H2SO4Hurts 40 most recent comments for H2SO4Hurts http://www.labspaces.net/blog/profile/15/H_SO_Hurts Tue, 19 Mar 2024 03:55:37 -0500 H2SO4Hurts Comment Feed http://www.labspaces.net/blog/profile/15/H_SO_Hurts http://www.labspaces.net/images/badge_large.png What I wish I knew...Before applying to graduate school - Comment by Brian Krueger, PhD <table> <tr><td> Jaeson, that's not true at most places.  Top tier, sure, but 1100+ should get you past the first filter of most PhD programs in the sciences. . . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=511&#comment10542 Mon, 24 Jun 2013 08:39:32 -0500 What I wish I knew...Before applying to graduate school - Comment by Jaeson <table> <tr><td> All I can say is that GRE's really do matter at the University of California....I had amazing grades, as well as a Master's degree with stellar grades, government scholarships, publication, conference presentation alongside other students from the UC which I wanted to be accepted to, and rec letters from three alumni and one very well known person in my subfield...to top it off I also had the p. . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=511&#comment10539 Wed, 19 Jun 2013 23:00:53 -0500 A coming of age for PacBio and long read sequencing? #AGBT13 - Comment by Michael Schatz <table> <tr><td> 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. . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1618&#comment10463 Tue, 26 Feb 2013 00:13:28 -0600 A coming of age for PacBio and long read sequencing? #AGBT13 - Comment by Brian Krueger, PhD <table> <tr><td> 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. . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1618&#comment10461 Mon, 25 Feb 2013 10:20:32 -0600 A coming of age for PacBio and long read sequencing? #AGBT13 - Comment by Jeremy Schmutz <table> <tr><td> 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. . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1618&#comment10459 Mon, 25 Feb 2013 08:01:15 -0600 A coming of age for PacBio and long read sequencing? #AGBT13 - Comment by Brian Krueger, PhD <table> <tr><td> 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? . . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1618&#comment10449 Sun, 24 Feb 2013 14:13:54 -0600 A coming of age for PacBio and long read sequencing? #AGBT13 - Comment by Jeremy Schmutz <table> <tr><td> 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. . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1618&#comment10448 Sun, 24 Feb 2013 13:01:55 -0600 A coming of age for PacBio and long read sequencing? #AGBT13 - Comment by Brian Krueger, PhD <table> <tr><td> 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! . . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1618&#comment10444 Sat, 23 Feb 2013 21:27:00 -0600 A coming of age for PacBio and long read sequencing? #AGBT13 - Comment by Shawn Baker <table> <tr><td> 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 . . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1618&#comment10443 Sat, 23 Feb 2013 21:17:36 -0600 A coming of age for PacBio and long read sequencing? #AGBT13 - Comment by Brian Krueger, PhD <table> <tr><td> Thanks Paul!&#160; I totally agree with your commentary on your site.&#160; I also read over that Bio-IT world interview.&#160; Great stuff there. http://www.bio-itworld.com/2013/1/18/moleculo-man-mickey-kertesz-illumina-long-read-acquisition.html . . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1618&#comment10442 Sat, 23 Feb 2013 21:10:19 -0600 A coming of age for PacBio and long read sequencing? #AGBT13 - Comment by Paul <table> <tr><td> I agree Brian, Illumina could have been a bit more forthcoming about Moleculo technology.&#160; I was disappointed with their claim of "10kb reads" when I found out they weren&#039;t all read as one piece. I wrote a little more on the issue here: www.checkmatescientist.net/2013. . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1618&#comment10441 Sat, 23 Feb 2013 17:35:14 -0600 So, you've dropped a cryovial or lost a sample box in your liquid nitrogen container...now what? - Comment by Mike Gruidl <table> <tr><td> 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 . . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1596&#comment10438 Fri, 22 Feb 2013 13:22:10 -0600 #AGBT day one talks and observations: WES/WGS, kissing snails, Poo bacteria sequencing - Comment by Brian Krueger, PhD <table> <tr><td> 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 ;) . . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1616&#comment10433 Thu, 21 Feb 2013 23:42:46 -0600 #AGBT day one talks and observations: WES/WGS, kissing snails, Poo bacteria sequencing - Comment by Dan Koboldt <table> <tr><td> Thanks for a nice summary of the day 1 plenary talks! A bit more depth and thought than Twitter allows is always appreciated! . . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1616&#comment10428 Thu, 21 Feb 2013 17:07:09 -0600 A peril of "Open" science: Premature reporting on the death of #ArsenicLife - Comment by Martin J Sallberg <table> <tr><td> 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. . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1555&#comment10419 Fri, 15 Feb 2013 06:18:19 -0600 So, you've dropped a cryovial or lost a sample box in your liquid nitrogen container...now what? - Comment by Erin <table> <tr><td> 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)  . . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1596&#comment10373 Tue, 15 Jan 2013 19:06:30 -0600 So, you've dropped a cryovial or lost a sample box in your liquid nitrogen container...now what? - Comment by Brian Krueger, PhD <table> <tr><td> No problem!  It should work better for that since beakers are bigger! . . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1596&#comment10320 Tue, 23 Oct 2012 07:33:23 -0500 So, you've dropped a cryovial or lost a sample box in your liquid nitrogen container...now what? - Comment by S <table> <tr><td> 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! . . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1596&#comment10319 Fri, 19 Oct 2012 12:42:20 -0500 Got fetal DNA on the brain? - Comment by Brian Krueger, PhD <table> <tr><td> How in the world did I miss that. I guess I was too focused on the methods and results...thanks for the links, Emily. . . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1601&#comment10304 Fri, 28 Sep 2012 17:02:26 -0500 Got fetal DNA on the brain? - Comment by GUEST COMMENT <table> <tr><td> Wonderful write up about this paper! Thanks Brian! I'll be sharing! . . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1601&#comment10303 Fri, 28 Sep 2012 15:07:10 -0500 Got fetal DNA on the brain? - Comment by Emily Willingham <table> <tr><td> I didn&#039;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&#160; </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1601&#comment10302 Fri, 28 Sep 2012 14:43:11 -0500 Memes about 'junk DNA' miss the mark on paradigm shifting science - Comment by Brian Krueger, PhD <table> <tr><td> 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. . . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1599&#comment10285 Sat, 08 Sep 2012 12:05:24 -0500 Memes about 'junk DNA' miss the mark on paradigm shifting science - Comment by Tristan Mumford <table> <tr><td> 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. </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1599&#comment10284 Fri, 07 Sep 2012 17:54:11 -0500 So, you've dropped a cryovial or lost a sample box in your liquid nitrogen container...now what? - Comment by Brian Krueger, PhD <table> <tr><td> My stupidity taught them an important lesson.  Always put the retainer wire back in :P  I meant to do it that way... . . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1596&#comment10265 Fri, 17 Aug 2012 11:50:26 -0500 So, you've dropped a cryovial or lost a sample box in your liquid nitrogen container...now what? - Comment by GUEST COMMENT <table> <tr><td> Way to go, Brian. Good think you taught that young 'un right. . . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1596&#comment10264 Fri, 17 Aug 2012 11:29:48 -0500 End to the sonication saga - Comment by Brian Krueger, PhD <table> <tr><td> It's ~1ug total DNA per lane   . . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1357&#comment10089 Fri, 23 Mar 2012 09:13:53 -0500 End to the sonication saga - Comment by kinder_ovni <table> <tr><td> I would like to ask the amount of sonicated DNA (in mg or ng) that you loaded in this gel. Thanks. . . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1357&#comment10086 Mon, 19 Mar 2012 15:41:19 -0500 A peril of "Open" science: Premature reporting on the death of #ArsenicLife - Comment by dopple95 <table> <tr><td> @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. . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1555&#comment9984 Thu, 23 Feb 2012 14:54:44 -0600 A peril of "Open" science: Premature reporting on the death of #ArsenicLife - Comment by David Sanders <table> <tr><td> 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. . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1555&#comment9976 Tue, 07 Feb 2012 11:24:44 -0600 A peril of "Open" science: Premature reporting on the death of #ArsenicLife - Comment by Brian Krueger, PhD <table> <tr><td> 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 . . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1555&#comment9971 Fri, 03 Feb 2012 10:02:13 -0600 A peril of "Open" science: Premature reporting on the death of #ArsenicLife - Comment by Alex Merz <table> <tr><td> There ARE many peer-reviewed papers already published that tell us that "arsenic life" is almost certainly nonsense. For example, it&#039;s been understood for decades that arsenodiester bonds are vastly less stable than phosphodiesters — by MANY orders of magnitude. We&#039;re talking bout relative half-lives of less than a tenth of a second versus more than ten million years.&#160; . . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1555&#comment9968 Thu, 02 Feb 2012 19:39:39 -0600 A peril of "Open" science: Premature reporting on the death of #ArsenicLife - Comment by Brian Krueger, PhD <table> <tr><td> 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. . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1555&#comment9967 Thu, 02 Feb 2012 10:53:34 -0600 A peril of "Open" science: Premature reporting on the death of #ArsenicLife - Comment by Doctor Zen <table> <tr><td> "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 . . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1555&#comment9966 Thu, 02 Feb 2012 10:40:26 -0600 Slides - From the Bench to the Blogosphere: Why every lab should be writing a science blog - Comment by Brian Krueger, PhD <table> <tr><td> Yep, one of them was :)  The other people were mostly communications people for different departments . . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1508&#comment9795 Mon, 24 Oct 2011 08:40:49 -0500 Slides - From the Bench to the Blogosphere: Why every lab should be writing a science blog - Comment by Psycasm <table> <tr><td> Any bloggers among them?. . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1508&#comment9794 Mon, 24 Oct 2011 02:34:26 -0500 Slides - From the Bench to the Blogosphere: Why every lab should be writing a science blog - Comment by Brian Krueger, PhD <table> <tr><td> 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. . . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1508&#comment9788 Fri, 21 Oct 2011 07:51:35 -0500 Slides - From the Bench to the Blogosphere: Why every lab should be writing a science blog - Comment by Psycasm <table> <tr><td> Nice. How was it received?   . . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1508&#comment9786 Fri, 21 Oct 2011 00:24:11 -0500 Fact Checking AARP: Why soundbytes about shrimp on treadmills and pickle technology are misleading - Comment by Brian Krueger, PhD <table> <tr><td> 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 :)   . . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1507&#comment9778 Mon, 17 Oct 2011 11:55:07 -0500 Fact Checking AARP: Why soundbytes about shrimp on treadmills and pickle technology are misleading - Comment by Redshift42 <table> <tr><td> 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. . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1507&#comment9777 Mon, 17 Oct 2011 11:33:55 -0500 A dose of batshit crazy: Bachmann would drill in the everglades if elected president - Comment by JaniceF <table> <tr><td> Doomed I say, we're doomed if she becomes president. . . . </td> </tr> </table> http://www.labspaces.net/view_blog.php?blogID=1462&#comment9650 Sun, 04 Sep 2011 16:31:36 -0500