I think this challenge is pointless. The race for speeding up genome sequencing has been going on for several years and this price will not change anything. It will not bring in new players and the ones that are already there are working fiercely on the problem anyway. Just this summer there were two different papers in Nature, I think, that introduced nano-scale sequencing techniques with a speedup of 100x compared to "traditional" techniques.
The foundation should spend its prize money on some other noble goal where the rewards are not already so high.
What is wrong with the Belville line of sets? That is very "girly". And I would think that girls would like the Harry Potter sets too. My daughter has enjoyd some Potter sets that come with lots of shiny pieces and small animals.
Then there are clickits: Make your own necklace, bracelet, whatever, using special pieces in the Lego system. This is somewhat outside the line of regular construction sets, but in the same spirit and still compatible. And lots of fun.
I don't understand this! How can they be without Lego?
Lego was my favourite toy as a child and I have made sure they have plenty of Lego today. There are plenty of sets that build more than what the instructions tell you. And if you don't like the sets currently available, buy some second hand!
Every child deserves some Lego.
People here really seem to love screen. Yet I cannot understand its lure. I use konsole and use tabs, giving my one terminal in each tab. It is easy to walk through the tabs with a keyboard shortcut and I can click to get the tab I want. What does screen have that konsole does not have? I just don't see it.
There are several suggestions to improve the current system actually, it is an active debate in that you can follow in Science and Nature. One suggestion I saaw recently was to include reviewing reviews. The idea was that low-quality referees would be weeded out after having received bad comments/points from authors. I have seen reviews that I think very little of, where the referee has done a very poor job. (On the other hand, I have also seen some great and very helpful reviews.)
Another suggestion that keeps coming up is to use anonymization of manuscript submission. Here, the basic idea is that the referee does not know who is being reviewed. That would balance the system more in favour of new and controversial authors and against the established ones with well respected names that gets them a free ride (a phenomenon that certainly exists). There are many cases where this procedure would not help much, because it would be so obvious who wrote it, but I can't see that it could hurt. In todays electronic submission systems, this should be easy to implement.
I suggest you look at the papers in recent issues of the journals and ask yourself in which "company" your article would look the best.
In this case, I don't think the impact factor lies. If memory serves me right, the impact factor for PLoS has even included article types that the editors did not see as prime citation material, such as editorials and essays, so the impact factor for PLoS might even be slightly disadvantaged. Look at the BMC journals for instance, they have been very successful too, and it is most likely the visibility of an open and online presence.
I have now looked at the feature list of Kile, and also its screenshoots, and I don't get it: When I use (X)Emacs together with AUXTeX and RefTeX etc, I have basically everything that Kile boasts. The only thing I could see Emacs not matching Kile on would be "Quick Preview", but that is not explained in the documentations so I am not sure about that one either.
Whenever I use XEmacs for LaTeX, I also have immediate access to spell checking, dynamic abbreviations (a felxible completion system), and every other crazy minor mode there is. Unless Kile is extensible with an integrated scripting environment, for example a Lisp environment, I don't think Kile can keep up with Emacs!
And yes, I am an Emacs fan boy.
Re:If you want decent scientific articles..
on
Bad Science in the Press
·
· Score: 2, Informative
If you have access to them, the big "science tabloids", Nature and Science, have very good summaries and explanations of their most important articles. You'd be surprised. It is now so strange, really, because they have a large reader base from very many disciplines and these people (usually scientists) want to know and understand what happens in other fields without having to have a PhD in those fields.
You can probably find them in your local college library. Have a look!
I have still to RTFP (put it on my list), but I did notice that this is an essay, and not a research article. As such, it probably did not go to peer review as it is more of a discussion piece.
I am also a long time user of xfig. Even though I never get used to the user interface, it works reliably and has the features I need. My favourite feature is that you can export your drawing in a large number of formats (EPS, PDF, mixes of EPS/PDF and (La)TeX, various pixmap formats, and nowadays SVG). As pointed out, the actual FIG format is human readable and I have done search-and-replace edits in FIG files that would have taken way too much clicking in any GUI drawing program. Actually, being able to import any EPS-picture and draw on top of it is also good.
One of my dream applications is xfig combined with a modern user interface...
For a recent presentation, I tried to edit an SVG illustration generated by a computer program (using GNU plotutils) in Inkscape. This did not work well for some reason, but maybe that is due to plotutils. I had to fall back to good old xfig!
I had lots of fun with my Sinclair Spectrum, my first computer, and then the Commodore 64 which I bought because so many friends had cool games for it. But the absolute best moment was when I managed to impress my grandfather.
I had sat down to write a program, in Basic of course, to solve a word puzzle, a kind of crossword, that was published every week in the local daily news paper. It was probably also my first program that solved a combinatorial problem. With surprisingly little effort, I got something that worked!
When my grandfather came over a few days later, I loaded the program and brought him in to my room to show the program. I knew that he did not understand the fun I had with my computers, but since he was really into these puzzles himselves, it gave me a great opportunity to show him what a computer could do and how it worked.
I declared that I could solve said puzzle with my computer, showed him the program and how it was built up, ran the program, and concluded by printing out the solution to the puzzle. I noticed to my disappointment that my grandfather had gotten a blank stare in his eyes and had just nodded through the little presentation. Being a good grandfather, he told me how clever that was, accepted the printout, and went out to talk to the others. Ah, well, "wrong generation" I thought to myself.
One minute later my grandfather dashed back into the room again, blurting out "but this is the solution!" He had taken another look at the printout and realized what I was talking about. He was impressed! And I was really proud.
First you point out that the Y chromosome does not follow Mendelian genetics, then that neither does mitochondrial DNA (mtDNA), but you conclude that one should use male samples. Why?
I believe the best thing would be to use both Y chromosome and mtDNA to be able to look at differences in the results in order to find weak conclusions.
A friend of mine has worked with dog populations and has mostly used mtDNA simply because it was the only well understood sequence data for the dog. There are additional advantages with mtDNA over Y chromosome data: It is a small genome and it is relatively easy to sequence large parts of it, or even the whole thing. The best property is though that in a single cell, with only one copy of Y, there are thousands of copies of mtDNA. If you are going to have people to send you data from far away, you will face the challenge of having the DNA degrading. It is then an advantage to have that genomic redundancy in mtDNA.
Yeah, but if actual users are saying the get more spam, it is likely that they see the spam themselves, I would say. So I would guess that people are getting increasingly used to spam. Sad.
Personally, I have no idea about my spam rates since I filter out spam myself in Thunderbird, plus that the organizations I belong to seem to do a good job of keeping some of the spam out using SpamAssasin and other tricks.
Yes, I am aware of the "Sokal affair", and consider it one of the most clever stunts in academia. I was under the impression that Sokal wrote it himself though, without the aid of software.
Wow, that is brilliant! And there is even a link to the "Dada engine" for setting up your own text generator. I'd say that this is the doom for automatic text analysis, at least if the the analysing program is publically distributed and therefore available to train the generator on.
I also read the paper describing "recursive transition networks", and it turns out that the idea comes from Hofstadter's "Gödel, Escher, Bach". I guess I have to actually read that book now... But, with that book in mind, does anyone know if there is a similar system for generating music? There is so much more freedom in music (you don't have to worry about logic, facts, and background knowledge) that this systems should be able to generate really cool music of various genres.
We also have a preprint server that is free that most astronomers post their articles to (except for Nature articles because Nature won't let them).
The Nature policy you claim is apparently not true. In the most recent issue of Nature, an editor writes:
So please let's put a myth about this journal to rest. As first stated in an editorial in 1997, and since then in our Guide to Authors, if scientists wish to display drafts of their research papers on an established preprint server before or during submission to Nature or any Nature journal, that's fine by us.
I don't really buy this paperwork reasoning. I mean, libraries have people employed taking care of subscriptions too, and their paperwork should be substantially reduced. Also, how much can the paperwork for the average researcher's check really cost?
I'd just like to see a link to some solid estimates I guess.
Well, what the article was saying was that there was overhead and paperwork that was the cost, not this shift of burden.
But, in my experience, large univiersities also have large libraries and they certainly have more journals than the ones that their researchers publish in if they worth their reputation. And most researchers I know read more journals than they publish in.
I am puzzled by the following quote from the article:
Moreover, Lightner notes that several large research universities have examined the potential cost of faculty publishing under an author-pays model and have concluded that, for them, open access would not be the most cost-effective publishing solution. He says the schools discovered they would pay more in author fees than it would cost to continue to pay to subscribe to journals from publishers, even at current high prices. That's not only because of the large number of faculty members publishing; it is also because of the additional overhead incurred in having to process paperwork, including individual purchase orders and cutting checks to pay the publishing fees.
Is this true? Anyone knows where is comes from? Since libraries are getting more and more sidestepped by the open publishing revolution, I'd expect some FUD floating around, but this is a strong statement that should be easily verified or countered.
I guess my problem is that I simply cannot see how the author-pays model would become more expensive for a university/organization.
I meant flashy in the sense of "very well funded", which I have heard they are, and "with high ambitions". The other poster was worried that the barcode project would take resources from good old traditional taxonomy.
That is a good wikipedia link you gave. I recommend it to people interesting in this thread.
I could rant on but, I think this project is of some use only if combined with traditional taxonomy. The danger is that a large flashy project like this will steal research dollars away from traditional taxonomy.
It is not like the field of taxonomy is without flashy projects. Consider the Tree of life project for instance.
Given the information in the Wiki you referred to, wouldn't you say that the barcodes could provide a starting point for good taxonomy projects?
I too am somewhat confused about the project too, since this is more or less done already today. Isn't 16S ribosomal DNA the standard "genetic bar code"?
But I think the project is about actually sampling the bar code from every known species. To some extent we are getting spoiled with all the genome data coming out, gene discovery projects, whole genome sequencing, gene expression data, et.c., and at least I have more or less come to expect to find the gene data I would like to have. However, the sequencing is not uniformly sampled: It is concentrated to the important model organisms and then patched out over the animals that some researcher has had an interest in.
A "16S-ribosome" project to complement the different genome projects could be pretty cool.
This would have blown me away a couple of months ago, but I have now seen the light that is
map24.com! Their maps, shown using a java applet, actually zooms way more smoothly and elegant than these google maps.
They have localized versions of their system to 18 different countries. In the EU-centric Google portals, searches for city names can also come up with a prominent map24 link.
If you are interested by maps.google, you really want to check it out! No I am not in any way affiliated with map24.
But I think Linus is actually using "evolution" with the correct interpretation. From what I have seen of Linux development, there is a high degree of redundancy in implementations. Then, the most fit solution survives!
Sure, sometimes solutions and implementations are influenced by each other, but that could be regarded as recombination...
Slashdot Mirror
I think this challenge is pointless. The race for speeding up genome sequencing has been going on for several years and this price will not change anything. It will not bring in new players and the ones that are already there are working fiercely on the problem anyway. Just this summer there were two different papers in Nature, I think, that introduced nano-scale sequencing techniques with a speedup of 100x compared to "traditional" techniques. The foundation should spend its prize money on some other noble goal where the rewards are not already so high.
What is wrong with the Belville line of sets? That is very "girly". And I would think that girls would like the Harry Potter sets too. My daughter has enjoyd some Potter sets that come with lots of shiny pieces and small animals. Then there are clickits: Make your own necklace, bracelet, whatever, using special pieces in the Lego system. This is somewhat outside the line of regular construction sets, but in the same spirit and still compatible. And lots of fun.
I don't understand this! How can they be without Lego? Lego was my favourite toy as a child and I have made sure they have plenty of Lego today. There are plenty of sets that build more than what the instructions tell you. And if you don't like the sets currently available, buy some second hand! Every child deserves some Lego.
People here really seem to love screen. Yet I cannot understand its lure. I use konsole and use tabs, giving my one terminal in each tab. It is easy to walk through the tabs with a keyboard shortcut and I can click to get the tab I want. What does screen have that konsole does not have? I just don't see it.
There are several suggestions to improve the current system actually, it is an active debate in that you can follow in Science and Nature. One suggestion I saaw recently was to include reviewing reviews. The idea was that low-quality referees would be weeded out after having received bad comments/points from authors. I have seen reviews that I think very little of, where the referee has done a very poor job. (On the other hand, I have also seen some great and very helpful reviews.)
Another suggestion that keeps coming up is to use anonymization of manuscript submission. Here, the basic idea is that the referee does not know who is being reviewed. That would balance the system more in favour of new and controversial authors and against the established ones with well respected names that gets them a free ride (a phenomenon that certainly exists). There are many cases where this procedure would not help much, because it would be so obvious who wrote it, but I can't see that it could hurt. In todays electronic submission systems, this should be easy to implement.
I suggest you look at the papers in recent issues of the journals and ask yourself in which "company" your article would look the best.
In this case, I don't think the impact factor lies. If memory serves me right, the impact factor for PLoS has even included article types that the editors did not see as prime citation material, such as editorials and essays, so the impact factor for PLoS might even be slightly disadvantaged. Look at the BMC journals for instance, they have been very successful too, and it is most likely the visibility of an open and online presence.
I have now looked at the feature list of Kile, and also its screenshoots, and I don't get it: When I use (X)Emacs together with AUXTeX and RefTeX etc, I have basically everything that Kile boasts. The only thing I could see Emacs not matching Kile on would be "Quick Preview", but that is not explained in the documentations so I am not sure about that one either.
Whenever I use XEmacs for LaTeX, I also have immediate access to spell checking, dynamic abbreviations (a felxible completion system), and every other crazy minor mode there is. Unless Kile is extensible with an integrated scripting environment, for example a Lisp environment, I don't think Kile can keep up with Emacs!
And yes, I am an Emacs fan boy.
If you have access to them, the big "science tabloids", Nature and Science, have very good summaries and explanations of their most important articles. You'd be surprised. It is now so strange, really, because they have a large reader base from very many disciplines and these people (usually scientists) want to know and understand what happens in other fields without having to have a PhD in those fields.
You can probably find them in your local college library. Have a look!
I have still to RTFP (put it on my list), but I did notice that this is an essay, and not a research article. As such, it probably did not go to peer review as it is more of a discussion piece.
One of my dream applications is xfig combined with a modern user interface...
For a recent presentation, I tried to edit an SVG illustration generated by a computer program (using GNU plotutils) in Inkscape. This did not work well for some reason, but maybe that is due to plotutils. I had to fall back to good old xfig!
I had sat down to write a program, in Basic of course, to solve a word puzzle, a kind of crossword, that was published every week in the local daily news paper. It was probably also my first program that solved a combinatorial problem. With surprisingly little effort, I got something that worked!
When my grandfather came over a few days later, I loaded the program and brought him in to my room to show the program. I knew that he did not understand the fun I had with my computers, but since he was really into these puzzles himselves, it gave me a great opportunity to show him what a computer could do and how it worked.
I declared that I could solve said puzzle with my computer, showed him the program and how it was built up, ran the program, and concluded by printing out the solution to the puzzle. I noticed to my disappointment that my grandfather had gotten a blank stare in his eyes and had just nodded through the little presentation. Being a good grandfather, he told me how clever that was, accepted the printout, and went out to talk to the others. Ah, well, "wrong generation" I thought to myself.
One minute later my grandfather dashed back into the room again, blurting out "but this is the solution!" He had taken another look at the printout and realized what I was talking about. He was impressed! And I was really proud.
I believe the best thing would be to use both Y chromosome and mtDNA to be able to look at differences in the results in order to find weak conclusions.
A friend of mine has worked with dog populations and has mostly used mtDNA simply because it was the only well understood sequence data for the dog. There are additional advantages with mtDNA over Y chromosome data: It is a small genome and it is relatively easy to sequence large parts of it, or even the whole thing. The best property is though that in a single cell, with only one copy of Y, there are thousands of copies of mtDNA. If you are going to have people to send you data from far away, you will face the challenge of having the DNA degrading. It is then an advantage to have that genomic redundancy in mtDNA.
Personally, I have no idea about my spam rates since I filter out spam myself in Thunderbird, plus that the organizations I belong to seem to do a good job of keeping some of the spam out using SpamAssasin and other tricks.
Yes, I am aware of the "Sokal affair", and consider it one of the most clever stunts in academia. I was under the impression that Sokal wrote it himself though, without the aid of software.
I also read the paper describing "recursive transition networks", and it turns out that the idea comes from Hofstadter's "Gödel, Escher, Bach". I guess I have to actually read that book now... But, with that book in mind, does anyone know if there is a similar system for generating music? There is so much more freedom in music (you don't have to worry about logic, facts, and background knowledge) that this systems should be able to generate really cool music of various genres.
So please let's put a myth about this journal to rest. As first stated in an editorial in 1997, and since then in our Guide to Authors, if scientists wish to display drafts of their research papers on an established preprint server before or during submission to Nature or any Nature journal, that's fine by us.
I'd just like to see a link to some solid estimates I guess.
But, in my experience, large univiersities also have large libraries and they certainly have more journals than the ones that their researchers publish in if they worth their reputation. And most researchers I know read more journals than they publish in.
I guess my problem is that I simply cannot see how the author-pays model would become more expensive for a university/organization.
I meant flashy in the sense of "very well funded", which I have heard they are, and "with high ambitions". The other poster was worried that the barcode project would take resources from good old traditional taxonomy.
I could rant on but, I think this project is of some use only if combined with traditional taxonomy. The danger is that a large flashy project like this will steal research dollars away from traditional taxonomy.
It is not like the field of taxonomy is without flashy projects. Consider the Tree of life project for instance.
Given the information in the Wiki you referred to, wouldn't you say that the barcodes could provide a starting point for good taxonomy projects?
But I think the project is about actually sampling the bar code from every known species. To some extent we are getting spoiled with all the genome data coming out, gene discovery projects, whole genome sequencing, gene expression data, et.c., and at least I have more or less come to expect to find the gene data I would like to have. However, the sequencing is not uniformly sampled: It is concentrated to the important model organisms and then patched out over the animals that some researcher has had an interest in.
A "16S-ribosome" project to complement the different genome projects could be pretty cool.
They have localized versions of their system to 18 different countries. In the EU-centric Google portals, searches for city names can also come up with a prominent map24 link.
If you are interested by maps.google, you really want to check it out! No I am not in any way affiliated with map24.
Sure, sometimes solutions and implementations are influenced by each other, but that could be regarded as recombination...