I think a lot of you are missing the point. Many of you have pointed out that the time frame is wrong because he missed it by such and such. But one must consider the search space in which the predictions are in context of . . . all future time which is a large search space. It is obvious that the earthquake occurred outside of the time frame of the prediction (let alone the geographic region), but there is promise to this line of research for sure, especially in light of the small margin of error in light of the backdrop of the search space. And yes, it would be nice to get it down to a day so people take safety measures.
To submit a more abstract statement, models (whether for earthquakes or materials science) such as these are growing in increasing importance as our evolving society learns to understand our surroundings.
It's difficult to evaluate all the various statistical packages. I would love to read some sort of comparison among the various packages, both commercial and free. For instance, which packages have some sort of GUI? What types of programming languages does each one use? How does each one scale? Is there a particular feature that separates a particular package?
Anyone?
It's time I wean myself off of excel particularly since the other day I couldn't even create a histogram since my dataset is more than ~64,000 data points, which is apparently excel's limit.
Does anyone in the community know of a good replacement for excel that scales well to many data points but also has some sort of user-interface so that I can do some visual manipulations if I want to. I understand that most of these packages come with their own interactive shell and languages, but I would like to have both the command-line interface and a visual interface (like that of excel), while still being able to scale to many data points.
Any suggestions?
"You and the parent just don't get it. The point of Free Software and Open Source Software is to create better software. Its not about making more money from the software. Its not even about making less money from the software. Its just about making better, more useful software."
I myself wholly believe that innovation is what is really important. But then why the insistence for the software to be free? Is there no innovation in software that someone needs to purchase?
When it comes down to it, there are plenty of examples both on the open-source and closed-source side of the fence where innovation clearly took a second seat. No matter which way we as a community cut it, it's time we all start being real serious about innovating. This certainly means that companies with billions and billions in liquid cash should stop sitting on top of cash cows and stagnating their software because it's about the revenue model and not how much one can aspire to innovate. It certainly also means organizations and companies adopting open-source as a weapon to compete against other companies, mostly based upon the low price point, need to realize that they lost on the innovation front and that innovation is ultimately going to save their organization and innovation is the right thing to pursue. Finally, I think all this certainly means that we would all like to stop seeing the same windows-clone-like desktop on many linux systems and see something different. What's up with the start button on all these linux desktops? True, MS has stagnated the OS technology in various ways, but I don't see linux blazing the trail on this front either.
On the contrary, bioinformaticists have gone to great lengths to usher in the field of genomics, proteomics, etc. and allow wet-lab researchers to achieve new wonders. This cannot be argued against very easily. Computational biologists put forth these tools so that more meaningful analysis is achieved. If people of computational nature feel threatened, why would we dedicate part of our research to put forth these very "tools" you say we are threatened by? I believe the common consensus is that "traditional" biologists feel threatened by these new approaches to the life sciences. I think there is room for both computational and wet-lab research. In fact, it should be said quite strongly that both are essential to help us usher in more positive discoveries.
No one here has said that wet-lab researchers cannot employ bioinformatics software. In fact, that is the whole point, they need to employ it. What has been said is that perl is not necessarily popular for bioinformatics, but instead is popular for simple text processing, which is common in many fields and should not be confused with the core of computational biology.
These "bench scientists" you refer to, are NOT bioinformaticists. That needs to be clear. They are primarly wet-lab researchers. Using a computer does not mean you are a bioinformaticist. Computers are used for a lot of things, including basic parsing, which according to you is enough to transform a wet-lab researcher into a bioinformaticist. The core of computational biology is the research and development of algorithms, mathematical models, and computational approaches in the life sciences. The work you describe is merely the basic use of a programming language. If I parse through files that contain small molecule compounds, that doesn't make me a cheminformaticist. If I parse through a file that contains action potentials, that does not make me a neuroinformaticist. Perl is simply popular because, like you say, "bench scientists" employ it in basic tasks.
I am a bioinformaticist and I don't use perl that much. I have often wondered why perl was so popular myself. I think a lot of it has to do with the misconception that perl is the only language that works with text files. So maybe I should back up for a minute . . . there a part of computational biology that has to go through the uglies of working with raw data in files . . . thus the need to parse through them and reformat them.
Almost every language has text processing capabilities. Here's a dirty little secret most people don't know . . . regular expressions for bioinformatics work is not as important as people would like you to believe. The fact of the matter is, most of the data bioinformatics researchers encounter is structured data. Simple string parsing and tokenization is all that is needed. Regulars expressions past the most simple are rarely encountered. In fact, a lot of the data a bioinformaticist encounters is in either XML, tab-delimited, or CSV. For the text processing part of my tasks, I have often used awk to blow my way right through a text file. Of course perl can do the same thing, but I'd like to point out that awk is great when so much of your data is in tabular format (we've got databases everywhere in this field). I also find Java's String, StringTokenizer, BufferedReader and Writer mixed with the FileReader and Writer classes to work great with text files too.
This brings me to my last point. Perl is horrible for some areas of bioinformatics. A lot of people employed in so-called bioinformatics positions spend like 90% of their day parsing through text files. Most people don't know that there are bioinformaticists who spend very little of their day doing that, but instead are developing algorithms and such that usually require a different language. For instance, I'd hate to run a Hidden Markov modeler with the Viterbi algorithm coded in Perl:) Or how about a massive simulation during haplotype reconstructions in perl? Or maybe a support vector machine in perl? Hee, you get the idea. For these tasks C is often chosen. Particularly if one employs parallel programming. I encourage bioinformaticists to explore other languages besides perl so that they have a vast array of expression for the multi-facted charges a computational biologist is expected to handle.
Also keep in mind that even though a 64-bit processor with a 64-bit memory manager in an OS will allow for increased memory addressing, the chipset must also support the addressable memory. 8 GB is the limit in most boxes.
I think what might be interesting in the future is the synergy between MRAM and full 64-bit processing . . . with MRAM cheap enough and abundant enough, virtual memory will be eliminated with applicatioins getting free reign across the entire addressable space that doubles as the entire storage space.
Has anyone else noticed that the schedule of when each Democratic primary takes place is all wrong? The way the current system is set up, it is almost always the case that the earlier primaries, such as Iowa and New Hampshire, have more of a vote than later primaries. This whole concept of "momentum" should not be a deciding factor in who will cinch the Democratic presidential nomination. It makes no sense that a Union would back out of supporting one candidate simply because another candidate is building this so-called "momentum". Huh? So is the union saying that it had no clue as to why they supported the candidate in the first place? Is this supposed union backing away from its core values and shifting their money to the front-runner? Whether we're talking about a union or an individual, isn't momentum such a strong phenomenon that the system should be changed? The status quo has it so that states with later primaries have less of a say in such an important election. The status quo has it so that votes in states like New Jersey, with their primary in June, have virtually no say in who claims the nomination because there is only one candidate left by the time people from that state can vote. In this year's election, most people's votes after New Hampshire's primary didn't seem to matter as much since a front-runner had already been decided. I think all this is said best by the following:
"Front-loading extravanganzas such as Super Tuesday and Mega Tuesday are the WMDs in presidential politics. They kill candidacies by the score. In the last three contested Republican presidential nominations, 1988, 1996, 2000, the campaign season began with 6, 10, 12 candidates respectively, in each case the race was conceded to the front-runner by the Ides of March."
I propose that the primaries are all held on the same day or that the results are not made public until after the winner is determined.
It's a failure of democracy to see a candidates message being drowned out or silenced simply because he/she is running out of money (for ads and ground worker help to get their message out) because people jump ship to support the front-runner so their resources aren't wasted. Every vote in every state should count just the same. It's no secret that states have been trying to move their primaries up earlier and earlier. California, with a whopping 400+ delegates, in 1996 moved their primary from the first Tuesday in June to the second Tuesday in March. Being discontent with that, the state moved its primary again in 2000 to the first Tuesday of March. Now, they are part of Mega Tuesday and Californians have more of a say. North Dakota made a similar move this year since candidates mostly never campaign in that state as if it didn't matter. Now, with an earlier primary, candidates actually visited North Dakota this year.
There are quite a few apps that chew up CPU while seemingly doing nothing. It's probably because the software is polling for input. Regardless, I simply issue the following command:
kill -STOP pid
To start the app again I issue:
kill -CONT pid
This stops all CPU waste from "resting" applications.
I think you're missing the heart of open-source too. You even used the word "customers" when you describe this so-called "freedom". Let's get one thing straight and on the table here . . . open-source IS about the love we hackers/programmers/software engineers have for software and our desire to share it with one another and learn from it. This is freedom. It is not about "customers" as you say.
And you fail to carry across a point with your comment regarding the fact you don't have to give away your software for free. No one can deny that the major selling point of how these large corporations are using open-source is the low price point (whether free or not). Open-source to these companies is a business tactic first and foremost. I'd hate to see open-source developers draw inspiration from a legion of corporate developers from a corporation that hopes that they can drive a wedge into someone else's product line by either giving the software away for free, or for an extremely low price.
I thought open-source developers simply write software because they love to and do not seek any compensation.
It's amazing how people haven't seen how IBM, Sun, etc. have hijacked true open-source and turned it into a capitalistic weapon.
To me, open-source will always be much more than simply being able to see the code and getting software for free. The heart of open-source software has been tarnished by these large corporations that use it to play "price point" wars with each other.
Slashdot Mirror
I think a lot of you are missing the point. Many of you have pointed out that the time frame is wrong because he missed it by such and such. But one must consider the search space in which the predictions are in context of . . . all future time which is a large search space. It is obvious that the earthquake occurred outside of the time frame of the prediction (let alone the geographic region), but there is promise to this line of research for sure, especially in light of the small margin of error in light of the backdrop of the search space. And yes, it would be nice to get it down to a day so people take safety measures. To submit a more abstract statement, models (whether for earthquakes or materials science) such as these are growing in increasing importance as our evolving society learns to understand our surroundings.
It's difficult to evaluate all the various statistical packages. I would love to read some sort of comparison among the various packages, both commercial and free. For instance, which packages have some sort of GUI? What types of programming languages does each one use? How does each one scale? Is there a particular feature that separates a particular package? Anyone?
It's time I wean myself off of excel particularly since the other day I couldn't even create a histogram since my dataset is more than ~64,000 data points, which is apparently excel's limit. Does anyone in the community know of a good replacement for excel that scales well to many data points but also has some sort of user-interface so that I can do some visual manipulations if I want to. I understand that most of these packages come with their own interactive shell and languages, but I would like to have both the command-line interface and a visual interface (like that of excel), while still being able to scale to many data points. Any suggestions?
I myself wholly believe that innovation is what is really important. But then why the insistence for the software to be free? Is there no innovation in software that someone needs to purchase?
When it comes down to it, there are plenty of examples both on the open-source and closed-source side of the fence where innovation clearly took a second seat. No matter which way we as a community cut it, it's time we all start being real serious about innovating. This certainly means that companies with billions and billions in liquid cash should stop sitting on top of cash cows and stagnating their software because it's about the revenue model and not how much one can aspire to innovate. It certainly also means organizations and companies adopting open-source as a weapon to compete against other companies, mostly based upon the low price point, need to realize that they lost on the innovation front and that innovation is ultimately going to save their organization and innovation is the right thing to pursue. Finally, I think all this certainly means that we would all like to stop seeing the same windows-clone-like desktop on many linux systems and see something different. What's up with the start button on all these linux desktops? True, MS has stagnated the OS technology in various ways, but I don't see linux blazing the trail on this front either.
On the contrary, bioinformaticists have gone to great lengths to usher in the field of genomics, proteomics, etc. and allow wet-lab researchers to achieve new wonders. This cannot be argued against very easily. Computational biologists put forth these tools so that more meaningful analysis is achieved. If people of computational nature feel threatened, why would we dedicate part of our research to put forth these very "tools" you say we are threatened by? I believe the common consensus is that "traditional" biologists feel threatened by these new approaches to the life sciences. I think there is room for both computational and wet-lab research. In fact, it should be said quite strongly that both are essential to help us usher in more positive discoveries. No one here has said that wet-lab researchers cannot employ bioinformatics software. In fact, that is the whole point, they need to employ it. What has been said is that perl is not necessarily popular for bioinformatics, but instead is popular for simple text processing, which is common in many fields and should not be confused with the core of computational biology.
These "bench scientists" you refer to, are NOT bioinformaticists. That needs to be clear. They are primarly wet-lab researchers. Using a computer does not mean you are a bioinformaticist. Computers are used for a lot of things, including basic parsing, which according to you is enough to transform a wet-lab researcher into a bioinformaticist. The core of computational biology is the research and development of algorithms, mathematical models, and computational approaches in the life sciences. The work you describe is merely the basic use of a programming language. If I parse through files that contain small molecule compounds, that doesn't make me a cheminformaticist. If I parse through a file that contains action potentials, that does not make me a neuroinformaticist. Perl is simply popular because, like you say, "bench scientists" employ it in basic tasks.
Almost every language has text processing capabilities. Here's a dirty little secret most people don't know . . . regular expressions for bioinformatics work is not as important as people would like you to believe. The fact of the matter is, most of the data bioinformatics researchers encounter is structured data. Simple string parsing and tokenization is all that is needed. Regulars expressions past the most simple are rarely encountered. In fact, a lot of the data a bioinformaticist encounters is in either XML, tab-delimited, or CSV. For the text processing part of my tasks, I have often used awk to blow my way right through a text file. Of course perl can do the same thing, but I'd like to point out that awk is great when so much of your data is in tabular format (we've got databases everywhere in this field). I also find Java's String, StringTokenizer, BufferedReader and Writer mixed with the FileReader and Writer classes to work great with text files too.
This brings me to my last point. Perl is horrible for some areas of bioinformatics. A lot of people employed in so-called bioinformatics positions spend like 90% of their day parsing through text files. Most people don't know that there are bioinformaticists who spend very little of their day doing that, but instead are developing algorithms and such that usually require a different language. For instance, I'd hate to run a Hidden Markov modeler with the Viterbi algorithm coded in Perl :) Or how about a massive simulation during haplotype reconstructions in perl? Or maybe a support vector machine in perl? Hee, you get the idea. For these tasks C is often chosen. Particularly if one employs parallel programming. I encourage bioinformaticists to explore other languages besides perl so that they have a vast array of expression for the multi-facted charges a computational biologist is expected to handle.
Also keep in mind that even though a 64-bit processor with a 64-bit memory manager in an OS will allow for increased memory addressing, the chipset must also support the addressable memory. 8 GB is the limit in most boxes. I think what might be interesting in the future is the synergy between MRAM and full 64-bit processing . . . with MRAM cheap enough and abundant enough, virtual memory will be eliminated with applicatioins getting free reign across the entire addressable space that doubles as the entire storage space.
Has anyone else noticed that the schedule of when each Democratic primary takes place is all wrong? The way the current system is set up, it is almost always the case that the earlier primaries, such as Iowa and New Hampshire, have more of a vote than later primaries. This whole concept of "momentum" should not be a deciding factor in who will cinch the Democratic presidential nomination. It makes no sense that a Union would back out of supporting one candidate simply because another candidate is building this so-called "momentum". Huh? So is the union saying that it had no clue as to why they supported the candidate in the first place? Is this supposed union backing away from its core values and shifting their money to the front-runner? Whether we're talking about a union or an individual, isn't momentum such a strong phenomenon that the system should be changed? The status quo has it so that states with later primaries have less of a say in such an important election. The status quo has it so that votes in states like New Jersey, with their primary in June, have virtually no say in who claims the nomination because there is only one candidate left by the time people from that state can vote. In this year's election, most people's votes after New Hampshire's primary didn't seem to matter as much since a front-runner had already been decided. I think all this is said best by the following: "Front-loading extravanganzas such as Super Tuesday and Mega Tuesday are the WMDs in presidential politics. They kill candidacies by the score. In the last three contested Republican presidential nominations, 1988, 1996, 2000, the campaign season began with 6, 10, 12 candidates respectively, in each case the race was conceded to the front-runner by the Ides of March." I propose that the primaries are all held on the same day or that the results are not made public until after the winner is determined. It's a failure of democracy to see a candidates message being drowned out or silenced simply because he/she is running out of money (for ads and ground worker help to get their message out) because people jump ship to support the front-runner so their resources aren't wasted. Every vote in every state should count just the same. It's no secret that states have been trying to move their primaries up earlier and earlier. California, with a whopping 400+ delegates, in 1996 moved their primary from the first Tuesday in June to the second Tuesday in March. Being discontent with that, the state moved its primary again in 2000 to the first Tuesday of March. Now, they are part of Mega Tuesday and Californians have more of a say. North Dakota made a similar move this year since candidates mostly never campaign in that state as if it didn't matter. Now, with an earlier primary, candidates actually visited North Dakota this year.
How can we tell the email is genuine? It's not that hard to spoof an email.
There are quite a few apps that chew up CPU while seemingly doing nothing. It's probably because the software is polling for input. Regardless, I simply issue the following command: kill -STOP pid To start the app again I issue: kill -CONT pid This stops all CPU waste from "resting" applications.
I love OS X!!! :)
Me so happy.
I think you're missing the heart of open-source too. You even used the word "customers" when you describe this so-called "freedom". Let's get one thing straight and on the table here . . . open-source IS about the love we hackers/programmers/software engineers have for software and our desire to share it with one another and learn from it. This is freedom. It is not about "customers" as you say. And you fail to carry across a point with your comment regarding the fact you don't have to give away your software for free. No one can deny that the major selling point of how these large corporations are using open-source is the low price point (whether free or not). Open-source to these companies is a business tactic first and foremost. I'd hate to see open-source developers draw inspiration from a legion of corporate developers from a corporation that hopes that they can drive a wedge into someone else's product line by either giving the software away for free, or for an extremely low price.
I thought open-source developers simply write software because they love to and do not seek any compensation. It's amazing how people haven't seen how IBM, Sun, etc. have hijacked true open-source and turned it into a capitalistic weapon. To me, open-source will always be much more than simply being able to see the code and getting software for free. The heart of open-source software has been tarnished by these large corporations that use it to play "price point" wars with each other.