but this is exactly the kind of nonsense that these Free/Open Source hypocrites don't like to talk about. "Oh dear, no way would I use Microsoft products. Everything should be free! Free software, free tech support, free ISPs, etc."
You have no idea what you are talking about. Free software is about freedom to reuse, redistribute, and change software that you use. That has nothing to do with whether you pay for the software or not. I have paid a lot of money for free software over the years, as have many other people. In fact, tech support and services are some of the main ways in which free software advocates recommend making money with free software.
Don't mean to sound vicious or judgemental or anything,
I don't question your scientific qualifications (which I don't know anything about), I question you judgement. I have been through several cycles of hype-and-bust in different academic disciplines. It derails scientific careers, slows down research, locks up scientific results in corporate vaults, and is generally destructive. It also attracts opportunists to fields in which they have no interest or skill.
Progress in bioinformatics has been steady over decades. Many of the capabilities we have now are based on methods and ideas developed a long time ago, although they have much more impact now with powerful PCs.
What we need is steady, continued public research funding in the application of computers to biological systems. What you advocate, and what follows from hyping up a field, rapid expansion and large new private investments, is destructive in the long run.
Of course they were. However back in the 60's, 70's or 80's or even 90's I could not perform quick sequence searches of various species, get a 3-D appreciation of a particular protein and then design and submit an antibody or drug for that sequence in an afternoon. In order to do this, I need databases that have been populated with information developed over decades and tools to mine those databases. That is some of what bioinformatics is about.
Since you admit that the technologies and software were already available decades ago, what is your point? Are you saying that bioinformatics is about being able to do something in an afternoon, as opposed to having to run it on a mainframe over a few days?
I never said that bioinformatics began with sequencing the human genome. Rather I was using it as an example as it was widely publicized and well known. Please re-read my previous comment.
You wrote:
Actually, bioinformatics is just starting out and the hype has not even begun.
A bit snippy are we?
No, not at all. It is simply evident from your post that you are a bit taken with the hype and a bit unfamiliar with the history of molecular biology, even if you talk at length and repeatedly about "T's, G's, C's, and A's".
First of all, it takes many months to get there and many to get back - regardless of whether you land or not.
Yes, but if you land, you need to figure out how to get several 200 pound people to land softly on the surface and them and their life support back into orbit. That's expensive. With mobile robots, you land them hard, explore, and leave them there. To get samples back, you only need to lift a few pounds into orbit--much simpler.
Remote-controlled robots can be controlled just as well from earth - ok, a round trip for a command and it's response takes a few minutes but why would that matter?
With subsecond delays, you get telepresence: people can interact fairly normally. With delays much greater than a second, you don't get telepresence anymore: every move needs to be worked out carefully on paper. And, yes, it does make a difference whether a mission takes a day (telepresence) or a year (many minutes delay for every move).
how can you provide a power source that would last long enough.
Plutonium or solar.
The value added by controlling it and not only looking at pictures taken when somebody else (= a scientist) controls it isn't that big.
Who says it would be just a toy? Amateur scientists and explorers have done lots of fun and interesting stuff.
Linux applications do work on different kinds of Linux distributions. But just like a Sony VCR works better with a Sony TV, a RedHat application works better with RedHat Linux.
And beyond electricity, gas, and audio, there are very few parts among consumer electronics and appliances that are interchangeable: the shelves from one refrigerator don't work in another, the remote from one VCR doesn't work with another, every manufacturer has different parts for their cars, etc.
The field is just starting to really contribute to society as a whole, with the first drugs developed using rational drug design being used in medical practice
Rational drug design has been around for a long time, and that is not the "first drug" designed rationally. Of course, decades ago, people couldn't do rational drug design by the kinds of large scale simulations we do today, but the principles of rational drug design were still the same.
Who wants just steady progress? Most people want exponential progress in medicine, and that will only happen if the field grows.
Using the term "exponential" similar to "rapid" generally suggest someone who has no idea about science; a steady 3% annual growth rate is "exponential growth", just like an an annual doubling.
In any case, the problem with the hype and bubble approach is that after a few years of spectacular growth and job opportunities, you get many years of spectacular failure and disappointment.
Bio-Informatics will profoundly change our lives but its Hype-factor will be less than the internet as people can not readily get a tactile "feel" for it as they can with the intenet.
Molecular biology will profoundly change our lives. Bioinformatics is only one of many tools of molecular biology.
Now get to my main point about the Internet being Hyped. Yes it was hyped, but rightly so. The famous remark by Elison "The Internet changes everything" is truer today than when it was uttered a few year ago.
The Internet did change everything, but, like bioinformatics, it was created quietly in the 1960's and grew steadily for several decades afterwards. The hype and feeding frenzy in the late 1990's hurt the further development of the Internet and thrust us into a recession.
So, optimism about both bioinformatics and the Internet is justified, but what commercial applications need is steady, continued investment, not a huge influx of people and money all at once.
Sure, it is: DNA sequence databases, genetic sequence analysis, simulations of regulatory networks, simulations of biochemical networks, 3D structural analysis of proteins, etc. were already in wide use in the early 1980's, and a lot of that goes back to the 1960's.
You are probably familiar with the relatively recent announcement of the human genome being sequenced.
But you are evidently not familiar with the history of biochemistry or molecular biology. Bioinformatics didn't start with the attempts to sequence of the human genome.
These are only two of literally millions of questions that can now be asked illustrating that this rough draft is only the beginning and it is only one genome out of many that has been sequenced
These are the same questions that people were asking before the sequencing of the human genome, and many people still believe that what the human genome project accomplished was not the most cost effective approach to answering them. And it is not the case anyway that the human genome project has delivered an end-to-end sequence of the human genome.
Contribution has nothing to do with using ANY OSS. Nothing. Nada. Zilch.
Sure it does: OSS exists only because of contributions.
There's not much in life for free, so if someone's dumb enough to actually give me something for free, I won't look a gift horse in the mouth.
Anybody is free to use free software. But if they want free software to work differently from the way it does, nobody has an obligation to fulfill their wishes; if nobody else volunteers, they either contribute the changes or pay for them.
Don't pick what is fashionable, pick what you are interested in. The biological sciences are very different from computer science and engineering. Chances are that if you weren't interested in the biological sciences when you picked your major, you still wouldn't be today.
What you can do, however, is apply computer science and engineering skills to biological problems: work as a developer or engineer for a biotech company or lab.
Yes, it's an important field. It's been an important field for decades. And it's going to continue to make steady progress, not because of, but in spite of the attention and hype, and the stupid patents and opportunism that come along with it.
There is only one answer: SOMEONE needs to convince me that I can be just as happy and productive in a Linux environment
Why does anybody "need" to do anything for you for free? If you like to switch, good for you. If you don't, well, that's your decision.
I also need some incentive (in this case that would be that Linux is free).
Linux is not "free" in the sense of "having no cost". You pay for Linux by contributing. If you don't contribute, please stay off the platform. And if you can't even make the minimal effort to determine for yourself whether Linux is good for you or not, it looks like you aren't planning on contributing anything down the road.
Hollywood's reality distortion
on
Old Age Simulator
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· Score: 4, Insightful
Hollywood distorts reality terribly: between make up, digital image enhancements, plastic surgery, and careful media managment, almost anybody and everybody seems to stay "youthful" until they unexpectedly die. Most Hollywood stars in real life don't look anything like what they look like on screen even when they are young.
If you exercise moderately and don't smoke, you'll extend your life somewhat and are at lower risk of some unpleasant diseases. Beyond that, it's out of your control.
A few people have good genes: it runs in the family. Maybe you do, too, but don't count on it.
Of course, fitness and healthy eating will tend to reduce the effects of aging no matter how good or bad your genes are, but don't count on being youthful at 70 no matter how virtuous you live.
Jack La Lanne is nearly 100 years old, yet he looks 65 and still works out every day. I was born in the 1970s, and I plan on living well into my 120s and 130s. I'm not kidding.
Sorry to burst your bubble, but that's mostly genetics. Medicine and public health have only extended the average lifespan, but the maximum human lifespan appears to have other limits on it and appears to have remained mostly constant throughout human history.
Unless there are major breakthroughs in human biology, gene therapy, and genetic engineering, count on between 70-80 years of life if you are lucky, and keep in mind that you could die any day no matter what you do.
There are plenty of solutions for running Windows DLLs on Linux, as well as for compiling Windows source code to run on Linux natively (e.g., Willow TWIN).
Even if there weren't, of if they can't use it for licensing reasons, it's easy to find the OS/library calls that a piece of software makes and write a wrapper that it can life in.
While using special hardware features may be hard, and while installing audio drivers can occasionally be tricky, the audio API on Linux is easier than on just about any other platform. Ditto for video playback under X11.
Either they just don't know what they are doing on Linux, or they are using the prejudice that "Linux has no multimedia support" as a lame excuse for not delivering a client they didn't really care much about anyway.
Rather than spending a huge amount of money on getting a few people up there, I think remotely controlled mobile robots would be much cooler. The moon is close enough that we could have a fleet of mobile robots up there, equipped with manipulators and high resolution stereoscopic cameras, and a direct radio link to earth. You could probably make that cheap enough that for a few thousand dollars, anyone could rent one for half an hour and be "almost there".
That's probably also how we should explore Mars: keep a control crew in orbit and only land mobile robots, controlled via telepresence from orbit.
but I'm glad for anything that would keep Tivo afloat.
Why? Is there any indication that other companies can't provide the same service just as well and possibly more cheaply?
I, for one, am rather disappointed that a couple of companies have tried to build patent fences around DVRs for what are pretty simple ideas that had been "in the air" for many years. Tivo's bankruptcy wouldn't necessarily free those patents, but at least it would demonstrate again that patent landgrabs don't assure commercial success.
I think this support for Tivo is similar to the support for Microsoft: people are saw awed by a product or feature that they don't stop to ask the question: how well could others do in this market if they had the chance?
(1) If it's published in a scientific, peer-reviewed publication, it must contain all the information to be reproducible; if it requires special materials for reproduction, the authors must make those evailable. Publishing irreproducible results goes by a different name: public relations and marketing, either for a company or a career; it has no place in science.
(2) If people put their names on a paper, they should define their contributions and be responsible for the results. If they don't want to accept responsibility for parts of a paper because they didn't work on it, they should say so clearly.
Unfortunately, it has become common practice for people to pad their publications through multiple authorships: five people writing five papers each only have one publication each, but five people putting their names on each other's publications have five publications each; so much more marketable for job hunting that works by counting publications.
It doesn't look like much is changing. In response to the Schoen affair, the American Physical Society weasled out of a requirement of academic responsibility by all authors; things are just continuing the way they are. And scientific papers with little more substance than press releases are becoming increasing common, in particular in the biomedical sciences, as companies promise the sky and find them good PR and marketing materials. And editors are afraid to reject that junk.
But since the peer review system and system of academic publications is becoming increasingly corrupt and useless, perhaps on-line publishing of results without peer review will become the norm. Then, it is really word-of-mouth and recommendations by known friends, as opposed to anonymous reviewers, that matter.
it's about what you can do with it. If you can't modify it and republish your modifications without the consent of the original author, it's missing the point--it just becomes even more of a trap as you fix someone else's bugs for free and become more and more dependent on undocumented (mis-)features. Many companies that "share" source under non-open-source licenses also attempt to impose "contamination" clauses on licensees--people who have seen their code can't work on competing products or open source alternatives afterwards. It's not only Microsoft that is trying to entrap users in this way, but Sun and other companies as well.
If you buy proprietary software, it should work without having source code access. Insist on well-documented APIs and preferably conformance to standards. For a proprietary vendor to give you source code access under a restrictive license is only an excuse for poor testing and quality control and an attempt to bind you to them further. Don't touch someone else's source code unless it comes with an open source compliant license or is in the public domain.
If I didn't use Windows so much I'd be using vim exclusively (but that's another fight altogether!).
Are you aware that there are excellent Windows-native GUI versions of vim? Check on the VIM site.
They may not be able to buy Forte or Eclipse but they can remove a significant development tool for the linux platform that allows the exact same project to run on solaris, linux, windows and mac os (to a lesser extent).
Delphi was great at the time as an alternative to C development on Windows. But today, C++ pretty much has won as the low-level object-oriented programming language; with wxWindows or Qt, you also get excellent cross-platform development support. And for high-level cross-platform development, you get Java. What do we need Delphi for?
Slashdot Mirror
It's fine for the company not to give you a Christmas gift. But a bobble head doll is just in seriously bad taste.
You have no idea what you are talking about. Free software is about freedom to reuse, redistribute, and change software that you use. That has nothing to do with whether you pay for the software or not. I have paid a lot of money for free software over the years, as have many other people. In fact, tech support and services are some of the main ways in which free software advocates recommend making money with free software.
Don't mean to sound vicious or judgemental or anything,
No, you just sound stupid.
Progress in bioinformatics has been steady over decades. Many of the capabilities we have now are based on methods and ideas developed a long time ago, although they have much more impact now with powerful PCs.
What we need is steady, continued public research funding in the application of computers to biological systems. What you advocate, and what follows from hyping up a field, rapid expansion and large new private investments, is destructive in the long run.
Since you admit that the technologies and software were already available decades ago, what is your point? Are you saying that bioinformatics is about being able to do something in an afternoon, as opposed to having to run it on a mainframe over a few days?
I never said that bioinformatics began with sequencing the human genome. Rather I was using it as an example as it was widely publicized and well known. Please re-read my previous comment.
You wrote:
A bit snippy are we?
No, not at all. It is simply evident from your post that you are a bit taken with the hype and a bit unfamiliar with the history of molecular biology, even if you talk at length and repeatedly about "T's, G's, C's, and A's".
Yes, but if you land, you need to figure out how to get several 200 pound people to land softly on the surface and them and their life support back into orbit. That's expensive. With mobile robots, you land them hard, explore, and leave them there. To get samples back, you only need to lift a few pounds into orbit--much simpler.
Remote-controlled robots can be controlled just as well from earth - ok, a round trip for a command and it's response takes a few minutes but why would that matter?
With subsecond delays, you get telepresence: people can interact fairly normally. With delays much greater than a second, you don't get telepresence anymore: every move needs to be worked out carefully on paper. And, yes, it does make a difference whether a mission takes a day (telepresence) or a year (many minutes delay for every move).
how can you provide a power source that would last long enough.
Plutonium or solar.
The value added by controlling it and not only looking at pictures taken when somebody else (= a scientist) controls it isn't that big.
Who says it would be just a toy? Amateur scientists and explorers have done lots of fun and interesting stuff.
And beyond electricity, gas, and audio, there are very few parts among consumer electronics and appliances that are interchangeable: the shelves from one refrigerator don't work in another, the remote from one VCR doesn't work with another, every manufacturer has different parts for their cars, etc.
Rational drug design has been around for a long time, and that is not the "first drug" designed rationally. Of course, decades ago, people couldn't do rational drug design by the kinds of large scale simulations we do today, but the principles of rational drug design were still the same.
Who wants just steady progress? Most people want exponential progress in medicine, and that will only happen if the field grows.
Using the term "exponential" similar to "rapid" generally suggest someone who has no idea about science; a steady 3% annual growth rate is "exponential growth", just like an an annual doubling.
In any case, the problem with the hype and bubble approach is that after a few years of spectacular growth and job opportunities, you get many years of spectacular failure and disappointment.
Molecular biology will profoundly change our lives. Bioinformatics is only one of many tools of molecular biology.
Now get to my main point about the Internet being Hyped. Yes it was hyped, but rightly so. The famous remark by Elison "The Internet changes everything" is truer today than when it was uttered a few year ago.
The Internet did change everything, but, like bioinformatics, it was created quietly in the 1960's and grew steadily for several decades afterwards. The hype and feeding frenzy in the late 1990's hurt the further development of the Internet and thrust us into a recession.
So, optimism about both bioinformatics and the Internet is justified, but what commercial applications need is steady, continued investment, not a huge influx of people and money all at once.
Sure, it is: DNA sequence databases, genetic sequence analysis, simulations of regulatory networks, simulations of biochemical networks, 3D structural analysis of proteins, etc. were already in wide use in the early 1980's, and a lot of that goes back to the 1960's.
You are probably familiar with the relatively recent announcement of the human genome being sequenced.
But you are evidently not familiar with the history of biochemistry or molecular biology. Bioinformatics didn't start with the attempts to sequence of the human genome.
These are only two of literally millions of questions that can now be asked illustrating that this rough draft is only the beginning and it is only one genome out of many that has been sequenced
These are the same questions that people were asking before the sequencing of the human genome, and many people still believe that what the human genome project accomplished was not the most cost effective approach to answering them. And it is not the case anyway that the human genome project has delivered an end-to-end sequence of the human genome.
Sure it does: OSS exists only because of contributions.
There's not much in life for free, so if someone's dumb enough to actually give me something for free, I won't look a gift horse in the mouth.
Anybody is free to use free software. But if they want free software to work differently from the way it does, nobody has an obligation to fulfill their wishes; if nobody else volunteers, they either contribute the changes or pay for them.
What you can do, however, is apply computer science and engineering skills to biological problems: work as a developer or engineer for a biotech company or lab.
Yes, it's an important field. It's been an important field for decades. And it's going to continue to make steady progress, not because of, but in spite of the attention and hype, and the stupid patents and opportunism that come along with it.
Why does anybody "need" to do anything for you for free? If you like to switch, good for you. If you don't, well, that's your decision.
I also need some incentive (in this case that would be that Linux is free).
Linux is not "free" in the sense of "having no cost". You pay for Linux by contributing. If you don't contribute, please stay off the platform. And if you can't even make the minimal effort to determine for yourself whether Linux is good for you or not, it looks like you aren't planning on contributing anything down the road.
If you exercise moderately and don't smoke, you'll extend your life somewhat and are at lower risk of some unpleasant diseases. Beyond that, it's out of your control.
Of course, fitness and healthy eating will tend to reduce the effects of aging no matter how good or bad your genes are, but don't count on being youthful at 70 no matter how virtuous you live.
Sorry to burst your bubble, but that's mostly genetics. Medicine and public health have only extended the average lifespan, but the maximum human lifespan appears to have other limits on it and appears to have remained mostly constant throughout human history.
Unless there are major breakthroughs in human biology, gene therapy, and genetic engineering, count on between 70-80 years of life if you are lucky, and keep in mind that you could die any day no matter what you do.
Even if there weren't, of if they can't use it for licensing reasons, it's easy to find the OS/library calls that a piece of software makes and write a wrapper that it can life in.
Either they just don't know what they are doing on Linux, or they are using the prejudice that "Linux has no multimedia support" as a lame excuse for not delivering a client they didn't really care much about anyway.
That's probably also how we should explore Mars: keep a control crew in orbit and only land mobile robots, controlled via telepresence from orbit.
Why? Is there any indication that other companies can't provide the same service just as well and possibly more cheaply?
I, for one, am rather disappointed that a couple of companies have tried to build patent fences around DVRs for what are pretty simple ideas that had been "in the air" for many years. Tivo's bankruptcy wouldn't necessarily free those patents, but at least it would demonstrate again that patent landgrabs don't assure commercial success.
I think this support for Tivo is similar to the support for Microsoft: people are saw awed by a product or feature that they don't stop to ask the question: how well could others do in this market if they had the chance?
(2) If people put their names on a paper, they should define their contributions and be responsible for the results. If they don't want to accept responsibility for parts of a paper because they didn't work on it, they should say so clearly.
Unfortunately, it has become common practice for people to pad their publications through multiple authorships: five people writing five papers each only have one publication each, but five people putting their names on each other's publications have five publications each; so much more marketable for job hunting that works by counting publications.
It doesn't look like much is changing. In response to the Schoen affair, the American Physical Society weasled out of a requirement of academic responsibility by all authors; things are just continuing the way they are. And scientific papers with little more substance than press releases are becoming increasing common, in particular in the biomedical sciences, as companies promise the sky and find them good PR and marketing materials. And editors are afraid to reject that junk.
But since the peer review system and system of academic publications is becoming increasingly corrupt and useless, perhaps on-line publishing of results without peer review will become the norm. Then, it is really word-of-mouth and recommendations by known friends, as opposed to anonymous reviewers, that matter.
If you buy proprietary software, it should work without having source code access. Insist on well-documented APIs and preferably conformance to standards. For a proprietary vendor to give you source code access under a restrictive license is only an excuse for poor testing and quality control and an attempt to bind you to them further. Don't touch someone else's source code unless it comes with an open source compliant license or is in the public domain.
Are you aware that there are excellent Windows-native GUI versions of vim? Check on the VIM site.
They may not be able to buy Forte or Eclipse but they can remove a significant development tool for the linux platform that allows the exact same project to run on solaris, linux, windows and mac os (to a lesser extent).
Delphi was great at the time as an alternative to C development on Windows. But today, C++ pretty much has won as the low-level object-oriented programming language; with wxWindows or Qt, you also get excellent cross-platform development support. And for high-level cross-platform development, you get Java. What do we need Delphi for?
Elegant object oriented languages really are a dime a dozen. If you want something like that, Eiffel or Oberon are other choices.
The Jikes compiler for Java is also very, very fast. And an open source compiler (I believe GNU Pascal) supports Object Pascal.