Recorded: 08 May 2012
So we knew, we had very serious competition that the competition was a group headed by Gene Myers at Celera, so Gene and I went to school together actually. I knew Gene very, very well. We were students together at the University of Colorado at Boulder.
I of course kept contact with Gene and, and I thought his program on the whole genome shotgun methodology with Webber was just amazing and was a huge fan of the methodology. And we had, we had worked on a number of combinatorial problems, we had the same advisor Andre Aaronfoit[?] at the University of Colorado who was a complete genius, poly-math, did everything and was very, very supportive of the work that both Gene and I did at that time in , in what was bioinformatics before the term was even popular and we’re talking about 1983, 1982, 1981. But, when Gene decided to leave Arizona and go to Celera it was because the opportunity was so extraordinary and I remember when he called me over to meet Craig at a, at one of the scientific meetings, we had a serious discussion about whether I should actually leave Santa Cruz and join that project as well and I decided not to, so we ended up competing instead of collaborating on this, this genome. So it was, it was fun. You know, Gene and I, when the competition was hot, we didn’t communicate that much, we were really too busy, there wasn’t any particular reason for us to communicate. At point Gene had a different problem that the public had. The public data was of a different character because we had information from the fingerprint map, we had information from the fact that it was done mostly clone by clone and so there was some locality information that was just not present in the P.O.P. [unintelligible] genome shotgun data.
And Gene, Gene had a bigger problem in many, in many ways, he had millions of genome pieces to put together in his jigsaw puzzle, we had about six hundred thousand to put together in ours because using Phil Green’s Phrap program, there are already in some assembly of the, of the genome segments. But nevertheless, the fact that Jim Kent came along at that time was a total game changer.
The public was in a desperate situation. As you know, Francis had made a deal with Craig Venter over pizza at Ari Patrinos’ house and that’s when we first found out about the deadline. We had a weekly call about the progress on the Human Genome Project and then suddenly, in the middle of the spring, it was announced by Francis Collins that in fact we would finish, and there would be an announcement on June 26th and we – the engineers were tearing their hair out. They were like: ‘Wait a minute this is no way to plan a project. You can’t tell us how long it is going to take. We don’t know how long it’s going to take to assemble all of these data.’ So, it was really, it just had to happen and that really created an extraordinary atmosphere of urgency.
We knew that Gene Myers and Granger Sutton and the team at Celera was going to do a good job, we knew they had an incredible computing resource at their facility and that they were exceedingly brilliant engineers. So the public was really up against a very stiff competition and the public had not planned for a massive computational problem, they had planned to sequence the genome clone-by-clone, piece-by-piece, and gradually assemble it into a finished project and finish it around 2005. And so this was an enormous acceleration of the schedule but it was also a complete change in computational strategy and computational demands and there was no planning, there had been no time to plan for resources to match that and so we had to come up completely seat-of-the-pants with a solution to this.
David Haussler (born 1953) is an American bioinformatician known for his work leading the team that assembled the first human genome sequence in the race to complete the Human Genome Project and subsequently for comparative genome analysis that deepens understanding the molecular function and evolution of the genome. He is a Howard Hughes Medical Institute Investigator, professor of biomolecular engineering and director of the Center for Biomolecular Science and Engineering at the University of California, Santa Cruz, director of the California Institute for Quantitative Biosciences (QB3) on the UC Santa Cruz campus, and a consulting professor at Stanford University School of Medicine and UC San Francisco Biopharmaceutical Sciences Department.