While it is true that global food production has resulted in an overabundance in terms of calories, nutritional content is the limiting factor. It was previously thought that fortification (think Wonder Bread (TM) and vitamins) would solve the nutrition problem, it has not and cannot. When people trot out the old story of distribution being at fault,it misses the real issue and causes people to assume that continued work in basic agricultural research (e.g. plant breeding) is no longer important. Many of the world's poor have enough calories, but are suffering from developmental disease (blindness) due to poor nutrition. Shipping commodity crops (e.g. corn, soybeans, wheat and rice)does not solve the nutrition problem. Vegetables that will grown in difficult conditions, locally by small farmers can.
Dr. Jefferson is interested in agricultural biotechnology. While most people who commented on this article have equated biotechnology to medical research, this is not the area in which open science is most needed. It is in the agricultural sector where funding is tight, profit margins slim and there was a long history of sharing materials and methods in the public (even private) sector that open science is desperately needed. In the 1980s, the ability to patent methods and living things in combination with the Bayh-Dole act started a chain of events which has diminished the ability of agricultural researchers to work for the public efficiently.
Some will argue that the ability of companies to patent materials and methods promotes research by promising a return. As a scientist working in the field of plant breeding I see that this is not the case here. Large biotech / seed companies are most interested in working on species which are grown widely (e.g. corn, soybeans and cotton) and on which they can make a profit due to economies of scale. Many minor crops which are important to those people who grow and consume them (particularly in the developing world) do not get the attention of the large companies. Plant breeding efforts must be regional because plants interact with their environment in ways that cannot be easily predicted. Therefore a variety bred for use in the midwest of the United States might not be suitable for use in the northeast let alone Africa or Asia. If the modern molecular biology tools which are useful are encumbered by patents which restrict their use (either directly or through licensing costs) the ability of people all over the world to benefit from scientific knowledge and use that knowledge to feed themselves is lost.
This problem is compounded by the fact that in the development of new varieties many genes / methods are included. Multiple parties might be patent holders in one variety which could easily price the variety out of the market. An example (which was resolved with complex negotiations) is the so called golden rice (contains increased vitamin A precursors) which involves about 30 different patents.
As others have pointed out, a system of open tools / technologies in the sciences is great for the many of the same reasons free software development works so well. There are some of us who are working to promote both of these things in the agricultural sciences. If we succeed, plant breeders in developing countries will be able to tackle the difficult problems which face their farmers and their people and they will be able to do it without having to rely on the generosity of the developed nations and / or multinational corporations.
The issue here is to take the raw data (essentially a picture file) and processing it into genotypes. The software that does this does it poorly with a lot of user intervention for a lot of money. There is no true need for it to be this way.
You are right in that we do want the genotype data stored in a relational database. The problem is getting to the data we want to put in the database.
Re:Wanted: Biohacker Help
on
Biohackathon
·
· Score: 1
I have had no response from the NCSA people regarding work on my project. Even with all the talk about cross-campus communication / cooperation, if it isn't flashy people are not interested in working on it. Regarding paying developers, that would be great, but my lab is underfunded as it is and was created with the purpose of being low cost so that agricultural researches could afford to do their work. There is plenty of money for medical related / genomics work, but for those people who are developing the disease resistant plant varieties the old fashion way (and feed the country while they are at it) the money is still pretty slim.
Additionally, I would like to be able to write a "Setting Up a Genetic Marker Lab Howto" using only open source software. If I can do this, other research facilities (particularly those who have little funding) will be able to replicate the setup and do this work in their own countries, giving them more control of their food supply.
Wanted: Biohacker Help
on
Biohackathon
·
· Score: 4, Interesting
I am the director of a core molecular biology laboratory with a focus on agricultural genotyping at a major midwestern university. I am happy to see that there is an interest in providing better downstream tools for data analysis.
My main area of concern however is the lack of good tools to take the raw data from sequencing machines and produce genotypes. Most software available is vendor specific, closed source, not very robust and extremely expensive. The closed source vendor specific solutions which are available lock up the data in proprietary databases, making it difficult to migrate to equipment from other vendors in the future and to get the data organized for many projects. All the software (including the few open source projects that exist) that I have evaluated has the same basic flaw, it starts with the premise that the lab will use them to screen against an existing database of genotypes (for disease or pedigree). These are fine medical applications (for which they were developed) but does not address the needs of the basic research laboratory which is working to discover the genotypes to begin with.
I would like to build an open source application that gives the user the freedom to choose the data collection platform, the freedom to move the data from one application to another and the freedom to improve and expand the application itself. I face two challenges: 1) Administration that says "open source, why would we want to use shareware". This one I'm addressing by building the information infrastructure using Linux. 2) Finding qualified programers that would like to work on the project. (I'm a pretty good admin, but am not a programmer).
The need for this work is great. In talking with other people in my field, I've found that the key thing they want to know is what software are you using to do the raw analysis. No one is satisfied with the current situation, but most of these are old school and don't know anything about opensource software. I've showed them that we can use existing open source software to run the lab. I'd like to show them that we can develop our own software to do some of the basic work. Any volunteers?
Slashdot Mirror
While it is true that global food production has resulted in an overabundance in terms of calories, nutritional content is the limiting factor. It was previously thought that fortification (think Wonder Bread (TM) and vitamins) would solve the nutrition problem, it has not and cannot. When people trot out the old story of distribution being at fault,it misses the real issue and causes people to assume that continued work in basic agricultural research (e.g. plant breeding) is no longer important. Many of the world's poor have enough calories, but are suffering from developmental disease (blindness) due to poor nutrition. Shipping commodity crops (e.g. corn, soybeans, wheat and rice)does not solve the nutrition problem. Vegetables that will grown in difficult conditions, locally by small farmers can.
Dr. Jefferson is interested in agricultural biotechnology. While most people who commented on this article have equated biotechnology to medical research, this is not the area in which open science is most needed. It is in the agricultural sector where funding is tight, profit margins slim and there was a long history of sharing materials and methods in the public (even private) sector that open science is desperately needed. In the 1980s, the ability to patent methods and living things in combination with the Bayh-Dole act started a chain of events which has diminished the ability of agricultural researchers to work for the public efficiently.
Some will argue that the ability of companies to patent materials and methods promotes research by promising a return. As a scientist working in the field of plant breeding I see that this is not the case here. Large biotech / seed companies are most interested in working on species which are grown widely (e.g. corn, soybeans and cotton) and on which they can make a profit due to economies of scale. Many minor crops which are important to those people who grow and consume them (particularly in the developing world) do not get the attention of the large companies. Plant breeding efforts must be regional because plants interact with their environment in ways that cannot be easily predicted. Therefore a variety bred for use in the midwest of the United States might not be suitable for use in the northeast let alone Africa or Asia. If the modern molecular biology tools which are useful are encumbered by patents which restrict their use (either directly or through licensing costs) the ability of people all over the world to benefit from scientific knowledge and use that knowledge to feed themselves is lost.
This problem is compounded by the fact that in the development of new varieties many genes / methods are included. Multiple parties might be patent holders in one variety which could easily price the variety out of the market. An example (which was resolved with complex negotiations) is the so called golden rice (contains increased vitamin A precursors) which involves about 30 different patents.
As others have pointed out, a system of open tools / technologies in the sciences is great for the many of the same reasons free software development works so well. There are some of us who are working to promote both of these things in the agricultural sciences. If we succeed, plant breeders in developing countries will be able to tackle the difficult problems which face their farmers and their people and they will be able to do it without having to rely on the generosity of the developed nations and / or multinational corporations.
The issue here is to take the raw data (essentially a picture file) and processing it into genotypes. The software that does this does it poorly with a lot of user intervention for a lot of money. There is no true need for it to be this way.
You are right in that we do want the genotype data stored in a relational database. The problem is getting to the data we want to put in the database.
I have had no response from the NCSA people regarding work on my project. Even with all the talk about cross-campus communication / cooperation, if it isn't flashy people are not interested in working on it. Regarding paying developers, that would be great, but my lab is underfunded as it is and was created with the purpose of being low cost so that agricultural researches could afford to do their work. There is plenty of money for medical related / genomics work, but for those people who are developing the disease resistant plant varieties the old fashion way (and feed the country while they are at it) the money is still pretty slim.
Additionally, I would like to be able to write a "Setting Up a Genetic Marker Lab Howto" using only open source software. If I can do this, other research facilities (particularly those who have little funding) will be able to replicate the setup and do this work in their own countries, giving them more control of their food supply.
I am the director of a core molecular biology laboratory with a focus on agricultural genotyping at a major midwestern university. I am happy to see that there is an interest in providing better downstream tools for data analysis.
My main area of concern however is the lack of good tools to take the raw data from sequencing machines and produce genotypes. Most software available is vendor specific, closed source, not very robust and extremely expensive. The closed source vendor specific solutions which are available lock up the data in proprietary databases, making it difficult to migrate to equipment from other vendors in the future and to get the data organized for many projects. All the software (including the few open source projects that exist) that I have evaluated has the same basic flaw, it starts with the premise that the lab will use them to screen against an existing database of genotypes (for disease or pedigree). These are fine medical applications (for which they were developed) but does not address the needs of the basic research laboratory which is working to discover the genotypes to begin with.
I would like to build an open source application that gives the user the freedom to choose the data collection platform, the freedom to move the data from one application to another and the freedom to improve and expand the application itself. I face two challenges: 1) Administration that says "open source, why would we want to use shareware". This one I'm addressing by building the information infrastructure using Linux. 2) Finding qualified programers that would like to work on the project. (I'm a pretty good admin, but am not a programmer).
The need for this work is great. In talking with other people in my field, I've found that the key thing they want to know is what software are you using to do the raw analysis. No one is satisfied with the current situation, but most of these are old school and don't know anything about opensource software. I've showed them that we can use existing open source software to run the lab. I'd like to show them that we can develop our own software to do some of the basic work. Any volunteers?