Take a copy of National enquirer and copy it 100 times.
insert lines from NI randomly into Shakespeare until you run out of lines to add.
Lose all punctuation, spellings, and write everything in lower case.
chop into 100 letter long bits.
copy twenty times.
discard half the bits.
now do a critical comparison between the characters in shakespeare and the characters in Ibsen treated the same way (except that for Ibsen use 'Kvinne og Klaer' instead of NI and it is all in Norwegian)
Ewan is one of the outstanding people in the field
I was thinking more along the lines of EMBOSS as well. I have been hacking a few bits on that and trying to get things going. Generally people like it a lot despite the command line.
Bioperl is cool. I put together a database indexing and retrieval script for my DBs with a non standard header. Works a charm (after tidying up a few wrinkles in the way my hack worked.)
We are looking to get ENSEMBL up and running shortly. It looks exciting and we want to build on it for our own purposes too.
Academic genomics has certainly produced a lot of good open source tools. ENSEMBL, EMBOSS, Bioperl, Biojava, Sean's HMMER and so on. Maybe we should start a new site? adopt_a_genome_scientist.org for those that can write good code but don't know what to write to meet those that know what they want doing but can't write code.
Nice to see a coherent account from an expert in the field.
Last time I checked the human 'rough draft' from the public project had about 80% of the sequence complete in draft form and in the public domain. The Celera project has nothing in the public domain except a few press releases.
I update my databases every night from the HGP. It is doubling in data volume approximately every 7 months and the doubling time is getting shorter.
Moores law eat your heart out.
The HGP is providing us with data faster than we can analyse it, and really opening up a whole new level of understanding of how things work. One of my colleagues complained to me after I had given a seminar on Genome analysis that his labs old laboroius techniques of analysing family pedigrees and careful selection of regions to look for genes was being blown apart by the public sequencing projects.
We are entering a new era of biology, one in which a biologist will need to be as handy with a keyboard as with a pipette. If you want to be a successful molecular biologist you will either need to be very, very good or have good data analysis skills.
Enough of a winge. Any open source programmers out there fancy getting involved in writing code to help with the human genome analysis? plenty of odd tasks to go round.
There is definitely a division between the scientists at certain 'public' research institutes whose management insist on contracts signed in blood etc. and those at others which are dependent more on the 'gift culture' for getting work done.
I am a bioinformaticist who is involved with a number of projects (most peripherally). Our aim is to provide tools that work for those that need them, so we GPL or LGPL almost everything. One spinoff of the major package I am involved with is that instead of paying a huge per processor fee for a package that is closed and requires expensive hardware to run, I can now put out a better package that is modifyable and extensible on a larger number of machines, each of which is far cheaper. Happy? ask my users in six months.
Progress? Standing on the shoulders of giants is a good way to get to see further. Before we had the OS package (EMBOSS for the interested) anyone wanting to write a new package had to start from scratch. Now, you just copy the bits that do what you want from the existing source, write a couple of new functions and have a new application in a day or two. With good design it is on the web based interface before the coding is even finished!!.
I expect a scientist saying 'I used this program' when they publish a paper to make that code available to other scientists to try to repeat the results and audit the accuracy of the work. It is understandable and acceptable to licence things to protect the original authors investment, but that does not mean closed source.
Enough ranting. Support your local open source scientists. EMBOSS, BioPerl, BioJava and so on.. That way we ALL get better tools to do better work. And the kudos go to the ones that dream up the best tools and ways to approach things.
Antisense technology is different to Gene Silencing. It can be used for gene silencing but also for other things.
Gene silencing can be performed through a number of different mechanisms. One of the more promising methods is ribozym (yes, without the e) technology which does work in vivo.
As for these genetic switches, the body comprises an extremely comples mechanism of feedback control. It operates on many many levels and one of the challenges molecular biology faces is how to cope with this. Data gathering is a huge task, microarray chips only address a tiny proportion of what we need to know in regard to how these mechanisms are controlled.
The current paper is interesting but like much of science can easily be dismissed by the 'knowledgeable but not expert' as 'standing on the shoulders of giants'.
As for evolution, with a small e it is a useful mathematical model for describing (no explaining) the relationships between different entities, with a large E it is a matter of pseudoscientific faith as to our origins.
Have a nice day.
Maybe/. should have some way of having expert moderators for such discussions. There are many good molecular biologists and bioinformaticians who cringe reading a lot of the inane drivel posted by the nonunderstanding.
Another cool feature would be kill lists so I don't have to read any anonymous posts...
This 'I need to accellerate out of trouble' syndrome is a symptom of poor driving to start with. Research in Sweden on speed limiters and drivers response to them showed that at first drivers were worried about this. Then, as they realised that leaning on the gas pedal and burnign adrenalin made no difference they relaxed, were more aware, and just didn't get into the situations where previously they had to 'accelerate away'. To think that people drive at a level of safety (risk homeostasis) gets close to the point, but my almost unjustifiable opinion is that people drive to a level of adrenalin. Some argue about freedom to drive how they will. That is all well and good but only as far as it doesn't impinge on other peoples freedom. Should you have the freedom to drive at 40 in a school zone eventhough you are perfectly capable of not crashing at that speed? of course not, because it impinges on my right to cross teh road in a reasonable degree of safety. (there is no jaywalking law in UK). I would consider your freedom arguments bogus, because they are based on your selfishness rather than a freedom for all. I concur more with your 'government monitoring' fears. It is however perfectly legitimate for a company to track where its vehicles are at any given time. I would prefer a car that is speed limited to one that is not for many reasons. I would not neccessarily want my presence tracked though I doubt any government has the power (financial as well as personnell) to do that. Anyway, enough rambling. I'll leave the americans to their rambling and 18K gundeaths vs UK 200ish and 50K auto deaths per year (vs UK 3K). (for the geographically challenged, US is less than five times the population of UK)..d
So what you are saying is that despite the much higher legal ownership of guns in the US (like I don't know anyone who owns a gun in UK, but do know a couple of people with a shotgun license)
the US public are so poor (wrt UK), so drug crazed that the violent crime rate is somehow held in check by a ready supply of deadly weapons?
And the violent crime rate has nothing to do with our police officers (in general) not being armed..
give me a break. If you have a very limited supply of deadly weapons then there can only be a limited number of deaths. If you have a large number of deadly weapons then there will be a correspondingly higher totall numebr of deaths EVEN IF the population are better trained in gun use etc.
The European Molecular Biology Open Software Suite should get an award of some kind here.
Reasons?
Usable and used now by tens of thousands of scientists worldwide which is a great advance on last year
Really nice design for the interface allowing it to be easily merged with any frontend you wish for easy incorporation into GUI apps, workflow schemes etc.
Open source by design, and updated every night
An extra man year of funding would make a massive difference and you'll also be contributing to basic scientific research.
Developed by Genome researchers for scientists worldwide
This is an interface that describes all the inputs to the programs. It means that the one program can be linked to whichever frontend you wish be it web, javabean, corba or whatever. Just parse the program description file (ACD file) and you are in..
A power failure in the sporveiers network between Majorstua and Tøyen. Heard about it at lunchtime (1200 GMT) as I was heading home and the T-bane stopped at Blindern. Didn't bother me, the bicycle is Y2K compliant (though I am not sure about the rider)
Slashdot Mirror
- Take the complete works of shakespeare
- Take a copy of National enquirer and copy it 100 times.
- insert lines from NI randomly into Shakespeare until you run out of lines to add.
- Lose all punctuation, spellings, and write everything in lower case.
- chop into 100 letter long bits.
- copy twenty times.
- discard half the bits.
- now do a critical comparison between the characters in shakespeare and the characters in Ibsen treated the same way (except that for Ibsen use 'Kvinne og Klaer' instead of NI and it is all in Norwegian)
The sequence is not the endIt is not the beginning of the end
It is merely the end of the beginning
I was thinking more along the lines of EMBOSS as well. I have been hacking a few bits on that and trying to get things going. Generally people like it a lot despite the command line.
Bioperl is cool. I put together a database indexing and retrieval script for my DBs with a non standard header. Works a charm (after tidying up a few wrinkles in the way my hack worked.)
We are looking to get ENSEMBL up and running shortly. It looks exciting and we want to build on it for our own purposes too.
Academic genomics has certainly produced a lot of good open source tools. ENSEMBL, EMBOSS, Bioperl, Biojava, Sean's HMMER and so on. Maybe we should start a new site? adopt_a_genome_scientist.org for those that can write good code but don't know what to write to meet those that know what they want doing but can't write code.
Last time I checked the human 'rough draft' from the public project had about 80% of the sequence complete in draft form and in the public domain. The Celera project has nothing in the public domain except a few press releases.
I update my databases every night from the HGP. It is doubling in data volume approximately every 7 months and the doubling time is getting shorter.
Moores law eat your heart out.
The HGP is providing us with data faster than we can analyse it, and really opening up a whole new level of understanding of how things work. One of my colleagues complained to me after I had given a seminar on Genome analysis that his labs old laboroius techniques of analysing family pedigrees and careful selection of regions to look for genes was being blown apart by the public sequencing projects.
We are entering a new era of biology, one in which a biologist will need to be as handy with a keyboard as with a pipette. If you want to be a successful molecular biologist you will either need to be very, very good or have good data analysis skills.
Enough of a winge. Any open source programmers out there fancy getting involved in writing code to help with the human genome analysis? plenty of odd tasks to go round.
Dr. David Martin European Molecular Biology Network node manager.
I am a bioinformaticist who is involved with a number of projects (most peripherally). Our aim is to provide tools that work for those that need them, so we GPL or LGPL almost everything. One spinoff of the major package I am involved with is that instead of paying a huge per processor fee for a package that is closed and requires expensive hardware to run, I can now put out a better package that is modifyable and extensible on a larger number of machines, each of which is far cheaper. Happy? ask my users in six months.
Progress? Standing on the shoulders of giants is a good way to get to see further. Before we had the OS package (EMBOSS for the interested) anyone wanting to write a new package had to start from scratch. Now, you just copy the bits that do what you want from the existing source, write a couple of new functions and have a new application in a day or two. With good design it is on the web based interface before the coding is even finished!!.
I expect a scientist saying 'I used this program' when they publish a paper to make that code available to other scientists to try to repeat the results and audit the accuracy of the work. It is understandable and acceptable to licence things to protect the original authors investment, but that does not mean closed source.
Enough ranting. Support your local open source scientists. EMBOSS, BioPerl, BioJava and so on.. That way we ALL get better tools to do better work. And the kudos go to the ones that dream up the best tools and ways to approach things.
Antisense technology is different to Gene Silencing. It can be used for gene silencing but also for other things.
Gene silencing can be performed through a number of different mechanisms. One of the more promising methods is ribozym (yes, without the e) technology which does work in vivo.
As for these genetic switches, the body comprises an extremely comples mechanism of feedback control. It operates on many many levels and one of the challenges molecular biology faces is how to cope with this. Data gathering is a huge task, microarray chips only address a tiny proportion of what we need to know in regard to how these mechanisms are controlled.
The current paper is interesting but like much of science can easily be dismissed by the 'knowledgeable but not expert' as 'standing on the shoulders of giants'.
As for evolution, with a small e it is a useful mathematical model for describing (no explaining) the relationships between different entities, with a large E it is a matter of pseudoscientific faith as to our origins.
Have a nice day.
Maybe /. should have some way of having expert moderators for such discussions. There are many good molecular biologists and bioinformaticians who cringe reading a lot of the inane drivel posted by the nonunderstanding.
Another cool feature would be kill lists so I don't have to read any anonymous posts...
This 'I need to accellerate out of trouble' syndrome is a symptom of poor driving to start with. Research in Sweden on speed limiters and drivers response to them showed that at first drivers were worried about this. Then, as they realised that leaning on the gas pedal and burnign adrenalin made no difference they relaxed, were more aware, and just didn't get into the situations where previously they had to 'accelerate away'. To think that people drive at a level of safety (risk homeostasis) gets close to the point, but my almost unjustifiable opinion is that people drive to a level of adrenalin. Some argue about freedom to drive how they will. That is all well and good but only as far as it doesn't impinge on other peoples freedom. Should you have the freedom to drive at 40 in a school zone eventhough you are perfectly capable of not crashing at that speed? of course not, because it impinges on my right to cross teh road in a reasonable degree of safety. (there is no jaywalking law in UK). I would consider your freedom arguments bogus, because they are based on your selfishness rather than a freedom for all. I concur more with your 'government monitoring' fears. It is however perfectly legitimate for a company to track where its vehicles are at any given time. I would prefer a car that is speed limited to one that is not for many reasons. I would not neccessarily want my presence tracked though I doubt any government has the power (financial as well as personnell) to do that. Anyway, enough rambling. I'll leave the americans to their rambling and 18K gundeaths vs UK 200ish and 50K auto deaths per year (vs UK 3K). (for the geographically challenged, US is less than five times the population of UK) ..d
So what you are saying is that despite the much higher legal ownership of guns in the US (like I don't know anyone who owns a gun in UK, but do know a couple of people with a shotgun license)
the US public are so poor (wrt UK), so drug crazed that the violent crime rate is somehow held in check by a ready supply of deadly weapons?
And the violent crime rate has nothing to do with our police officers (in general) not being armed..
give me a break. If you have a very limited supply of deadly weapons then there can only be a limited number of deaths. If you have a large number of deadly weapons then there will be a correspondingly higher totall numebr of deaths EVEN IF the population are better trained in gun use etc.
And this is totally off the point.
..d
The European Molecular Biology Open Software Suite should get an award of some kind here.
Reasons?Visit the EMBOSS home page for more details. ..d
This is an interface that describes all the inputs to the programs. It means that the one program can be linked to whichever frontend you wish be it web, javabean, corba or whatever. Just parse the program description file (ACD file) and you are in..
Have a look atThe EMBOSS project for more details.Nothing to do with Y2K (isn't that 2048?)
A power failure in the sporveiers network between Majorstua and Tøyen.
Heard about it at lunchtime (1200 GMT) as I was heading home and the T-bane stopped at Blindern.
Didn't bother me, the bicycle is Y2K compliant (though I am not sure about the rider)
..d
If you really don't want cookies, alias cookies.txt to /dev/null
No problems then, unless you actually want the benefits cookies allow.
..d