Difference between revisions of "Open Source Scientific Research"

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The main platform for the scientific community in the 20th century was the peer-reviewed scientific journal. A scientist writes a paper, submits it for review by other scientists and, if it is found to be up-to-standard, the paper is published in a copyrighted journal and made available to subscribers. The intellectual property rights to the paper are owned by the journal.
 
The main platform for the scientific community in the 20th century was the peer-reviewed scientific journal. A scientist writes a paper, submits it for review by other scientists and, if it is found to be up-to-standard, the paper is published in a copyrighted journal and made available to subscribers. The intellectual property rights to the paper are owned by the journal.
  
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This model has many advantages: the main one being that poorly conducted experiments are filtered out by the peer-review process. On the other hand, subscription to journals is often expensive (e.g. It costs $200 a year to subscribe to ''Nature''), limiting access to scientific knowledge. Negative results (e.g. finding that a certain drug has no effect on a disease) are rarely published in such journals, as space in the journal is limited and tends to be given to more interesting positive results.  
+
This model has many advantages: the main one being that poorly conducted experiments are filtered out by the peer-review process. On the other hand, subscription to journals is often expensive (e.g. It costs $200 a year to subscribe to ''Nature''), limiting access to scientific knowledge.  
 +
 
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Negative results (e.g. finding that a certain drug has no effect on a disease) are rarely published in such journals, as space in journals is limited and tends to be given to more interesting positive results. Scientists are often reluctant to publish negative results - particularly where the research is intended to show the effectiveness of a certain drug. This leads to {{wp|Publication_bias|publication bias}}, where data is skewed towards the positive simply because the negative results have been withheld. If scientific studies are conducted openly, all data - whether positive or negative - can come to light.
  
 
An alternative to the peer-reviewed journal is open scientific research. This means posting scientific papers freely on the Internet for anyone to access, without intellectual property restrictions.  
 
An alternative to the peer-reviewed journal is open scientific research. This means posting scientific papers freely on the Internet for anyone to access, without intellectual property restrictions.  
  
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The most obvious and most important advantage of open access publishing is that scientists have much more research available to them.  
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The most obvious and most important advantage of open access publishing is that scientists have much more research available to them. Researchers also have an incentive to publish openly; open publications are much more likely to be cited, and thus develop the researcher's professional reputation.  
  
 
A different kind of peer-review then takes place, an open peer-review like what we see on Wikipedia. Other scientists can rate the paper or comment on it, allowing the best research to rise to the top. Data-mining algorithms can link related research studies together, showing studies that use similar methodologies together, even aggregating the results of several studies.
 
A different kind of peer-review then takes place, an open peer-review like what we see on Wikipedia. Other scientists can rate the paper or comment on it, allowing the best research to rise to the top. Data-mining algorithms can link related research studies together, showing studies that use similar methodologies together, even aggregating the results of several studies.
  
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Open collaboration in science allows scientific experiments to be global collaborations of interested parties around the  world. This allows for greater ''n'' numbers, as data can be aggregated from a large number of researchers. This leads to more reliable results.
 
Open collaboration in science allows scientific experiments to be global collaborations of interested parties around the  world. This allows for greater ''n'' numbers, as data can be aggregated from a large number of researchers. This leads to more reliable results.
  
 
A key tenet of the scientific method is that all experiments be repeatable. When anyone can read about an experiment and replicate it for themselves, false results - due to sloppy design, fluke or fraud - are neutralized. By making scientific papers open, experiments can be repeated by anyone, not just subscribers. This will ultimately lead to more reliable scientific results.
 
A key tenet of the scientific method is that all experiments be repeatable. When anyone can read about an experiment and replicate it for themselves, false results - due to sloppy design, fluke or fraud - are neutralized. By making scientific papers open, experiments can be repeated by anyone, not just subscribers. This will ultimately lead to more reliable scientific results.
  
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There are already millions of papers and datasets contributed to open scientific platforms. [http://www.ncbi.nlm.nih.gov/genbank/ GenBank] is a public library of over 120 million DNA nucleotide sequences and the proteins they produce. The [http://www.plos.org/ Public Library of Science] publishes open scientific journals in eight different areas. [http://www.thehumanbrainproject.com The Human Brain Project] is a huge collaborative project that aims to share all known data about the human brain.
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There are already millions of papers and datasets contributed to open scientific platforms and 20% of all scientific journals are now open access. [http://www.ncbi.nlm.nih.gov/genbank/ GenBank] is a public library of over 120 million DNA nucleotide sequences and the proteins they produce. The [http://www.plos.org/ Public Library of Science] publishes open scientific journals in eight different areas. [http://www.thehumanbrainproject.com The Human Brain Project] is a huge collaborative project that aims to share all known data about the human brain.
  
 
===Grassroots science===
 
===Grassroots science===
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===Open computing resources for science===
 
===Open computing resources for science===
 
Another application of open collaboration to scientific research is allowing people to contribute processing power to computing for scientific research. Rather than have a supercomputer crunching numbers in a lab, thousands of people's personal computers around the world can be used. This has been very successful at helping calculate how proteins fold {{em}} see http://folding.stanford.edu. The [http://www.opensciencegrid.org/ Open Science Grid] is a cloud supercomputer used for data-rich research.
 
Another application of open collaboration to scientific research is allowing people to contribute processing power to computing for scientific research. Rather than have a supercomputer crunching numbers in a lab, thousands of people's personal computers around the world can be used. This has been very successful at helping calculate how proteins fold {{em}} see http://folding.stanford.edu. The [http://www.opensciencegrid.org/ Open Science Grid] is a cloud supercomputer used for data-rich research.
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===Open collaborative mathematics===
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The [http://en.wikipedia.org/wiki/Timothy_Gowers#Polymath_Project Polymath Project] was an experiment to see if massive open collaboration could solve a deep problem in mathematics called the Density Hales-Jewett Theorem. A proof was reached within six weeks and published in an open access journal. This is extraordinarily fast research by the standards of mathematics and promises a new, more productive way of doing mathematics.
  
 
===Links===
 
===Links===
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* http://www.biomedcentral.com/
 
* http://www.biomedcentral.com/
 
* [http://www.scientificamerican.com/article.cfm?id=science-2-point-0 Scientific American: Science 2.0 -- Is Open Access Science the Future?]
 
* [http://www.scientificamerican.com/article.cfm?id=science-2-point-0 Scientific American: Science 2.0 -- Is Open Access Science the Future?]
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Latest revision as of 16:10, 4 December 2011

Unlike publishing in journals, open notebook science allows scientists to benefit from the commentary and suggestions of their peers as they work. They do not have to wait until after the experiment is over - when it is often too late to correct errors anyway.

Scientific research can also be done in a spirit of open collaboration. Scientific papers can be made available online to be read and reviewed (a process known as open publishing or open access), and the raw data collected from scientific studies can also be made publicly available (known as open notebook science). Some scientists 11px-Wikipedia_logo.jpg are even taking this to the point of keeping detailed logs of everything done in their lab - all procedures, results, measurements - in a blog-style notebook that is updated in real time.

The main platform for the scientific community in the 20th century was the peer-reviewed scientific journal. A scientist writes a paper, submits it for review by other scientists and, if it is found to be up-to-standard, the paper is published in a copyrighted journal and made available to subscribers. The intellectual property rights to the paper are owned by the journal.

This model has many advantages: the main one being that poorly conducted experiments are filtered out by the peer-review process. On the other hand, subscription to journals is often expensive (e.g. It costs $200 a year to subscribe to Nature), limiting access to scientific knowledge.

Negative results (e.g. finding that a certain drug has no effect on a disease) are rarely published in such journals, as space in journals is limited and tends to be given to more interesting positive results. Scientists are often reluctant to publish negative results - particularly where the research is intended to show the effectiveness of a certain drug. This leads to publication bias 11px-Wikipedia_logo.jpg, where data is skewed towards the positive simply because the negative results have been withheld. If scientific studies are conducted openly, all data - whether positive or negative - can come to light.

An alternative to the peer-reviewed journal is open scientific research. This means posting scientific papers freely on the Internet for anyone to access, without intellectual property restrictions.

The most obvious and most important advantage of open access publishing is that scientists have much more research available to them. Researchers also have an incentive to publish openly; open publications are much more likely to be cited, and thus develop the researcher's professional reputation.

A different kind of peer-review then takes place, an open peer-review like what we see on Wikipedia. Other scientists can rate the paper or comment on it, allowing the best research to rise to the top. Data-mining algorithms can link related research studies together, showing studies that use similar methodologies together, even aggregating the results of several studies.

Open collaboration in science allows scientific experiments to be global collaborations of interested parties around the world. This allows for greater n numbers, as data can be aggregated from a large number of researchers. This leads to more reliable results.

A key tenet of the scientific method is that all experiments be repeatable. When anyone can read about an experiment and replicate it for themselves, false results - due to sloppy design, fluke or fraud - are neutralized. By making scientific papers open, experiments can be repeated by anyone, not just subscribers. This will ultimately lead to more reliable scientific results.

There are already millions of papers and datasets contributed to open scientific platforms and 20% of all scientific journals are now open access. GenBank is a public library of over 120 million DNA nucleotide sequences and the proteins they produce. The Public Library of Science publishes open scientific journals in eight different areas. The Human Brain Project is a huge collaborative project that aims to share all known data about the human brain.

Grassroots science

Large areas of science have become dominated by highly institutionalised, heavily funded research projects. This has not only engendered public mistrust and fear of science, it has also led to a huge bias towards research that can serves commercial and military interests.

A new model of science is becoming possible thanks to two trends. The first is that equipment is becoming cheaper as a result of technological evolution. The second is that information is now being shared openly on a scale that dwarfs anything ever seen before.

Computer science, where hackers and hobbyists have always been in the vanguard, is the leading example of this. There are stirrings of biotechnology being done in this way, thanks to the equipment becoming much cheaper. There are now hackerspaces springing up for biotechnology, online communities for biohackers and cheap and open-source equipment available.

Open computing resources for science

Another application of open collaboration to scientific research is allowing people to contribute processing power to computing for scientific research. Rather than have a supercomputer crunching numbers in a lab, thousands of people's personal computers around the world can be used. This has been very successful at helping calculate how proteins fold — see http://folding.stanford.edu. The Open Science Grid is a cloud supercomputer used for data-rich research.

Open collaborative mathematics

The Polymath Project was an experiment to see if massive open collaboration could solve a deep problem in mathematics called the Density Hales-Jewett Theorem. A proof was reached within six weeks and published in an open access journal. This is extraordinarily fast research by the standards of mathematics and promises a new, more productive way of doing mathematics.

Links

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