tag:blogger.com,1999:blog-36768584.post4367112405066365013..comments2024-03-03T18:49:34.382-05:00Comments on Omics! Omics!: Ripples from 454's Shutdown AnnouncmentKeith Robisonhttp://www.blogger.com/profile/04765318239070312590noreply@blogger.comBlogger6125tag:blogger.com,1999:blog-36768584.post-62090558697936798712013-12-11T15:33:04.481-05:002013-12-11T15:33:04.481-05:00This is in Reply to Rick's comment about every...This is in Reply to Rick's comment about every Uni wanting to build a super computing center. I have been pushing to get our center to look at cloud based solutions for data analysis however there are two huge hurdles. One is the speed of data transfer to the cloud which is a huge hinderance if you don't have a 10gigy line and the other big problem we've encountered is that a lot of the work we do is now considered protected health information and a lot of the big guns in the offsite cloud storage space won't sign a Business Associates Agreement (BAA) which basically says they're liable for any breaches that result in the release of PHI. So for those two reasons we're FORCED into keeping all of the computing analysis local.Brian Kruegerhttps://www.blogger.com/profile/13456672262242780223noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-29729467752075483872013-10-24T07:52:08.098-04:002013-10-24T07:52:08.098-04:00Quick 454 runs are a fallacy. For one scientist to...Quick 454 runs are a fallacy. For one scientist to go through the whole 454 workflow takes about 2 days of full-on bench work (emPCR setup & dispense, emPCR, emulsion breaking, bead enrichment, 454 pre-wash, sequencing reagent prep, PTP loading and a 10 hour run). Alternatively a MiSeq run is 30 minutes of hands-on and 27 hours of furiously refreshing BaseSpace for 30 hours until the run has finished.<br />Of course, it's quicker than the HiSeq, but the HiSeq produces significantly more data at a faster rate (HiSeq >1Gb per hour, 454 ~50Mb per hour)Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-25862552447290584952013-10-22T02:08:27.694-04:002013-10-22T02:08:27.694-04:00The quantum yield of bioluminescence is quite high...The quantum yield of bioluminescence is quite high, 40-90% depending on whom you believe (http://www.nature.com/nphoton/journal/v2/n1/full/nphoton.2007.251.html). However, the problem is likely that of a 1-photon emitter, i.e., every strand produces ~0.5 photons, and unlike photoluminescence, cannot be regenerated. With a typical Illumina cluster size of ~1000 templates you would get ~500 photons emitted in all directions. A high-NA optical system needed to resolve the clusters would collect at most of a few percent of that, so you are looking at tens of photons, not enough to overcome Schott noise. This is just speculation, possibly ill-informed.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-11972292971991856642013-10-21T11:45:44.718-04:002013-10-21T11:45:44.718-04:00James:
1000bp reads are great -- but for some de ...James:<br /><br />1000bp reads are great -- but for some de novo assembly they are shockingly short. For the good stuff in the bugs I work in, 4Kb sometimes isn't long enough!Keith Robisonhttps://www.blogger.com/profile/04765318239070312590noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-39180201216993610592013-10-21T11:18:53.288-04:002013-10-21T11:18:53.288-04:00That was a great summary Keith. A big change for m...That was a great summary Keith. A big change for me was Illumina's announcment at AGBT 2011 or 12 of the 600bp reads on MiSeq. It was clear that from thenon Illumina's read length would increase. I suspect 1000bp is achievable and longer may be possible. Once we get 1B 1000bp reads is there any need for anything else?James@cancerhttps://www.blogger.com/profile/02825715598810395734noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-50781574203421957452013-10-21T10:54:58.833-04:002013-10-21T10:54:58.833-04:00Leaving aside the Ion Torrent and miSeq -- both of...Leaving aside the Ion Torrent and miSeq -- both of which can be lab level instruments -- I suspect most PIs are already subscribing to "sequencing-as-a-service" model but at a local level. The customers using our hiSeq, for example, aren't allow to "touch the machine". We provide a service to them but they could be sending their samples to anyone anywhere. <br /><br />There is a mentality of "the university must have a sequencing center" (sort of like your point behind the "I need my own box" mentality) similar to "the university must have a super-computing center". There is a lot to be said about having local people who you can talk to doing your sequencing work. However this mentality may also fade over time.<br />Rickhttps://www.blogger.com/profile/09945270829932237628noreply@blogger.com