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Blasted Bioinformatics!?Bioinformatics lessons learned the hard way, bugs, gripes, and maybe topical paper reviews too...
http://blastedbio.blogspot.com/
Bioinformatics lessons learned the hard way, bugs, gripes, and maybe topical paper reviews too...
http://blastedbio.blogspot.com/
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Blasted Bioinformatics!? | blastedbio.blogspot.com Reviews
https://blastedbio.blogspot.com
Bioinformatics lessons learned the hard way, bugs, gripes, and maybe topical paper reviews too...
blastedbio.blogspot.com
Blasted Bioinformatics!?: BLAST! No frequency ratios needed for composition-based statistics
https://blastedbio.blogspot.com/2014/10/deltablast-rpsblast-no-frequency-ratios.html
Bioinformatics lessons learned the hard way, bugs, gripes, and maybe topical paper reviews too. No frequency ratios needed for composition-based statistics. While working on updating the NCBI BLAST wrapper for Galaxy. For any changes in the new BLAST 2.2.30 release. I hit a cryptic error message from deltablast. Deltablast -query rhodopsin proteins.fasta -subject four human proteins.fasta -evalue 1e-08 -outfmt "6 qseqid sseqid score" -rpsdb /data/blastdb/cdd delta. The same applies to the rpsblast. And f...
Blasted Bioinformatics!?: Column headers in BLAST+ tabular and CSV output
https://blastedbio.blogspot.com/2014/11/column-headers-in-blast-tabular-and-csv.html
Bioinformatics lessons learned the hard way, bugs, gripes, and maybe topical paper reviews too. Column headers in BLAST tabular and CSV output. In the last couple of years, my preferred BLAST output format has switched from BLAST XML to plain tabular output. The main reason for this it is easier to parse, and now gives easy access to more fields - BLAST 2.2.28 added descriptions and taxonomy output. To the tabular and CSV output, but the cumulative effect is BLAST XML has been lagging behind. 6 = tabular,.
Blasted Bioinformatics!?: 2014-12
https://blastedbio.blogspot.com/2014_12_01_archive.html
Bioinformatics lessons learned the hard way, bugs, gripes, and maybe topical paper reviews too. BLAST Christmas Wish List. Please could you ask the Elves at the NCBI to deliver the following BLAST feature requests for Christmas 2014? PS Do they think I have been naughty or nice with my BLAST blog posts. Subscribe to: Posts (Atom). View my complete profile. BLAST Christmas Wish List. Simple template. Template images by luoman.
Blasted Bioinformatics!?: BLAST+ 2.2.29 upset by [key=value] entries in queries
https://blastedbio.blogspot.com/2014/04/error-1431-fasta-reader-ignoring-modifiers.html
Bioinformatics lessons learned the hard way, bugs, gripes, and maybe topical paper reviews too. BLAST 2.2.29 upset by [key=value] entries in queries. I recently got a weird error/warning message (repeated) in my BLAST stderr output,. Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any. This turns out to be due to having. Update (31 October 2014):. This was fixed in BLAST 2.2.30 (released yesterday). On the BLAST FTP site.
Blasted Bioinformatics!?: 2014-11
https://blastedbio.blogspot.com/2014_11_01_archive.html
Bioinformatics lessons learned the hard way, bugs, gripes, and maybe topical paper reviews too. Column headers in BLAST tabular and CSV output. In the last couple of years, my preferred BLAST output format has switched from BLAST XML to plain tabular output. The main reason for this it is easier to parse, and now gives easy access to more fields - BLAST 2.2.28 added descriptions and taxonomy output. To the tabular and CSV output, but the cumulative effect is BLAST XML has been lagging behind.
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etalog: November 2012
http://etalog.blogspot.com/2012_11_01_archive.html
More of a comment than a question. Thursday, November 8, 2012. Journal article: Biopython's Bio.Phylo. We're not known for the timeliest reporting here at etalog, but FYI, our article on the Bio.Phylo module for phylogenetics in Biopython is now up in its final form on the BMC Bioinformatics:. BioPhylo: A unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython. To get started, though, I recommend the main documentation:. Phylo is currently chapter 12). In Boston about th...
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...
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 ...
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...
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).
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...
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 ...
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).
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.
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).
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Blasted Beat | Hot new Music
Skip to primary content. Please bang my sexy wife. Skip to secondary content. So you wanna make beats huh? March 6, 2013. This is the beginning of a segment that will teach you to make beats. I have no experience with making beats, so you should be all caught up. Gotta Kick off this Blog right. The Next Episode – Dr. Dre (ft. Kurupt, Snoop Dogg, Nate Dogg) (Hedegaard Remix). February 27, 2013. So you wanna make beats huh? Gotta Kick off this Blog right.
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Blasted Bill's Place of ranting and not of reading your LJ.
Blasted Bills Place of ranting and not of reading your LJ. Please Help I3 Detroit. Jan 7th, 2011 06:43 am. I3 Detroit needs your help to win a laser cutter. To do this: register for an Instructables account (free) at http:/ ow.ly/3xzb6. Then go to our project page and click vote - http:/ ow.ly/3xzbM. That's it. For 20 seconds of your time you will help i3 Detroit win a $8,000 piece of equipment for the community to use at the shop. Please help. Full specs on the laser cutter below. 16 x 12 (406 x 305 mm).
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Blasted Bioinformatics!?
Bioinformatics lessons learned the hard way, bugs, gripes, and maybe topical paper reviews too. Entrez eSpell can't resolve PubmedSpellSrv. Another quick bug report blog post, this time NCBI Entrezs espell is currently broken returning:. Couldnt resolve #PubmedSpellSrv, the address table is empty. BLAST 2.7.0 segmentation fault with HTML output. Ive not managed to blog much at all this year ( parenthood. 160;under both Mac and Linux when requesting HTML output. Mozilla Science Fellowship application 2016.
blasted books - Home
Novellas - short stories - essays - opuscula. Please read our 'about' page to get a feel for the sort of works we are looking for. Affect people and rage begets rage. Maxwell Armstrong's literary debut is a dark, energetic and visceral narrative interspersed with humorous and touching renderings. Flowing prose at times strays into the poetic while he studies the causality of behaviour and explores the effects of choices that some of us may need to make. Create a free website. Start your own free website.
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