5 ms·

Yes, but the HGP didn't make a full sequence either, using their scaffold-based contig assembly. Both groups declared a truce and announced they were "finished

by dekhn 3y ago

Yes, but the HGP didn't make a full sequence either, using their scaffold-based contig assembly. Both groups declared a truce and announced they were "finished with the first draft" 35 years ago: https://www.nytimes.com/1987/12/13/magazine/the-genome-project.html https://www.nytimes.com/1987/12/13/magazine/the-genome-proje... 33 years ago: https://www.nytimes.com/1990/06/05/science/great-15-year-project-to-decipher-genes-stirs-opposition.html https://www.nytimes.com/1990/06/05/science/great-15-year-pro... 29 years ago: the competition gets fierce https://www.nytimes.com/1994/02/22/science/scientist-at-work-j-craig-venter-a-bold-short-cut-to-human-genes.html https://www.nytimes.com/1994/02/22/science/scientist-at-work... 24 years ago: the race is alive! https://www.nytimes.com/1999/03/23/science/who-ll-sequence-human-genome-first-it-s-up-to-phred.html https://www.nytimes.com/1999/03/23/science/who-ll-sequence-h... 23 years ago: draft is complete https://archive.nytimes.com/www.nytimes.com/library/national/science/062600sci-human-genome.html https://archive.nytimes.com/www.nytimes.com/library/national... 20 years ago: https://www.nytimes.com/2003/04/15/science/once-again-scientists-say-human-genome-is-complete.html https://www.nytimes.com/2003/04/15/science/once-again-scient... 2 years ago: https://archive.nytimes.com/www.nytimes.com/library/national/science/062600sci-human-genome.html https://archive.nytimes.com/www.nytimes.com/library/national... The celera approach using shotgun was tricky because assembling the bits required a great deal of computational finesse and horsepower; "The final assembly computations were run on Compaq’s new AlphaServer GS160 because the algorithms and data required 64 gigabytes of shared memory to run successfully." At the time the GS160 was the monster machine, a classic big iron UNIX, which could be tightly clustered- unified IO/filesystem between all the machines. The primary author of the shotgun assembly was Gene Myers, who previously had written BLAST, and invented the Suffix Array with Udi Manber. The public project had its own issues, as many of the teams assigned to work on it still had the "cottage industry/artisinal/academic" approach, then Eric Lander came along and turned it into an industrial process, and parlayed that into running the Broad Institute, a privately funded MIT/Harvard research institute in Boston. These days petabytes of sequence data are generated every day and stored in clouds. The genome has been a fundamental tool for shaping our studies of humans, although its true potential for understanding complex phenotypes remains elusive.

sublinear 3y ago
> The primary author of the shotgun assembly was Gene Myers, who previously had written BLAST... So... um... BLAST processing?
- heyoni 3y ago
  I think blast is for mapping sequences on existing genomes, which uses similar algorithms but applied for a different purpose.
jghn 3y ago
Lets not forget how Perl Saved The Human Genome Project [1], which I remember seeing in a print magazine at the time. As someone who is in the genomics world now as a software person, I find it amusing that I've gotten more into perl over the last year or so. It has its place, in the way that grep/sed/awk/etc does. [1] https://news.ycombinator.com/item?id=30327812 https://news.ycombinator.com/item?id=30327812
- dekhn 3y ago
  Lincoln Stein is great, and perl was certainly critical to many processes, but it was and remains fairly niche in genomics, which used much more C++, Java, and later Python. IMHO the person who "saved the genome project" was WJ Kent, who developed the assembler, BLAT, that the public project needed. I strive to point out that he wasn't a sole hero, nor was Lincoln. What I really like about BLAT is that while Celera was using Big Iron UNIX (massive 64-bit 64GB machines with 10s of terabytes of central high performance storage), BLAT ran on a cluster of linux machines, right around the time that people were waking up to the fact that linux was becoming a useful tool for scientific data processing. BLAT's design allowed it to work on a cluster of cheaper/smaller machines, while celera's algorithm really needed a massive shared memory single machine. it was sort of a microcosm of the larger battle being fought between Big iron UNIX and little intel linux at the time.
  - jfoutz 3y ago
    I know hn isn't the place for memes, but, I'm obligated. Imagine what they could do with a beowulf cluster of pentium pros?

by dekhn 3y ago

sublinear 3y ago

> The primary author of the shotgun assembly was Gene Myers, who previously had written BLAST... So... um... BLAST processing?

heyoni 3y ago
I think blast is for mapping sequences on existing genomes, which uses similar algorithms but applied for a different purpose.

jghn 3y ago

Lets not forget how Perl Saved The Human Genome Project [1], which I remember seeing in a print magazine at the time. As someone who is in the genomics world now as a software person, I find it amusing that I've gotten more into perl over the last year or so. It has its place, in the way that grep/sed/awk/etc does. [1] https://news.ycombinator.com/item?id=30327812 https://news.ycombinator.com/item?id=30327812

dekhn 3y ago
Lincoln Stein is great, and perl was certainly critical to many processes, but it was and remains fairly niche in genomics, which used much more C++, Java, and later Python. IMHO the person who "saved the genome project" was WJ Kent, who developed the assembler, BLAT, that the public project needed. I strive to point out that he wasn't a sole hero, nor was Lincoln. What I really like about BLAT is that while Celera was using Big Iron UNIX (massive 64-bit 64GB machines with 10s of terabytes of central high performance storage), BLAT ran on a cluster of linux machines, right around the time that people were waking up to the fact that linux was becoming a useful tool for scientific data processing. BLAT's design allowed it to work on a cluster of cheaper/smaller machines, while celera's algorithm really needed a massive shared memory single machine. it was sort of a microcosm of the larger battle being fought between Big iron UNIX and little intel linux at the time.
- jfoutz 3y ago
  I know hn isn't the place for memes, but, I'm obligated. Imagine what they could do with a beowulf cluster of pentium pros?