that generates enormous amounts of data. Such data needs to be analysed automatically, and if we can tie in the published knowledge, the value of the data increases.
If you are interested in systems like these, look up the works of Andrade, Valencia, Bork, Ouzounis, and their collaborators!
Lars
__
Sure structures and motifs are good to have, but there are a lot of structures out there that we don't know much more about. And the issue here is about interactions, beyond simple statements like "this is a catalytic protein" or whatever.
Can one give Pubgene a pdb or fasta file-- and find papers on homolougous genes or structurally similar proteins-- or must one use BLAST, or a fold recognition algoritm prior to searching Pubgene?
No, you are supposed to have a set of genes names that you are working with. Homology can be asses elsewhere. What you can ask this system is about known and inferred interactions out there.
Lars
__
That is the basis for their technique yes. The thing is that they are using this transitively. If gene A is mentioned together with B in one paper, and then B is shown to work together with C in another, then that is evidence for A and C having some sort of relationship. There are problems with this approach, and I think the authors are aware of it (have not had access to the article yet). For example, if a paper is talking about a certain new technology, it could bring out examples from various systems in the cell, and thus mentioning genes that are quite unrelated.
Another thing to consider is that scientist don't just go around randomly picking a gene and studying it. There are generally reasons why the gene is interesting, and those genes are studied more than others.
This may be true historically, but we are entering a whole new era in genomics. Industrial science is here. The fashionable experiments today are genomewide, studying for example the workings of a large set (thousands) of genes at the the time. Genes are no longer selected for sociological reasons, but based on predictions on various aspects of the gene. "Are there reasons to believe that this gene encodes a protein sitting in the cell membrane? Let's include it in out experiment because it is then probably doing interesting signalling."
With industrial genomics and a higher publication rate than ever, new tools are needed to sift through the data. These Norwegians provides one attempt at addressing this.
Lars
__
Every other free software project starts off with the intent to get rid of bloat, get better stability, yadda yadda, better color combinations, yadda, XML, yadda. And then I see a feature list which equals or exceeds that competition. In this particular case, we have things such as all-GUI configuration tools and a key combo to highlight the mouse pointer would you have misplaced it on your vast 21" desktop.
Don't get me wrong: I think it is really cool that people try to one-up each other on free software, but should I really believe all these claims of superiority? I have not tried out XFce, but surely there is something that has been sacrificed? Can this beast be both lean and mean? Any data points? IMHO, if you make claims about being slim and bloat-free, you need to provide some evidence in that direction. Otherwise, just be proud over your featue list!
Lars
__
Oh come on. With this line of reasoning nothing software-related would work, and certainly not proprietary-software based businesses, given last year's fall-outs.
I have not used or downloaded Nautilus myself, but IMHO they have a sound business plan: Invest in a software that grows popular and people use for free to have them hooked on services you charge for. Not unreasonable. What magical touch does theKompany use to make them so superior?
Lars
__
Well, implement it the right way then: If you forward calls to phone 1 to another phone 2, you pay for a call from 1 to 2. This is how it is done in Sweden.
Lars
__
I don't know about Benefon, but Spectronics have been around for a while. I remember reading about them as an interesting challenger of the big guys at the beginning of the GSM revolution a few years back. I presume they have been making a fortune as a supplier/developer for the big corporations during recent years.
It is not so surprising that small independent (have no idea about their indepence actually) company can build a phone since most GSM circuitry are standard components nowadays. The hard part will be to market the gadget. Some say the mobile phone market is more marketing driven that technology driven these days.
Lars
__
I have several times taken delight in being able to read source code to understand why something is going wrong. One does not need to understand a whole system to detect a misuse of a feature. Remember that we are not only talking about the kernel here, but all the auxiliary libraries as well.
On the same note, there have been occasions when I have not been able to understand why something is going wrong with a proprietary system---and there has been no fast way of looking up why.
Lars
__
EtherNet to the home is being deployed in large scale here in Sweden right now. Best of all, my neighbourhood is scheduled to be done in April. Rumour has it that you will automatically get your own virtual private network over the LAN. So my neighbours will not have an advantage over other 31337 hackers on the Net.
Lars
__
Well, you are not really forced to use an Info browser. I just searched using Google and found a site with a info2html tool.
For me, however, the main argument is that there is an excellent info browser in my programming editor and it is very easy to switch from programming to reading. OK, so there is the W3 browser implemented in elisp, but it does not quite cut it for me. The web pretty much need a "real" GUI browser.
And there is no way you will be able to have a ready-to-print typeset manual using an HTML format. If you have a manual in Info, there are sources marked up using texi, and then you have a TeX backend. It is unbeatable for printing quality. To me this is one of the most remarkable aspects of Info. The markup is so carefully chosen that a document is instantly ready for both pleasurable online viewing and printing.
Lars
__
When it comes to collection of citations, I believe you are basically out of luck if you rely on PubMed as your primary source. As others have pointed out, the situation is quite different in CS, math, and other (typically formula-heavy) fields. I have actually considered making a PubMed front-end that searches their database for you (they provide URLs delivering the result as XML) and then reformat for BibTex. Who is interested?
Regarding management of citations however, I don't believe you can get anything better than using (X)Emacs in conjunction with the right modes. For managing your citation file(s), you have the BibTeX mode which is marvellously simple. For writing your paper, you use AUCTeX mode and the RefTeX minor mode. With RefTeX, you can search the citation database without leaving your emacs session and choose among matching citations to get the one you want in at the point. There is also support for managing references to figures and tables. For example, you can list all labels (to equations, figures, and tables) in a buffer, indented after sectioning.
But the inquirer confuses me regarding one thing. It is listed as a feature that EndNote can renumber your citations. In Latex, who cares?! You get all those details for free.
Lars
__
I don't much about Gnome and their help system, but I think it is sad if they are not using the man pages.
However, one should not see the Gnu Info system as a competitor, as they have totally different purposes. The man page should be fairly short and give you a speedy answer. The Info manual should give you access to complete manuals for large systems. For instance, a complete bash manual does not belong in a man page. Yes, I know it is there, but how managable is it? Then on the other hand, I should not have to use an Info browser to get the command line options for 'cat'.
In Info, you get easily navigated sections, hyperlinks, and a good index system. In addition, a manual set in Info can also be beautifully printed on paper since there is an excellent TeX backend. The result is beyond what you can get using HTML!
Lars
__
While not a true GUI solution, (X)Emacs offers the command M-x manual-entry which loads the man-page in a buffer. You may then navigate using scrollbars if you are so inclined and, more importantly, click on references to other man-pages to get those in its own buffer.
Make sure to have keyboard shortcut for that command in your C-mode. It makes for a speedy lookup of the function name you have by the point.
The strength of using man-pages in an emacs buffer become apparent when repeatedly working with very long man-pages.
Lars
__
I don't know what he actually coded in though.
Lars
__
They measure things such as the number of fragments (fewer=better) and their lengths (longer=better) and estimated coverage of the genome.
There is also a less biased comparison over at the Nature website. I don't know if you can get to read it without a paid subscription though. Their findings are less controversial, saying that the statistics are similar for the two assemblies, but that the annotations (i.e. descriptions of what is actually there, comparison: A group photo with note on peoples names and their relationships) are better in the public version.
Lars
__
I agree with you on your thoughts on socialized versus free-market health systems. The idea of non-profit insurance companies is however something I'd recommend not spending any energy on.
Here in Sweden, cooperative non-profit initiatives is an old idea, still with a large trusting following. In particular, we have a large cooperative insurance provider (non-health care, since we have socialized medicine and insurance here) that is basically indistuingishable from other companies. In fact, they have a pretty bad reputation with some people. The only reason they are so big is probably through momentum and people thinking that a cooperative business (I believe it is owned through unions and consumer organisations) must be good. This is not true!
The point is that in an efficient and functioning market, as I believe the insurance industry is in most countries, there is no point in having a non-profit provider. History suggests that they are not more efficient and competative than other companies.
Lars
__
You can have free-market medicine catering to a publicly-funded insurance system. The competition will be there, both on the care side and the insurance side.
To me, the point is that the more insurance companies are able to predict, the more important it becomes for society to step up and help those with unfortunate genetic dispositions. This is a moral responsibility.
Lars
__
As the article mostly discusses scientific literature, I don't see how the AAP can have a case. When I go download an online article from a publisher today, it is not conceptually different from when I go and physically "download" same article from a shelf, only much more efficient. It is speedier for me, and at least in theory it is more efficient for both libraries and publishers as they have to deal with less papercopies. I can do this both in academia and in a corporate environment and they typically have their paper subscriptions "upgraded" to online access.
Where do the publishers loose money here? People rarely hand around PDF files, so I don't think there is much pirating. It is probably less PDF-copying around than papercopying, simply because the PDF files are much more accessible than the paper versions.
In fact, if the publishers keep track of downloading, they have more control on the journal distribution and usage than in the "old paper world" where they would have no idea how many paper copies a library have made from an article.
Lars
__
These projects cannot be done without the cooperation of health authorities, simply because they sit on data (not only samples that you could drive around and collect, but medical records) that are essential to the project.
if you don't put rule and laws to regulate the market, don' t expect the market to regulate itself!
Right. And that is why I don't want these health authorities to create monopolies by selling exclusive rights!
Now, please, let's keep Hitler out of this. OK?
Lars
__
You are also not understanding what they are selling in Iceland and Sweden. It is not your genes or genome that is taken away from you; You can take it to anyone else to sell it or whatever. The deal is about the exlusive cooperation of healt authorities and the access to data and statistics that same authorities have collected.
One controversial issue is of course whether anonymous medical records belong to the originator or not. Representants of the people(s) have decided that is OK, but understanding it is a controversial issue, and very much an issue of trust, they have made it possible for people not to participate. I don't understand what more you can ask for.
What is really debatable is whether a government should be able to sell those publicly owned rights to one single company, shutting out everyone else.
Lars
__