dskernel.blogspot.com

The Bioinformatics Adventure

A list of interesting papers on optical mapping. At GYDLE inc., I work on optical mapping problems, and sometimes I find solutions to these problems. To tackle efficiently any problem, the error model for the problem must be understood. To write software that deals well with a given type of data, this type of data has to be understood, and one must be able to separate the good data from the bad data. Some of these papers describe error models for optical mapping. Links to this post. At Gydle Inc, we are ...

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The Bioinformatics Adventure | dskernel.blogspot.com Reviews

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A list of interesting papers on optical mapping. At GYDLE inc., I work on optical mapping problems, and sometimes I find solutions to these problems. To tackle efficiently any problem, the error model for the problem must be understood. To write software that deals well with a given type of data, this type of data has to be understood, and one must be able to separate the good data from the bad data. Some of these papers describe error models for optical mapping. Links to this post. At Gydle Inc, we are ...

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the bioinformatics adventure,posted by,sébastien boisvert,no comments,algorithm design,software design,software development,test development,ticket management,data analysis,data curation,gydle optical aligner,gydle optical alignment aligner,xmap alignment

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The Bioinformatics Adventure | dskernel.blogspot.com Reviews

https://dskernel.blogspot.com

A list of interesting papers on optical mapping. At GYDLE inc., I work on optical mapping problems, and sometimes I find solutions to these problems. To tackle efficiently any problem, the error model for the problem must be understood. To write software that deals well with a given type of data, this type of data has to be understood, and one must be able to separate the good data from the bad data. Some of these papers describe error models for optical mapping. Links to this post. At Gydle Inc, we are ...

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dskernel.blogspot.com

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The Bioinformatics Adventure: Nice public microbiome datasets for metagenomics

http://dskernel.blogspot.com/2013/10/nice-public-microbiome-datasets-for.html

Nice public microbiome datasets for metagenomics. Edit 2013-10-29: added humongous dataset from Qin et al. 2012. There are at least. 3 huge datasets for metagenomics. One of the challenge is to analyze all the data simultaneously in an integrative fashion. That's where Ray Surveyor will do when ready! Ray Surveyor will generate a Gramian Matrix, and also a Pairwise Distance Matrix. All of this is based on reference-free algorithms. Here are some huge datasets:. 406 GiB (compressed with gzip). Pulling nex...

2

The Bioinformatics Adventure: July 2014

http://dskernel.blogspot.com/2014_07_01_archive.html

Is it required to use different priority in a high-performance actor system? I was reading a log file from an actor computation. In particular, I was looking at the outcome of a kmer counting computation performed with Argonnite, which runs on top of Thorium. Argonnite is an application in the BIOSAL project and Thorium is the engine of the BIOSAL project (which means that all BIOSAL applications run on top of Thorium). In the current code, every actor is classified in normal by default. Node/0 worker/5 ...

3

The Bioinformatics Adventure: March 2014

http://dskernel.blogspot.com/2014_03_01_archive.html

On my way to the postdoctorate. Change is always ongoing. Change is good. In evolution processes, it is typically a balance between compartmentalization processes and consolidation processes. On 10 April 2014 (THE planned date). My schedule is not too far off my initial 2010 planning. I am really looking forward to join Argonne National Laboratory to work. Computing, Environment and Life Sciences) directorate. Technically I will be with MCS. According to Peter B. Littlewood. I really look forward to work...

4

The Bioinformatics Adventure: The convergence of HPC and cloud computing

http://dskernel.blogspot.com/2015/07/the-convergence-of-hpc-and-cloud.html

The convergence of HPC and cloud computing. Computer is an imaginary system that can sustain one exaflops (10 18 floating point operations per second.) Such an object is needed in science and engineering, mostly for simulating virtual versions of objects found in the real world, such as proteins, planes, and cities. Important requirements for such a computer are 1) memory bandwidth, 2) floating point operation throughput, 3) low network latency, and so on. An Interview with Berkeley Lab's Horst Simon).

5

The Bioinformatics Adventure: October 2013

http://dskernel.blogspot.com/2013_10_01_archive.html

Pulling next-generation sequences from the European Nucleotide Archive (ENA). Today, I have read the abstract (and the methods) of a PNAS (Proceedings of the National Academy of Sciences) paper entitled Evolutionary dynamics of Staphylococcus aureus. During progression from carriage to disease. In this paper, researchers sequenced the DNA of a high number of Staphylococcus aureus. Isolates from patients over a certain period of time. This is science. The INSDC has 3 members (alphabetical order):. Here ar...

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News And Views | (n=1) by Peter D'Adamo

http://n-equals-one.com/blogs/category/news-and-views

Archive for the 'News and Views' Category. Published by Peter D'Adamo. Under Diet and Nutrition. A study purporting to ‘debunk’ the blood type diet theory has recently been published. [1,2] However, a closer look at the study’s experimental design raises serious questions about its conclusions, including whether in fact the participants were actually following the blood type diet at all, and given its other parameters, would it have even been […]. 63 responses so far. Published by Peter D'Adamo.

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Despised Theories | (n=1) by Peter D'Adamo

http://n-equals-one.com/blogs/category/despised-theories

Archive for the 'Despised Theories' Category. Published by Peter D'Adamo. A look at the core data used in the PLOS Study [1] debunking the Blood Type Diet (BTD) finds support for the researcher’s conclusions that if your experimental subjects eat potato chips, sandwiches, pizza, ‘beans,’ mac-and-cheese, French Fries and processed meat products while doing 13.7% of the Blood Type Diet, their final cardiometabolic markers will […]. 13 responses so far. Published by Peter D'Adamo. I object, your honor!

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Glycobiology | (n=1) by Peter D'Adamo

http://n-equals-one.com/blogs/category/glycobiology-2

Archive for the 'Glycobiology' Category. Thoughts on the Immortality of the Crab. Published by Peter D'Adamo. The deepest problem: of the immortality of the crab, is that a soul it has, a little soul in fact … That if the crab dies entirely in its totality with it we all die for all of eternity Miguel de Unamuno, ‘The Immortality of the Crab’ Pensar en la inmortalidad del cangrejo (‘Thinking […]. 2 responses so far. Published by Peter D'Adamo. One response so far. Published by Peter D'Adamo. Carbohydrate...

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It Is I | (n=1) by Peter D'Adamo

http://n-equals-one.com/blogs/about

Published by Peter D'Adamo. I am Peter D’Adamo, a naturopathic physician, author, researcher-educator, Ivesian, software developer, music systems pre-programmer and air-cooled engine enthusiast. I have an abiding interest in glycobiology, principally the ABO blood groups, the secretor (FUT2) polymorphisms and the computer language Perl. As applied to genomic and information systematics). What I especially like about Perl is its tremendous utility in Web based interfaces. 10 responses so far. Vi su pregun...

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Uncategorized | (n=1) by Peter D'Adamo

http://n-equals-one.com/blogs/category/uncategorized

Archive for the 'Uncategorized' Category. Published by Peter D'Adamo. A look at the core data used in the PLOS Study [1] debunking the Blood Type Diet (BTD) finds support for the researcher’s conclusions that if your experimental subjects eat potato chips, sandwiches, pizza, ‘beans,’ mac-and-cheese, French Fries and processed meat products while doing 13.7% of the Blood Type Diet, their final cardiometabolic markers will […]. 13 responses so far. Published by Peter D'Adamo. Under Diet and Nutrition.

n-equals-one.com

Nutrigenomics | (n=1) by Peter D'Adamo

http://n-equals-one.com/blogs/category/nutrigenomics

Archive for the 'Nutrigenomics' Category. Published by Peter D'Adamo. A look at the core data used in the PLOS Study [1] debunking the Blood Type Diet (BTD) finds support for the researcher’s conclusions that if your experimental subjects eat potato chips, sandwiches, pizza, ‘beans,’ mac-and-cheese, French Fries and processed meat products while doing 13.7% of the Blood Type Diet, their final cardiometabolic markers will […]. 13 responses so far. Published by Peter D'Adamo. Under Diet and Nutrition.

n-equals-one.com

Places | (n=1) by Peter D'Adamo

http://n-equals-one.com/blogs/places

Published by Peter D'Adamo. Technical books I’ve written. Popular books I’ve written. An Older Blog of Mine. Subscribe to the comments on this post. Fats, Blood Groups and the Intestines. Blood groups, secretor status and the microbiome. Tracking the Blood Type Diet. On Wrecker of Civilization. On Wrecker of Civilization. On It Is I. On Wrecker of Civilization. Arts and Letters Daily. N=1) by Peter D'Adamo. Become my Facebook friend.

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Bioinformatics | (n=1) by Peter D'Adamo

http://n-equals-one.com/blogs/category/bioinformatics

Archive for the 'Bioinformatics' Category. Published by Peter D'Adamo. I’ve been gone for a while. Sorry. It’s been a busy time for me. I’ve spent most of the year coding a genomic analysis program called Opus 23 Pro. Opus 23 Pro is a suite of apps that provide a development environment for precision medicine. It allows the clinician to […]. Comments Off on Opus 23. Tracking the Blood Type Diet. Published by Peter D'Adamo. Comments Off on Tracking the Blood Type Diet. Published by Peter D'Adamo. One of t...

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dskernel.blogspot.com

The Bioinformatics Adventure

A list of interesting papers on optical mapping. At GYDLE inc., I work on optical mapping problems, and sometimes I find solutions to these problems. To tackle efficiently any problem, the error model for the problem must be understood. To write software that deals well with a given type of data, this type of data has to be understood, and one must be able to separate the good data from the bad data. Some of these papers describe error models for optical mapping. Links to this post. At Gydle Inc, we are ...

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It's all about Family

It's all about Family. Tuesday, January 8, 2013. 6 Months in Pictures. I don't think I can begin to catch up on all that has happened in the last six months. I will try to mention the big things and then you can enjoy some fun photo documentation of our work and play. This year threatens to be a busy one but we are looking forward to it in a lot of ways. Chance is getting some help blowing out his birthday candles. Grandma and Grandpa Kerns brought some puppets over for Chance's B-day. Way to wear it.

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Sevgili Meslektaşlarım, Göreve başladığımız 10 Şubat 2014 tarihinden itibaren en hızlı ve en etkin şekilde siz değerli meslektaşlarımızın ve sektörümüzün sorunlarına çare bulmak için yönetim. Yeni Yılınız Kutlu Olsun. 2018'in, Sağlıklı, Mutlu, Huzurlu ve Refah Dolu Geçmesi Dileğiyle. Yeni Yılınız Kutlu Olsun. HABERİN DEVAMI ». Şükran ve Saygıyla Anıyoruz. Türkiye Cumhuriyeti'nin kurucusu ve yeniliklerin sahibi olan Atatürk, fikirleri ile her zaman yaşayacak ve yaşatılacaktır. HABERİN DEVAMI ». HABERİN DE...

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