H2SO4Hurts

A coming of age for PacBio and long read sequencing? #AGBT13 - Comment by Michael Schatz

Tue, 26 Feb 2013 00:13:28 -0600

Hi Brian, I am certainly interested in both continuity and accuracy of PacBio sequencing. However, I no longer fear the 15% error rate like I first did, because we have more-or-less worked out the error model and algorithms that will let us "polish out" the vast majority of those errors. From a purely theoretical model, the consensus accuracy from even 20% random sequencing errors never. . .

A coming of age for PacBio and long read sequencing? #AGBT13 - Comment by Brian Krueger, PhD

Mon, 25 Feb 2013 10:20:32 -0600

Great stuff Jeremy! You bring up good points about gaps and bioinformatics. Despite the advances in technology, there is a lot of extra work that goes into assembling a de novo genome on the back end. Prior to my work at Duke I ran a de novo virus sequencing core lab at the University of Florida and even with small non-repetitive genomes we still had to do a alot of gap filling with Sange. . .

A coming of age for PacBio and long read sequencing? #AGBT13 - Comment by Jeremy Schmutz

Mon, 25 Feb 2013 08:01:15 -0600

Brian,I don't know why shatz doesn't appear to be concerned about the accuracy of Pacbio for plant applications. You would have to ask him. We operate in different spaces- shatz is concerned about linking and increasing contiguity for drafty draft quality genome space, I'm concerned about going beyond everything that is already doable now with illumina and 454 with a bit of effort and what. . .

A coming of age for PacBio and long read sequencing? #AGBT13 - Comment by Brian Krueger, PhD

Sun, 24 Feb 2013 14:13:54 -0600

Hey Jeremy, thanks for the clarification! I really enjoyed your talk and seeing Moleculo in action. I just wish we knew more details about how it worked. One question though, why do you think Schatz told everyone to not worry about the errors anymore if the PacBio data still isn't optimal in your dealings with it? . . .

A coming of age for PacBio and long read sequencing? #AGBT13 - Comment by Jeremy Schmutz

Sun, 24 Feb 2013 13:01:55 -0600

Hey Brian- good post, I don't like Moleculo because they do the work (i dont have problem reconstructing sub assemblies of millions of reads:) although many people do appreciate the ease of data collection. I like the technology because it does something with a plastic shoebox they we need do by handling freezers worth of clones- bin very small amounts of target DNA into a local assembly. Assembli. . .

A coming of age for PacBio and long read sequencing? #AGBT13 - Comment by Brian Krueger, PhD

Sat, 23 Feb 2013 21:27:00 -0600

Shawn, thanks for the added insight. Jeremy also sent me an email about this. I asked him to post his comment here to clear up some of my own hand waving! . . .

A coming of age for PacBio and long read sequencing? #AGBT13 - Comment by Shawn Baker

Sat, 23 Feb 2013 21:17:36 -0600

Brian, thanks for the review of AGBT - it's especially helpful for those of us who couldn't attend. But I think you're giving PacBio slightly too much credit on improving their error rate. They have made tremendous strides on the analysis front, but their raw error rate is still quite high, with an accuracy that ranges between 83%-87% (depending on which chemistry is used). The very impressive . . .

A coming of age for PacBio and long read sequencing? #AGBT13 - Comment by Brian Krueger, PhD

Sat, 23 Feb 2013 21:10:19 -0600

Thanks Paul! I totally agree with your commentary on your site. I also read over that Bio-IT world interview. Great stuff there. http://www.bio-itworld.com/2013/1/18/moleculo-man-mickey-kertesz-illumina-long-read-acquisition.html . . .

A coming of age for PacBio and long read sequencing? #AGBT13 - Comment by Paul

Sat, 23 Feb 2013 17:35:14 -0600

I agree Brian, Illumina could have been a bit more forthcoming about Moleculo technology. I was disappointed with their claim of "10kb reads" when I found out they weren't all read as one piece. I wrote a little more on the issue here: www.checkmatescientist.net/2013. . .

So, you've dropped a cryovial or lost a sample box in your liquid nitrogen container...now what? - Comment by Mike Gruidl

Fri, 22 Feb 2013 13:22:10 -0600

OK, I had to do this when I took over a lab. The cryo unit had tubes and other debris in the bottom and thawing the unit was not an option. To solve the problem, I attached a 6 inch diameter wire strainer to an old broom handle with worm gear hose clamps. Then you just remove a few of the towers and dip your 'metal net' into the liquid nitrogen to find your tube. This works best if you . . .

#AGBT day one talks and observations: WES/WGS, kissing snails, Poo bacteria sequencing - Comment by Brian Krueger, PhD

Thu, 21 Feb 2013 23:42:46 -0600

Dan, I totally agree. I wish more attendees would participate in the global conversation. Some day these things might even be live streamed for everyone to see and comment. I guess for now people are stuck with coverage from the early adopters ;) . . .

#AGBT day one talks and observations: WES/WGS, kissing snails, Poo bacteria sequencing - Comment by Dan Koboldt

Thu, 21 Feb 2013 17:07:09 -0600

Thanks for a nice summary of the day 1 plenary talks! A bit more depth and thought than Twitter allows is always appreciated! . . .

A peril of "Open" science: Premature reporting on the death of #ArsenicLife - Comment by Martin J Sallberg

Fri, 15 Feb 2013 06:18:19 -0600

Being scooped is no problem in a non-competetive context. Pure science Wiki (http://purescience.wikia.com) is an Internet platform for the pure scientific method without any of the prestige-obsession that makes academia unscientific. The topic pages "How to avoid hoaxes in science", "Advice of wa. . .

So, you've dropped a cryovial or lost a sample box in your liquid nitrogen container...now what? - Comment by Erin

Tue, 15 Jan 2013 19:06:30 -0600

Thanks! You are #1 on the list now, and the first thing I saw when I googled the same dilema. The first thing I thought was "fwew! I'm not the only one!" and the 2nd thing was "fwew, I may not have to transfer all the other samples and drain the dewer to get them back!" WebRep Overall rating This site has no rating(not enough votes) . . .

So, you've dropped a cryovial or lost a sample box in your liquid nitrogen container...now what? - Comment by Brian Krueger, PhD

Tue, 23 Oct 2012 07:33:23 -0500

No problem! It should work better for that since beakers are bigger! . . .

So, you've dropped a cryovial or lost a sample box in your liquid nitrogen container...now what? - Comment by S

Fri, 19 Oct 2012 12:42:20 -0500

Dropped a beaker in the tank...don't ask.. but I'm going to try your method! Thanks for sharing! You're a life saver! . . .

Got fetal DNA on the brain? - Comment by Brian Krueger, PhD

Fri, 28 Sep 2012 17:02:26 -0500

How in the world did I miss that. I guess I was too focused on the methods and results...thanks for the links, Emily. . . .

Got fetal DNA on the brain? - Comment by GUEST COMMENT

Fri, 28 Sep 2012 15:07:10 -0500

Wonderful write up about this paper! Thanks Brian! I'll be sharing! . . .

Got fetal DNA on the brain? - Comment by Emily Willingham

Fri, 28 Sep 2012 14:43:11 -0500

I didn't come up with the explanation you describe; rather, the authors offered it in the discussion: "The most likely source of male Mc in female brain is acquisition of fetal Mc from pregnancy with a male fetus. In women without sons, male DNA can also be acquired from an abortion or a miscarriage

Memes about 'junk DNA' miss the mark on paradigm shifting science - Comment by Brian Krueger, PhD

Sat, 08 Sep 2012 12:05:24 -0500

There's quite a bit of research into creating DNA storage and DNA computers, but I was just using that as an easy to understand analogy about why having a lot of junk cluttering the genome could be a disadvantage. No doubt there's a ceratin amount of stuff we don't use anymore. . . .

Memes about 'junk DNA' miss the mark on paradigm shifting science - Comment by Tristan Mumford

Fri, 07 Sep 2012 17:54:11 -0500

Really if you use genetics as an analog to a computer the genome is like the hard drive on a computer of unknown architecture with an unknown file system running an operating system and programs. Currently we seem to be at the point where a disk image can be dumped and a few patterns can be recognised and fiddled with using a hex editor, then dumped back to the disk to see what the changes do.

So, you've dropped a cryovial or lost a sample box in your liquid nitrogen container...now what? - Comment by Brian Krueger, PhD

Fri, 17 Aug 2012 11:50:26 -0500

My stupidity taught them an important lesson. Always put the retainer wire back in :P I meant to do it that way... . . .

So, you've dropped a cryovial or lost a sample box in your liquid nitrogen container...now what? - Comment by GUEST COMMENT

Fri, 17 Aug 2012 11:29:48 -0500

Way to go, Brian. Good think you taught that young 'un right. . . .

End to the sonication saga - Comment by Brian Krueger, PhD

Fri, 23 Mar 2012 09:13:53 -0500

It's ~1ug total DNA per lane . . .

End to the sonication saga - Comment by kinder_ovni

Mon, 19 Mar 2012 15:41:19 -0500

I would like to ask the amount of sonicated DNA (in mg or ng) that you loaded in this gel. Thanks. . . .

A peril of "Open" science: Premature reporting on the death of #ArsenicLife - Comment by dopple95

Thu, 23 Feb 2012 14:54:44 -0600

@David Sanders, just because 40 mM arsenate shouldn't be limiting, that doesn't mean that some other requirement wasn't limiting. Do you expect the growth curve to go exponentially upward forever? Brian, thank you for writing this story and calling out the main stream media as well as scientific outlets like Nature News who should know better. If people thought that the original NASA pre. . .

A peril of "Open" science: Premature reporting on the death of #ArsenicLife - Comment by David Sanders

Tue, 07 Feb 2012 11:24:44 -0600

Brian, I think you have made the mistake of thinking Arsenic Life was ever alive. It was stillborn. There was no evidence provided in the Science paper of incorporation of arsenic into any biomolecule. There was no real evidence of growth on arsenate. Look at Supplementary Table 1 anc compare it to the description of the data in the text. This misrepresentation of the d. . .

A peril of "Open" science: Premature reporting on the death of #ArsenicLife - Comment by Brian Krueger, PhD

Fri, 03 Feb 2012 10:02:13 -0600

Alex Merzsaid: A complete manuscript with full data and a reasonably complete description of the experimental methods. I can see the rebuttal from Wolfe-Simon already, "The Refield group used the wrong growth conditions, media, etc." The . . .

A peril of "Open" science: Premature reporting on the death of #ArsenicLife - Comment by Alex Merz

Thu, 02 Feb 2012 19:39:39 -0600

There ARE many peer-reviewed papers already published that tell us that "arsenic life" is almost certainly nonsense. For example, it's been understood for decades that arsenodiester bonds are vastly less stable than phosphodiesters — by MANY orders of magnitude. We're talking bout relative half-lives of less than a tenth of a second versus more than ten million years. . . .

A peril of "Open" science: Premature reporting on the death of #ArsenicLife - Comment by Brian Krueger, PhD

Thu, 02 Feb 2012 10:53:34 -0600

That's a great point Zen. But are FTLN a good example that science reporting should aspire to? How many people stopped following the debate after the first story? How many of those people still think that FTLN exist? I'd bet a fair amount still have the original soundbyte in their head. Reporting on data that has not been fully vetted and peer reviewed is doing a disservice to the commu. . .

A peril of "Open" science: Premature reporting on the death of #ArsenicLife - Comment by Doctor Zen

Thu, 02 Feb 2012 10:40:26 -0600

"Reporting on data that has not gone through the peer review process as if it were truth is not responsible journalism." I have also been shocked, SHOCKED, I say, to see a paper deposited in arXiv being reported around the world by researchers and journalists alike. Nobody commented that it hadn't been accepted in a peer-reviewed journal. Except I'm not talking about Redfield's . . .

Slides - From the Bench to the Blogosphere: Why every lab should be writing a science blog - Comment by Brian Krueger, PhD

Mon, 24 Oct 2011 08:40:49 -0500

Yep, one of them was :) The other people were mostly communications people for different departments . . .

Slides - From the Bench to the Blogosphere: Why every lab should be writing a science blog - Comment by Psycasm

Mon, 24 Oct 2011 02:34:26 -0500

Any bloggers among them?. . .

Slides - From the Bench to the Blogosphere: Why every lab should be writing a science blog - Comment by Brian Krueger, PhD

Fri, 21 Oct 2011 07:51:35 -0500

Pretty well. It was in a not very ideal part of campus, so only about 10 people showed up, but I'm going to try to give it again over in the hospital sometime next month. . . .

Slides - From the Bench to the Blogosphere: Why every lab should be writing a science blog - Comment by Psycasm

Fri, 21 Oct 2011 00:24:11 -0500

Nice. How was it received? . . .

Fact Checking AARP: Why soundbytes about shrimp on treadmills and pickle technology are misleading - Comment by Brian Krueger, PhD

Mon, 17 Oct 2011 11:55:07 -0500

Totally agree, and that's why it's so annoying that they targetted 2 science projects. The amount of money they're talking about is insignificant when compated to the budget or the debt. Why throw science under the bus? We make all of the drugs and therapies that keep old people alive :) . . .

Fact Checking AARP: Why soundbytes about shrimp on treadmills and pickle technology are misleading - Comment by Redshift42

Mon, 17 Oct 2011 11:33:55 -0500

It's also infuriating because the real threat to Social Security and Medicare isn't some nickel-and-dime tradeoff between that and a few science grants, it's the insistence that "we're broke" and everything must be cut rather than let any tax cuts expire. With only a passing mention of "tax loopholes", this ad implicitly buys into that mindset, apparently in the belief that outrage, no matter h. . .

A dose of batshit crazy: Bachmann would drill in the everglades if elected president - Comment by GirlPostdoc

Sun, 04 Sep 2011 16:31:36 -0500

Doomed I say, we're doomed if she becomes president. . . .

A dose of batshit crazy: Bachmann would drill in the everglades if elected president - Comment by Alchemystress

Sun, 04 Sep 2011 09:11:23 -0500

I can't say just how much this woman pisses me off... . . .

A true day in lab - Comment by Brian Krueger, PhD

Mon, 22 Aug 2011 14:23:53 -0500

Haha, I covered our EH&S guidelines concerning eating in lab in my last post. The Desk area is considered food safe. . . .