I used Endnote because of a few cool capabilities.
- You would copy/paste text-citation mix to a new document (from several previous papers/thesis of yours) and it would order the citation numbers (as in IEEE and numbered format) and produce a final reference list.
- You could have multiple types of documents (Journal, Conference paper etc.)
- The numbers were always in the order of usage,
- The formats could be changed and the whole document would be updated immediately.
- The database could be saved on a cloud storage (and be available on all PCs)
- You could download Endnote files on IEEE, Elsevier (scopus, sciencedirect) and other websites.
How does Zotero fare in the features I mentioned? I used it a few years ago but it lacked integration with MS Word, so I just gave up on it.
It does all of the above, and then some.For starters its has an interface that makes sense, unlike Endnote's which is a random pile of features accrued over the years. Capturing sources takes just one click within your browser. The only exception from your list is that the journals don't provide citation style files (you refer to them as Endnote files) for zotero. However this doesn't matter. You can find pretty much any style you want at http://www.zotero.org/styles. I think they have the formatting files for several thousand journals and the list keeps growing. One very useful feature of Zotero is the ability to have multiple groups with which you can share different libraries online. It comes handy both for collaborative writing and for teaching. I switched from endnote couple of years ago, when Zotero wasn't nearly as mature as it is now and i haven't looked back.
The judge over-stepped in this case & is legislating from the bench.
No he did not. What he said was: “Our review of the statute’s plain language leads us to conclude that the primary evil sought to be avoided is the distraction the driver faces when using his or her hands to operate the phone,” and “because it is undisputed that the appellant used his wireless telephone while holding it in his hand as he drove his vehicle,”. So the person who got convicted was not merely using the phone as navigation aid, as the article would like you to believe. Instead he was holding in his hand, while driving. As the Judge rightfully points out this is prohibited by California law:
" The statute prohibits driving “while using a wireless telephone,”except when the phone is “specifically designed and configured to allow hands-free listening and talking, and is used in that manner while driving.” ( 23123, subd. (a), emphasis added). The term “using” is nowhere defined in the statute, but if the Legislature had intended to limit the application of the statute to “conversing” or“listening and talking,” as appellant maintains, it could have done so.".
So if you have your phone on a mount and use it as navigation aid, without operating it (as you should also do with regular GPS devices), it is perfectly fine according to California law and the current judgment has no bearing on such cases.
Many robocallers wait for sound (like you saying 'Ahoy') before they play the recording. If you just pick the receiver and listen the software quickly hangs up. I imagine it does the same if it detects a fax signal or voice mail 'ping'.
This is a regulatory issue (unlike many other technical issues where the US government is more than happy to legislate on). Require phone companies to block spoofed phone numbers and alert law enforcement for their point of origin, unless they are explicitly authorized by the owner of the phone number. Phone companies have the technical capability to do this. What they lack is the incentive to do it. A simple fine would be more than enough to convince them them that it doesn't make business sense to allow robocalls from spoofed phone numbers. We don't even need new laws for this. I would imagine that FTC and FCC have the authority to put such regulations in place under existing laws like once that establish the 'Do not call' list and outlaw wirefraud. Where I can get my $50K?
US coal exports to China were on track to double last year and demand for US metallurgical coal, the high-heat content coking coal that is used for steelmaking, is so great in Asia that shipments make a round-the-world journey from Appalachia as they are sent by train to the port of Baltimore, where they steam to sea through the Chesapeake Bay, then south across the Atlantic Ocean and around Africa's Cape of Good Hope to reach Asian ports.
All I can say is WOW! Does anybody remember the times when the industrial west was importing cheap raw materials from third world countries to support its manufacturing?
I second this. Have fun and travel. Depending how your life turns, this literally may be your last opportunity for the next 20-30 years to see the world. Five years is a bit optimistic for biological sciences PhD these days. Then you will have to get a job (or a postdoc), you may have family and kids..... None of these are conducive to long periods away from home.
This will create thousands of jobs in the furniture industry. Congress should mandate that all new furniture on the market be self destructing to help the US industry. I know it would be mostly made in Asia, but it will be design by US high-tech companies (mostly, maybe) that one day will grow to be the Apple's or IBM's of the furniture industry. The world will envy us.
'I believe in evading and disintermediating the state. It seemed to be something we could build an organization around.Just like Bitcoin can circumvent financial mechanisms.'
This was published couple of years ago by Gibson and Venter. You can even buy a kit from New England Biolobas (very fine company I must say). What the software does is to save you little effort in writing the perl/python scripts for automating the design. I wouldn't call this a big hurdle for the would be terrorists.
Runs on cheap hardware, the OS is offered for free and somebody else takes care of developing the ecosystem with no strings attached. So if you are a carrier you can offer a "good enough" smart phone for the price of a feature phone. I bet it will be an instant success in developing countries markets and as a first phone for kids in developed countries (hence the Sprint and DT interest in it). The only serious competition it can face is from Android. It will be interesting to see if Google will bother maintaining android codebase that can run on low end phones or just pay to be the default search engine on the Firefox phones and make money on ads and clicks.
Why is an injury lawyer’s marketing campaign posted at all on Slashdot, let alone next to an unrelated LA time article? The article quoted in the second part of the post actually says exactly the opposite of what the post states. Does anybody on slashdot know what 'editor' means? What grades did the slashdot editors get on reading and comprehension on elementary school?
I agree with you. "Higher" wasn't the best choice of words, and I have had my encounters of irreproducible and not well supported but otherwise "innovative" discoveries in Science.
>> The Warren-Davis paper was rejected by both Science and Nature before its acceptance by the Proceedings of the National Academy of Science, perhaps suggesting the degree to which the 'mouse model' has become entrenched within the medical research community.
Or maybe it was rejected because it isn't a good paper? Just a thought.
I would say it is a very good paper, but Science and Nature have somewhat higher benchmark for accepting papers: the paper has to be truly innovative and to open new directions for research. The PNAS paper that the post links to is very well research and convincingly shows how bad the mouse models for sepsis are in representing the human disease. Well, we know that animal models have quirks and some are really bad, and some are really good. So this is one more addition to the first list, which is very important if you are trying to develop a drug for sepsis, but not really ground braking. Their main conclusion is that we need to do genome wide profiling to compare the responses of the animal models to the responses in humans to make sure they match. I can point you to a half a dozen papers that have come to the same conclusion. My guess is that if they have used the data to develop or suggest a new animal model that can do a better job, the paper would have been enthusiastically accepted in the Science and Nature journals. This is probably what they would do next.
NSF plans to cut the funding for the National Radio Astronomy Observatory at Green Bank. So I guess the kids will soon have WiFi and cell phones. This is a good thing, right?
By definition large manipulative bets would be outliers. Calculate the odds by reducing the weight of the outliers and provide both weighted and unweighted odds to the participants.
Well this is some seriously good news. The bloody thing was not only completely useless but was sucking the life out of my desktop. It should have never been enabled by default.
We have a pretty good idea on this one. Specific polymerases have specific sequences which they respond to, defining the start sequences of genes. It is possible we have missed some polymerase, but the likelihood is low given the extensive searches which have been done for them. As well, regions which are genes have a distinctively different character than regions which are not genes (at least in the general sense).
You justify an assumption with assumption. The core promoter sequences are so degenerate that they can be found pretty much anywhere. This has lead to misannotation of long genes as multiple single genes. There are a number other causes of annotation errors.
Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies
Alexandra M. Schnoes, Shoshana D. Brown, Igor Dodevski, Patricia C. Babbitt
Misannotations of rRNA can now generate 90% false positive protein matches in metatranscriptomic studies.
Tripp HJ, Hewson I, Boyarsky S, Stuart JM, Zehr JP.
There are also numerous examples of manually curated entries that are wrong because people studied non-existent proteins as a result of cloning artifacts or ignoring nonsense mediated decay. Here is one example where a transcripts containing unspliced introns that are eliminated by NMD have been studied and ascribed a function Zhu J, Chen X. MCG10, a novel p53 target gene that encodes a KH domain RNA-binding protein, is capable of inducing apoptosis and cell cycle arrest in G(2)-M. Mol Cell Biol. 2000 Aug;20(15):5602-18. (accessions AF257770, AF257771)
2. We can predict the protein sequence from the sequence of the gene.
We also have a pretty good idea about this, due to decades and decades of biologists trying to figure out the answer to this problem. The genetic code turns out to differ in some organisms from what we think of as the default. Sometimes multiple amino acids are coded for by the same sequence of bases, and so multiple proteins are produced from the identical coding region of DNA. Sometimes proteins are produced with modified amino acids, which are not explicitly coded for in the DNA of the gene, but rather by the activity of other proteins defined elsewhere by DNA. (This is a stochastic process and interference in the distribution of outcomes can sometimes result in pathological consequences.) In some organisms, the DNA is decompressed into RNA which is then translated into protein in a more typical way. (Extra bases are incorporated into the RNA in a repeatable way that results in amino acids added which were not defined in the sequence of DNA of the gene being added to proteins.) There's a whole bunch of stuff on alternate splicing, which we explicitly know that we don't know how to predict, that produces variations in protein sequence from a single gene sequence.
Your pretty good idea is applicable to about 60% of the long reading frames and even less applicable to short ORFs: Ingolia NT, Lareau LF, Weissman JS. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell. 2011 Nov 11;147(4):789-802.. Mind you this does not include processes like RNA editing, that can further complicate how we predict protein sequence based on gene sequence.
3. One protein can not be the product of two genes.
There are plenty of ways in which two separate genes can produce an identical protein. This actually happens ALL THE TIME in mammals, since we have two copies of every gene and most of these pairs have identical sequence. Even if the genes produce the identical protein through different mechanisms, if the protein is identical... then the protein is identical.
I wasn't commenting on ploidity. I had in mind things like trans-spli
That is all nice, but most of these prediction algorithms are based on one or more of the following assumptions, which are not always true:
1. We have accurate mapping of the genes.
2. We can predict the protein sequence from the sequence of the gene.
3. One protein can not be the product of two genes.
4. We have a good understanding of what the functions of the proteins in the training set are.
5. If two proteins have similar sequence, they must have similar functions.
6. One protein has one function.
7. A protein has a function.
So any prediction should be taken with a grain of salt and experimentally verified, which brings us back to "... with its inherent difficulty and expense, experimental characterization of function cannot scale up to accommodate the vast amount of sequence data already available...."
This is not going to help much, especially if the choice is not binary. Of course you can vastly increase the number of pilots to reduce the noise. But then again it may just turn into something like this.
Slashdot Mirror
I used Endnote because of a few cool capabilities.
- You would copy/paste text-citation mix to a new document (from several previous papers/thesis of yours) and it would order the citation numbers (as in IEEE and numbered format) and produce a final reference list. - You could have multiple types of documents (Journal, Conference paper etc.) - The numbers were always in the order of usage, - The formats could be changed and the whole document would be updated immediately. - The database could be saved on a cloud storage (and be available on all PCs) - You could download Endnote files on IEEE, Elsevier (scopus, sciencedirect) and other websites.
How does Zotero fare in the features I mentioned? I used it a few years ago but it lacked integration with MS Word, so I just gave up on it.
It does all of the above, and then some.For starters its has an interface that makes sense, unlike Endnote's which is a random pile of features accrued over the years. Capturing sources takes just one click within your browser. The only exception from your list is that the journals don't provide citation style files (you refer to them as Endnote files) for zotero. However this doesn't matter. You can find pretty much any style you want at http://www.zotero.org/styles. I think they have the formatting files for several thousand journals and the list keeps growing. One very useful feature of Zotero is the ability to have multiple groups with which you can share different libraries online. It comes handy both for collaborative writing and for teaching. I switched from endnote couple of years ago, when Zotero wasn't nearly as mature as it is now and i haven't looked back.
Where are my mod points when I need them. Please mod the parent up!
The judge over-stepped in this case & is legislating from the bench.
No he did not. What he said was: “Our review of the statute’s plain language leads us to conclude that the primary evil sought to be avoided is the distraction the driver faces when using his or her hands to operate the phone,” and “because it is undisputed that the appellant used his wireless telephone while holding it in his hand as he drove his vehicle,”. So the person who got convicted was not merely using the phone as navigation aid, as the article would like you to believe. Instead he was holding in his hand, while driving. As the Judge rightfully points out this is prohibited by California law:
" The statute prohibits driving “while using a wireless telephone,”except when the phone is “specifically designed and configured to allow hands-free listening and talking, and is used in that manner while driving.” ( 23123, subd. (a), emphasis added). The term “using” is nowhere defined in the statute, but if the Legislature had intended to limit the application of the statute to “conversing” or“listening and talking,” as appellant maintains, it could have done so.".
So if you have your phone on a mount and use it as navigation aid, without operating it (as you should also do with regular GPS devices), it is perfectly fine according to California law and the current judgment has no bearing on such cases.
Many robocallers wait for sound (like you saying 'Ahoy') before they play the recording. If you just pick the receiver and listen the software quickly hangs up. I imagine it does the same if it detects a fax signal or voice mail 'ping'.
This is a regulatory issue (unlike many other technical issues where the US government is more than happy to legislate on). Require phone companies to block spoofed phone numbers and alert law enforcement for their point of origin, unless they are explicitly authorized by the owner of the phone number. Phone companies have the technical capability to do this. What they lack is the incentive to do it. A simple fine would be more than enough to convince them them that it doesn't make business sense to allow robocalls from spoofed phone numbers. We don't even need new laws for this. I would imagine that FTC and FCC have the authority to put such regulations in place under existing laws like once that establish the 'Do not call' list and outlaw wirefraud. Where I can get my $50K?
US coal exports to China were on track to double last year and demand for US metallurgical coal, the high-heat content coking coal that is used for steelmaking, is so great in Asia that shipments make a round-the-world journey from Appalachia as they are sent by train to the port of Baltimore, where they steam to sea through the Chesapeake Bay, then south across the Atlantic Ocean and around Africa's Cape of Good Hope to reach Asian ports.
All I can say is WOW! Does anybody remember the times when the industrial west was importing cheap raw materials from third world countries to support its manufacturing?
Or you can add "license.icopyright.net/rights/" to your adblock filter list and never see the stupid overlay ever again.
I sure hope you are joking.
I second this. Have fun and travel. Depending how your life turns, this literally may be your last opportunity for the next 20-30 years to see the world. Five years is a bit optimistic for biological sciences PhD these days. Then you will have to get a job (or a postdoc), you may have family and kids ..... None of these are conducive to long periods away from home.
This will create thousands of jobs in the furniture industry. Congress should mandate that all new furniture on the market be self destructing to help the US industry. I know it would be mostly made in Asia, but it will be design by US high-tech companies (mostly, maybe) that one day will grow to be the Apple's or IBM's of the furniture industry. The world will envy us.
'I believe in evading and disintermediating the state. It seemed to be something we could build an organization around.Just like Bitcoin can circumvent financial mechanisms.'
What's this? Exercise in syllogism?
Price isn't the only determinant of whether something is a 'routine part of medicine'.
yes it is, do you know how much money your doctor can make by adding this to your routine blood work?
This was published couple of years ago by Gibson and Venter. You can even buy a kit from New England Biolobas (very fine company I must say). What the software does is to save you little effort in writing the perl/python scripts for automating the design. I wouldn't call this a big hurdle for the would be terrorists.
Runs on cheap hardware, the OS is offered for free and somebody else takes care of developing the ecosystem with no strings attached. So if you are a carrier you can offer a "good enough" smart phone for the price of a feature phone. I bet it will be an instant success in developing countries markets and as a first phone for kids in developed countries (hence the Sprint and DT interest in it). The only serious competition it can face is from Android. It will be interesting to see if Google will bother maintaining android codebase that can run on low end phones or just pay to be the default search engine on the Firefox phones and make money on ads and clicks.
Why is an injury lawyer’s marketing campaign posted at all on Slashdot, let alone next to an unrelated LA time article? The article quoted in the second part of the post actually says exactly the opposite of what the post states. Does anybody on slashdot know what 'editor' means? What grades did the slashdot editors get on reading and comprehension on elementary school?
... that happy people do not use Twitter.
Don't forget Bruce Willis, who just did the fifth Die Hard movie. He's gotta be an old fart by now.
Ok, I am confused. Is the example of the Die Hard 5 movies supposed to support or counter the parent's point of view. Please clarify.
I agree with you. "Higher" wasn't the best choice of words, and I have had my encounters of irreproducible and not well supported but otherwise "innovative" discoveries in Science.
>> The Warren-Davis paper was rejected by both Science and Nature before its acceptance by the Proceedings of the National Academy of Science, perhaps suggesting the degree to which the 'mouse model' has become entrenched within the medical research community.
Or maybe it was rejected because it isn't a good paper? Just a thought.
I would say it is a very good paper, but Science and Nature have somewhat higher benchmark for accepting papers: the paper has to be truly innovative and to open new directions for research. The PNAS paper that the post links to is very well research and convincingly shows how bad the mouse models for sepsis are in representing the human disease. Well, we know that animal models have quirks and some are really bad, and some are really good. So this is one more addition to the first list, which is very important if you are trying to develop a drug for sepsis, but not really ground braking. Their main conclusion is that we need to do genome wide profiling to compare the responses of the animal models to the responses in humans to make sure they match. I can point you to a half a dozen papers that have come to the same conclusion. My guess is that if they have used the data to develop or suggest a new animal model that can do a better job, the paper would have been enthusiastically accepted in the Science and Nature journals. This is probably what they would do next.
NSF plans to cut the funding for the National Radio Astronomy Observatory at Green Bank. So I guess the kids will soon have WiFi and cell phones. This is a good thing, right?
By definition large manipulative bets would be outliers. Calculate the odds by reducing the weight of the outliers and provide both weighted and unweighted odds to the participants.
Well this is some seriously good news. The bloody thing was not only completely useless but was sucking the life out of my desktop. It should have never been enabled by default.
1. We have accurate mapping of the genes.
We have a pretty good idea on this one. Specific polymerases have specific sequences which they respond to, defining the start sequences of genes. It is possible we have missed some polymerase, but the likelihood is low given the extensive searches which have been done for them. As well, regions which are genes have a distinctively different character than regions which are not genes (at least in the general sense).
You justify an assumption with assumption. The core promoter sequences are so degenerate that they can be found pretty much anywhere. This has lead to misannotation of long genes as multiple single genes. There are a number other causes of annotation errors.
There are also numerous examples of manually curated entries that are wrong because people studied non-existent proteins as a result of cloning artifacts or ignoring nonsense mediated decay. Here is one example where a transcripts containing unspliced introns that are eliminated by NMD have been studied and ascribed a function Zhu J, Chen X. MCG10, a novel p53 target gene that encodes a KH domain RNA-binding protein, is capable of inducing apoptosis and cell cycle arrest in G(2)-M. Mol Cell Biol. 2000 Aug;20(15):5602-18. (accessions AF257770, AF257771)
2. We can predict the protein sequence from the sequence of the gene.
We also have a pretty good idea about this, due to decades and decades of biologists trying to figure out the answer to this problem. The genetic code turns out to differ in some organisms from what we think of as the default. Sometimes multiple amino acids are coded for by the same sequence of bases, and so multiple proteins are produced from the identical coding region of DNA. Sometimes proteins are produced with modified amino acids, which are not explicitly coded for in the DNA of the gene, but rather by the activity of other proteins defined elsewhere by DNA. (This is a stochastic process and interference in the distribution of outcomes can sometimes result in pathological consequences.) In some organisms, the DNA is decompressed into RNA which is then translated into protein in a more typical way. (Extra bases are incorporated into the RNA in a repeatable way that results in amino acids added which were not defined in the sequence of DNA of the gene being added to proteins.) There's a whole bunch of stuff on alternate splicing, which we explicitly know that we don't know how to predict, that produces variations in protein sequence from a single gene sequence.
Your pretty good idea is applicable to about 60% of the long reading frames and even less applicable to short ORFs: Ingolia NT, Lareau LF, Weissman JS. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell. 2011 Nov 11;147(4):789-802.. Mind you this does not include processes like RNA editing, that can further complicate how we predict protein sequence based on gene sequence.
3. One protein can not be the product of two genes.
There are plenty of ways in which two separate genes can produce an identical protein. This actually happens ALL THE TIME in mammals, since we have two copies of every gene and most of these pairs have identical sequence. Even if the genes produce the identical protein through different mechanisms, if the protein is identical... then the protein is identical.
I wasn't commenting on ploidity. I had in mind things like trans-spli
That is all nice, but most of these prediction algorithms are based on one or more of the following assumptions, which are not always true:
So any prediction should be taken with a grain of salt and experimentally verified, which brings us back to " ... with its inherent difficulty and expense, experimental characterization of function cannot scale up to accommodate the vast amount of sequence data already available ...."
This is not going to help much, especially if the choice is not binary. Of course you can vastly increase the number of pilots to reduce the noise. But then again it may just turn into something like this.