Re: Is Churchill revolutionary?
On Thu, Feb 12, 2015 at 11:36:40AM +0100, Roland Fehrenbacher wrote: > > "Andreas" == Andreas Tille writes: > > Andreas> Hi, On Wed, Feb 11, 2015 at 11:24:35AM -0600, Scott > Andreas> Christley wrote: > > >> These are essentially data-parallel solutions. What I’ve found is > >> that most of these workflows utilizing existing software, > >> e.g. BWA for alignment and GATK for variant calling, ... > > Andreas> Anybody interested in packaging GATK > > Andreas>https://github.com/broadgsa/gatk > > Not sure whether their licensing permits redistribution within Debian. > Check https://github.com/broadgsa/gatk/tree/master/licensing Without checking I was assuming we are free to distribute the public part which should be covered by https://github.com/broadgsa/gatk/blob/master/licensing/public_license.txt I admit I have not checked all details but if there is some vital interest by some team members we could try to negotiate with the authors. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20150212105148.gc30...@an3as.eu
Re: Is Churchill revolutionary?
> "Andreas" == Andreas Tille writes: Andreas> Hi, On Wed, Feb 11, 2015 at 11:24:35AM -0600, Scott Andreas> Christley wrote: >> These are essentially data-parallel solutions. What I’ve found is >> that most of these workflows utilizing existing software, >> e.g. BWA for alignment and GATK for variant calling, ... Andreas> Anybody interested in packaging GATK Andreas>https://github.com/broadgsa/gatk Not sure whether their licensing permits redistribution within Debian. Check https://github.com/broadgsa/gatk/tree/master/licensing -- Roland --- http://www.q-leap.com / http://qlustar.com --- HPC / Storage / Cloud Linux Cluster OS --- -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/21724.6.690063.758...@gargle.gargle.howl
Re: Is Churchill revolutionary?
> "Gert" == Gert Wollny writes: Gert> On Wed, 2015-02-11 at 17:31 +, Jorge Sebastião Soares Gert> wrote: >> Hey, >> >> Maybe this is one more of those articles that have been published >> lately with the intent to verify the attention reviewers and >> journals pay to submissions: Gert> I don't think so, the paper appears in a BMC journal, and so Gert> far all review I got from other journals from this publisher Gert> were quite thorough. Besides, they really applied for a patent Gert> for the method: Gert> http://www.google.com/patents/US20130311106 Gert> I skimmed the paper, and what they claim is that they found a Gert> parallelization strategy that gives close to optimal scaling Gert> which really seems to make a difference when using *lots* of Gert> processors. It's not my field of work, so I can't comment on Gert> the details. Since I'm not a Bioinformtician, I ask myself: Are there tools in DebMed (or otherwise free) to achieve the same results, even if currently not as performing? If so, I'd be interested to look at them and see how they can be optimized to achieve similar performance. If their tasks are data-parallel a lot of the performance gain might come from a great HW setup. What would be needed is some kind of benchmark everyone in the field is familiar with. Cheers, Roland --- http://www.q-leap.com / http://qlustar.com --- HPC / Storage / Cloud Linux Cluster OS --- -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/21724.32876.213381.965...@gargle.gargle.howl
Re: Is Churchill revolutionary?
Hi, On Wed, Feb 11, 2015 at 11:24:35AM -0600, Scott Christley wrote: > These are essentially data-parallel solutions. What I’ve found is that > most of these workflows utilizing existing software, e.g. BWA for > alignment and GATK for variant calling, ... Anybody interested in packaging GATK https://github.com/broadgsa/gatk Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20150212072111.ga28...@an3as.eu
Re: Is Churchill revolutionary?
On Feb 11, 2015, at 9:32 AM, Roland Fehrenbacher wrote: > > Anyone can judge the real impact of this? > Other groups have worked on similar capability. http://bioinformatics.oxfordjournals.org/content/early/2014/02/12/bioinformatics.btu071.abstract These are essentially data-parallel solutions. What I’ve found is that most of these workflows utilizing existing software, e.g. BWA for alignment and GATK for variant calling, but they take different approaches to splitting the large data set, running the tools on that data in parallel, and then merging the results. Churchill does look to be pretty fast though. cheers Scott -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/f6e05551-75ba-4619-93f1-4924b071e...@me.com
Re: Is Churchill revolutionary?
On Wed, 2015-02-11 at 17:31 +, Jorge Sebastião Soares wrote: > Hey, > > Maybe this is one more of those articles that have been published > lately with the intent to verify the attention reviewers and journals > pay to submissions: I don't think so, the paper appears in a BMC journal, and so far all review I got from other journals from this publisher were quite thorough. Besides, they really applied for a patent for the method: http://www.google.com/patents/US20130311106 I skimmed the paper, and what they claim is that they found a parallelization strategy that gives close to optimal scaling which really seems to make a difference when using *lots* of processors. It's not my field of work, so I can't comment on the details. Best Gert -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/1423677504.5513.8.ca...@gmail.com
Re: Is Churchill revolutionary?
Hey, Maybe this is one more of those articles that have been published lately with the intent to verify the attention reviewers and journals pay to submissions: http://www.fastcompany.com/3041493/body-week/why-a-fake-article-cuckoo-for-cocoa-puffs-was-accepted-by-17-medical-journals Best, Jorge On Wed, Feb 11, 2015 at 3:32 PM, Roland Fehrenbacher wrote: > > "Andreas" == Andreas Tille writes: > > Andreas> Hi Roland, On Wed, Feb 11, 2015 at 12:51:21PM +0100, Roland > Andreas> Fehrenbacher wrote: > >> > Andreas> I did not found any download or even any project page of > Andreas> the software. > >> > >> The link is at the very end of the article. Here for reference: > >> http://churchill.nchri.org/ > > Andreas> Ahh, my bad to do a simple web search instead of reading. > Andreas> However, I can confirm that nothing happens after > Andreas> "Agree"-ing to the license terms ... :-( > > Thanks for checking. Hmm, seems to be some quickly hacked up page then ... > > Andreas> Somebody who has some vital interest should probably > Andreas> contact the authors. > > Anyone can judge the real impact of this? > > Roland > > --- > http://www.q-leap.com / http://qlustar.com > --- HPC / Storage / Cloud Linux Cluster OS --- > > > -- > To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org > with a subject of "unsubscribe". Trouble? Contact > listmas...@lists.debian.org > Archive: > https://lists.debian.org/21723.30221.23789.120...@gargle.gargle.howl > >
Re: Is Churchill revolutionary?
> "Andreas" == Andreas Tille writes: Andreas> Hi Roland, On Wed, Feb 11, 2015 at 12:51:21PM +0100, Roland Andreas> Fehrenbacher wrote: >> Andreas> I did not found any download or even any project page of Andreas> the software. >> >> The link is at the very end of the article. Here for reference: >> http://churchill.nchri.org/ Andreas> Ahh, my bad to do a simple web search instead of reading. Andreas> However, I can confirm that nothing happens after Andreas> "Agree"-ing to the license terms ... :-( Thanks for checking. Hmm, seems to be some quickly hacked up page then ... Andreas> Somebody who has some vital interest should probably Andreas> contact the authors. Anyone can judge the real impact of this? Roland --- http://www.q-leap.com / http://qlustar.com --- HPC / Storage / Cloud Linux Cluster OS --- -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/21723.30221.23789.120...@gargle.gargle.howl
Re: Is Churchill revolutionary?
Hi Roland, On Wed, Feb 11, 2015 at 12:51:21PM +0100, Roland Fehrenbacher wrote: > > Andreas> I did not found any download or even any project page of > Andreas> the software. > > The link is at the very end of the article. Here for reference: > http://churchill.nchri.org/ Ahh, my bad to do a simple web search instead of reading. However, I can confirm that nothing happens after "Agree"-ing to the license terms ... :-( Somebody who has some vital interest should probably contact the authors. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20150211131614.gh29...@an3as.eu
Re: Is Churchill revolutionary?
> "Andreas" == Andreas Tille writes: Andreas> Hi Roland, On Tue, Feb 10, 2015 at 06:39:30PM +0100, Roland Andreas> Fehrenbacher wrote: >> To the DebMed sequencing experts out there: >> >> Is this ( >> http://www.gizmag.com/churchill-fast-human-genome-analysis/35944/ >> ) just marketing fuzz or really as much of a breakthrough as it >> sounds? Andreas> I personally can't say. >> PS: I can't download the code, but you guys could check. Andreas> I did not found any download or even any project page of Andreas> the software. The link is at the very end of the article. Here for reference: http://churchill.nchri.org/ Cheers, Roland --- http://www.q-leap.com / http://qlustar.com --- HPC / Storage / Cloud Linux Cluster OS --- -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/21723.16953.736654.378...@gargle.gargle.howl
Re: Is Churchill revolutionary?
Hi Roland, On Tue, Feb 10, 2015 at 06:39:30PM +0100, Roland Fehrenbacher wrote: > To the DebMed sequencing experts out there: > > Is this ( > http://www.gizmag.com/churchill-fast-human-genome-analysis/35944/ ) just > marketing fuzz or really as much of a breakthrough as it sounds? I personally can't say. > PS: I can't download the code, but you guys could check. I did not found any download or even any project page of the software. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20150211103456.gc29...@an3as.eu
