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MQN Spaces for Drug Discovery: Part 5 « Zombie Process
https://zombieprocess.wordpress.com/2014/01/14/mqn-spaces-for-drug-discovery-part-5
2 AM, out of caffeine. Once more, I'm a… Zombie Process. What is a Zombie Process? MQN Spaces for Drug Discovery: Part 5. Tuesday, 14 Jan 2014. Continued from part 4. Böhm HJ, Flohr A, Stahl M. 2004. Scaffold hopping. Drug Discovery Today: Technologies. Blum LC, van Deursen R, and Reymond JL. 2011. Visualisation and subsets of the chemical universe database GDB-13 for virtual screening. J Comput Aided Mol Des. J Chem Inf Model. This entry was posted in bioinformatics. And tagged drug discovery. Notify me...
Metrics for Multi-Class Classifiers: A Case Study « Zombie Process
https://zombieprocess.wordpress.com/2014/03/18/metrics-for-multi-class-classifiers-a-case-study
2 AM, out of caffeine. Once more, I'm a… Zombie Process. What is a Zombie Process? Metrics for Multi-Class Classifiers: A Case Study. Tuesday, 18 Mar 2014. As I mentioned in my prior post. Assessing classifiers can be a difficult task. In this post, I’ll look at an example of a multi-class classification problem, and discuss good metrics for assessing the performance of tools designed to solve the problem. We will look at three secondary structure tools for this analysis:. Now, the matrix for PHD:. How s...
Calculating Percent Identity from SAM Files « Zombie Process
https://zombieprocess.wordpress.com/2013/05/21/calculating-percent-identity-from-sam-files
2 AM, out of caffeine. Once more, I'm a… Zombie Process. What is a Zombie Process? Calculating Percent Identity from SAM Files. Tuesday, 21 May 2013. This means that with 200bp Illumina reads, the alignments might include a CIGAR string like 200M, which does not indicate a 100% identity. Can be used to postprocess a SAM-formatted file in order to add MD fields to the records:. Samtools fillmd -S file.sam genomic.fna file.md.sam. SRR062334.404 0 gi 378696079 ref NC 016809.1 1804559 22. 5AA-AAA-AA5:- 6C@ ;?
Mike Strosaker « Zombie Process
https://zombieprocess.wordpress.com/author/strosaker
2 AM, out of caffeine. Once more, I'm a… Zombie Process. What is a Zombie Process? Author Archives: Mike Strosaker. Hidden Markov Models in Python. Friday, 21 Mar 2014. I recently created a new GitHub repository for a Python module that I wrote to implement arbitrary HMMs: https:/ github.com/mstrosaker/hmm. A brief primer on HMMs. I think that HMMs are best described by an example. We will look at this toy model:. This is why it’s described as a. S1 – S1 – S1: 0.5 (initial probability of ...S1 – S1...
MQN Spaces for Drug Discovery: Part 1 « Zombie Process
https://zombieprocess.wordpress.com/2014/01/06/mqn-spaces-for-drug-discovery-part-1
2 AM, out of caffeine. Once more, I'm a… Zombie Process. What is a Zombie Process? MQN Spaces for Drug Discovery: Part 1. Monday, 6 Jan 2014. The original title of the project was:. Assessment of the Utility of MQN Property Spaces for Drug Discovery. I undertook a study to establish whether the representational power of the MQN system is sufficient for cheminformatics tasks that are relevant to drug discovery programs. This objective is characterized by three hypotheses:. Van Deursen R, Blum LC, and Reym...
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Improving performance on Linux (mostly Power): April 2008
http://well-itdepends.blogspot.com/2008_04_01_archive.html
Improving performance on Linux (mostly Power). Monday, April 7, 2008. What "one thing" do you want in the Linux kernel? An interesting question came by this week. If I could have one free wish, one thoughtful choice, one wise selection, what would I want in the Linux kernel? I was of course assured that my choice didn't mean I'd get it, but it was an interesting hallway poll for the day. I suspect the answers were being pulled together as input for this week's Linux Foundation meetings. Cool technology w...
Improving performance on Linux (mostly Power): July 2008
http://well-itdepends.blogspot.com/2008_07_01_archive.html
Improving performance on Linux (mostly Power). Thursday, July 17, 2008. RHEL 5.2 and HPC performance hints. Re-building a RHEL 5 kernel for Power. We linked this in under the HPC Central wiki page where several of us are playing around with adding descriptive how-to's for HPC workloads based on practical experience. Follow the link to the Red Hat Enterprise Linux. Page, which is where the kernel page is linked in. We plan to replicate these pieces for SUSE Linux Enterprise Server next month. Paul Murphy ...
Improving performance on Linux (mostly Power): April 2010
http://well-itdepends.blogspot.com/2010_04_01_archive.html
Improving performance on Linux (mostly Power). Wednesday, April 7, 2010. Open-source - patents - and what about performance? Interesting debates arise around us every day. The latest "patent pledge" excitement on the web is interesting to watch. I tried to dig through and read the details of the various lists of patents, but the eyes glaze and I have to wonder who's pulling who's chain. Linux Foundation - open source patent pledge. Admit'ably, my world is focused primarily on helping customers tune and i...
Improving performance on Linux (mostly Power): June 2011
http://well-itdepends.blogspot.com/2011_06_01_archive.html
Improving performance on Linux (mostly Power). Monday, June 6, 2011. Gcc performance - getting better all of the time. There's quite a bit going on in the world of Linux on Power, where teams have been focused on improvements for gcc performance. Lately, a series of articles have been published on DeveloperWorks which nicely highlight the performance gains that gcc (packaged in the Advance Toolchain) provides over the gcc packaged with the Linux operating system. Naturally, your mileage will vary. Perfor...
Improving performance on Linux (mostly Power): Busy time for 2.6.32 kernel on Power7
http://well-itdepends.blogspot.com/2010/05/busy-time-for-2632-kernel-on-power7.html
Improving performance on Linux (mostly Power). Friday, May 21, 2010. Busy time for 2.6.32 kernel on Power7. Red Hat's RHEL 6 is already in beta (from last month):. Http:/ press.redhat.com/2010/04/21/red-hat-enterprise-linux-6-beta-available-today-for-public-download/. Novell just announced their latest service pack for SLES 11 which among other things upgrades the kernel to 2.6.32:. Http:/ www.novell.com/promo/suse/sle11sp1.html. Http:/ bluebiou.rice.edu/. Subscribe to: Post Comments (Atom). Mark Cathcar...
Improving performance on Linux (mostly Power): gcc performance - getting better all of the time
http://well-itdepends.blogspot.com/2011/06/gcc-performance-getting-better-all-of.html
Improving performance on Linux (mostly Power). Monday, June 6, 2011. Gcc performance - getting better all of the time. There's quite a bit going on in the world of Linux on Power, where teams have been focused on improvements for gcc performance. Lately, a series of articles have been published on DeveloperWorks which nicely highlight the performance gains that gcc (packaged in the Advance Toolchain) provides over the gcc packaged with the Linux operating system. Naturally, your mileage will vary. Perfor...
Improving performance on Linux (mostly Power): May 2008
http://well-itdepends.blogspot.com/2008_05_01_archive.html
Improving performance on Linux (mostly Power). Monday, May 5, 2008. PowerVM Lx86. Technology that works. Running Linux 32-bit x86 apps on Power systems. Slick. Super-easy with Linux. And does it work? Now, as a performance analyst, I'm often asked: "Is it a performance play? My quick answer: "Nah - not usually." But for everything I've tried: "It just works" - which in and of itself is pretty cool. You really want the best performance for your app? Http:/ www.transitive.com/customers/apple. IBM's product...
Improving performance on Linux (mostly Power): June 2008
http://well-itdepends.blogspot.com/2008_06_01_archive.html
Improving performance on Linux (mostly Power). Sunday, June 29, 2008. Building a distro kernel on Power - not so bad. This should be simple. And when you know all the steps, it is. But I was surprised how challenging it's been to find easy examples of the steps to re-build a commercially shipping "distro" kernel, in this case the SLES 10 sp1 kernel. For the SLES 10 sp1 (and sp2) kernel re-build instructions, see. Recently Jon Tollefson was playing around on the SLES 10 sp2 kernel and found that there's a...
Improving performance on Linux (mostly Power): SC10 - supercomputing conference
http://well-itdepends.blogspot.com/2010/11/sc10-supercomputing-conference.html
Improving performance on Linux (mostly Power). Friday, November 19, 2010. SC10 - supercomputing conference. Just got back from Supercomputing 2010. The annual conference provides a good perspective of the progress of "super computers", across universities, researchers, and industry. In recent years, the implementation of supercomputing has been slowly evolving towards a mix of compute core technologies, emerging more strongly along the lines of heterogeneous computing. As usual, the latest Top 500. List ...
Improving performance on Linux (mostly Power): October 2008
http://well-itdepends.blogspot.com/2008_10_01_archive.html
Improving performance on Linux (mostly Power). Wednesday, October 22, 2008. Who's stealing my CPU cycles? This "steal" term is a tad unfortunate. It's been suggested that a more gentle term of "sharing" would be preferred for customers. But digging around the source code I found the term "steal" is fairly pervasive. And what's in the code, tends to end up in the man pages. Ah well. The term "hardware thread" is with respect to the processor core. Each processor core can have two active hardware threa...
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Zombie Process « 2 AM, out of caffeine. Once more, I'm a… Zombie Process.
2 AM, out of caffeine. Once more, I'm a… Zombie Process. What is a Zombie Process? Hidden Markov Models in Python. Friday, 21 Mar 2014. I recently created a new GitHub repository for a Python module that I wrote to implement arbitrary HMMs: https:/ github.com/mstrosaker/hmm. A brief primer on HMMs. I think that HMMs are best described by an example. We will look at this toy model:. This is why it’s described as a. S1 – S1 – S1: 0.5 (initial probability of being in state 1) * 0.5 (prob...S1 – S1 ...
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We're committed to the art of advancing the. Software customer experience, for you, and. For your users. We are software artists. Craftsmanship is key.". More About Our Process. Micro-transactions and digital payments will never be the same. Food Feedback is a mobile app that connects people who want to share the beautiful meals they create with food coaches they choose. Eat healthy, eat beautiful, eat honest. PublishMe enables users to create, edit and share vibrant, attractive presentations on the iPad.
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