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User: brian.fristensky

gravatar for brian.fristensky
Reputation:
130
Status:
Trusted
Location:
Canada/University of Manitoba
Website:
http://home.cc.umanito...
Last seen:
1 month, 4 weeks ago
Joined:
3 years, 5 months ago
Email:
b***************@umanitoba.ca

I'm an Associate Professor in the Department of Plant Science at the University of Manitoba.

 

Posts by brian.fristensky

<prev • 24 results • page 1 of 3 • next >
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Answer: A: file and directory management best practices
... At the risk of sounding stodgy, I'd say that there is no substitute for deliberate and thoughtful organization right from the beginning. Search tools sometimes work, but are often more trouble than they're worth. An example would be most university web sites. If you try to do keyword seaches, you ge ...
written 9 weeks ago by brian.fristensky • 130
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Comment: C: Resources to learn genome assembly workflow for small genomes (like viruses)
... All Open source, and local. There are a few exceptions to the "local" part, in that you can run a BLAST+ search either using locally-installed copies of NCBI databases, or send the search to be run at NCBI. In either case, output pops up on your screen. As further enticement, BIRCH now sends email ...
written 9 weeks ago by brian.fristensky • 130
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Comment: C: Resources to learn genome assembly workflow for small genomes (like viruses)
... While there's no denying the power of the command line, [the BIRCH system][1] gives you the best of both worlds: An intuitive object-oriented set of GUI applications that run hundreds of common bioinformatics programs, which can also be run at the command line when that is more convenient. Assembli ...
written 9 weeks ago by brian.fristensky • 130
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Answer: A: Which tools do you miss?
... As a software developer, you might be intrigued by [Biolegato][1], a programmable GUI that makes it easy for biologists to run command-line programs. BioLegato is a Java application that lets the user set parameters in menus that are specified using PCD, a simple language that my lab has developed s ...
written 10 weeks ago by brian.fristensky • 130
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News: Software: BIRCH Bioinformatics System 3.70
... BIRCH 3.70 is now available for download at [http://home.cc.umanitoba.ca/~psgendb/local/public_html/BIRCH3.70announcement.html][1] NEW: - improvements and updates for multiple alignment and phylogeny - personalized user settings for BIRCH environment, including NCBI Entrez API keys - NCBI En ...
assembly genome news alignment rna-seq sequence written 3 months ago by brian.fristensky • 130
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Answer: A: How to extract certain CDS from a GenBank file in linux terminal
... See the BIRCH tutorial CREATING DATASETS OF RELATED SEQUENCES at [http://home.cc.umanitoba.ca/~psgendb/birchhomedir/BIRCHDEV/public_html/tutorials/bioLegato/dataset/dataset.html][1] [1]: http://home.cc.umanitoba.ca/~psgendb/birchhomedir/BIRCHDEV/public_html/tutorials/bioLegato/dataset/dataset.h ...
written 3 months ago by brian.fristensky • 130
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Comment: A: Preferred cloud environment for genomics.
... The term "cloud" can mean a lot of things, but a loose definition would mean that the programs and databases are on a server, but you run them from the desktop. You get the full power of the server, with the convenience of working from any computer you happen to be on. HOW you access the server can ...
written 3 months ago by brian.fristensky • 130
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Answer: A: how to run blastp against nr databse locally
... The entire process of installing BLAST databases and running BLAST searches is automated using the BioLegato applications found in the BIRCH system [http://home.cc.umanitoba.ca/~psgendb][1]. The following videos show BioLegato in action: Installing BLAST databases on your own computer [https://www ...
written 3 months ago by brian.fristensky • 130
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Answer: A: Trimmomatic paired-end mode question
... You didn't include the PE option to tell trimmomatic that you are giving it two paired end files. I put the PE option into your command line: java -jar /opt/anaconda3/pkgs/trimmomatic-0.39-1/share/trimmomatic-0.39-1/trimmomatic.jar PE -threads 16 -phred33 ${SRR}_1.fastq.gz ${SRR}_2.fastq.gz $ ...
written 3 months ago by brian.fristensky • 130
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Answer: A: Size of the nr database fasta file?
... The BIRCH system has a comprehensive point and click system for installing, managing and searching BLAST databases on your local computer. The documentation for local blast databases is found at [http://home.cc.umanitoba.ca/%7Epsgendb/birchadmin/blastdb/BLASTDB.html][1]. The link "Figuring out Disk ...
written 3 months ago by brian.fristensky • 130

Latest awards to brian.fristensky

Scholar 9 weeks ago, created an answer that has been accepted. For A: file and directory management best practices
Autobiographer 9 weeks ago, has more than 80 characters in the information field of the user's profile.
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Extract specific genes from a FASTA file.
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