dskernel.blogspot.com
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...
dskernel.blogspot.com
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 ...
dskernel.blogspot.com
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...
dskernel.blogspot.com
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).
dskernel.blogspot.com
The Bioinformatics Adventure: November 2013
http://dskernel.blogspot.com/2013_11_01_archive.html
27th November 2013 in Liverpool. Twitter superstar Nick Loman. Has organized a great meeting in Liverpool (United Kingdom) called Beatles and Bioinformatics! On 27th November 2013. I just gave my keynote talk. About Ray and metagenomics. I am currently attending the new great talks. You can watch the live talks from Beatles and Bioinformatics! On the YouTube channel called pathogenomics. Also, the CGR (Center for Genomic Research) Course in Metagenomics (held on 28th and 29th November 2013 in Liverpool).
dskernel.blogspot.com
The Bioinformatics Adventure: The Spark Notebook from creator Kate Matsudaira
http://dskernel.blogspot.com/2015/08/the-spark-notebook-from-creator-kate.html
The Spark Notebook from creator Kate Matsudaira. I received my Spark Notebook. What is the Spark Notebook, you may ask. Combines form and function. The Spark Notebook project raised funding on Kickstarter. The way I see it, the Spark Notebook is an agenda (a 6-month agenda) with additional features. These features include (from the guide. The Spark Notebook comes with a guide. How did I learn about the existence of the Spark Notebook? The other types of videos that I like on the AWS YouTube channel are t...
dskernel.blogspot.com
The Bioinformatics Adventure: Is it required to use different priority in a high-performance actor system ?
http://dskernel.blogspot.com/2014/07/is-it-required-to-use-different.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 ...
dskernel.blogspot.com
The Bioinformatics Adventure: July 2015
http://dskernel.blogspot.com/2015_07_01_archive.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).
dskernel.blogspot.com
The Bioinformatics Adventure: October 2014
http://dskernel.blogspot.com/2014_10_01_archive.html
Profiling the Thorium actor model engine with LTTng UST. Thorium is an actor model engine in C 1999. It uses MPI and Pthreads. The latency (in Thorium) when sending small messages between actors recently came to my attention. In this post, LTTng-UST is used to generate actor message delivery paths annotated with time deltas in each step. I have been working with perf for a while now, but found it only useful mostly for hardware counters. T $thread -o $thread.perf.data. A friend of mine ( Francis Giraldeau.
dskernel.blogspot.com
The Bioinformatics Adventure: June 2014
http://dskernel.blogspot.com/2014_06_01_archive.html
The actor model of computation. Has Professor Carl Hewitt in it. Hewitt is the original creator of the concept of actors. Hewitt created the concept of actors in 1973 with Bishop, and Steiger. Everything is in this paper and it's 11 page. If you have little time, you can read only the bottom of page 12 of Gul Agha's PhD thesis. Http:/ dspace.mit.edu/bitstream/handle/1721.1/6952/AITR-844.pdf. Page 12, section "2.1.3 Actors". If you have more time:. Hewitt, Bishop, Steiger 1973. Hewitt and Baker 1977.
