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Jean-Yves Sgro wrote a new post, A great Unix tutorial suitable for beginners 1 month, 4 weeks ago
More than once I have written my own tutorials for learning how to use the command line within the bash shell in the context of a Unix or Unix-like computer. Recently I found a very well done tutorial that, while […]
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Jean-Yves Sgro wrote a new post, PCA as Metro-Maps & Hierarchical Clustering on Principal Components 4 months, 4 weeks ago
The iris dataset is perhaps one of the most famous datasets used to learn and teach statistics and now machine learning. Being curious about this dataset lead me last time to the TableConvert.com web site that I […]
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Jean-Yves Sgro wrote a new post, TableConvert.com – free tabular data formats converter 5 months ago
This is a repost of my post on the Biochemistry department: tableconvert-com-free-tabular-data-formats-converter
Tabular formats
When I first came to Madison in 1986 as a postdoc with Biochemistry professor […]
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Jean-Yves Sgro wrote a new post, Bioawk for handling bioinformatics formats 5 months, 1 week ago
Today I found a new tool: bioawk that was written by Heng Li who also wrote samtools and bwa.
I first discovered it ont this blog: bioawk-basics (Bioinformatics Workbooks)
There is also a short tutorial on G […]
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Jean-Yves Sgro wrote a new post, A Boy And His Atom: The World’s Smallest Movie 5 months, 3 weeks ago
Moving atoms
For some reason a paper copy of “Chemical and Engineering News” (November 11, 2019 – Vol 97 Issue 44) ended up in my hands, and I almost missed this fun section named: “30 years of moving atoms: How […] -
Jean-Yves Sgro wrote a new post, GREP was written overnight – Birth and Name 5 months, 3 weeks ago
I use grep very often, and I made-up and acronym that made sense to me: Get REgular ExPression
But I discovered this YouTube video that gives an accurate historical recounting of its birth and where its name […]
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Jean-Yves Sgro wrote a new post, Visualizing gzipped compressed text files 5 months, 3 weeks ago
Even though I have been using computers all my life there are still many aspects of computing that are mysterious to me, and I am sure many others…
One of my favorite quotes is “A leads to B leads to C” […]
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Jean-Yves Sgro wrote a new post, Beyond Docker? Binder 2.0 6 months ago
Binder 2.0
As just an “end-user” of software for data analysis it is sometimes difficult to just catch up with what’s available, and I end-up discovering new things simply browsing the web looking for something […] -
Jean-Yves Sgro wrote a new post, STAR index for human genome – overcoming the hardware barriers 6 months ago
Recently I was testing a Docker image to run a container for Next Gen sequencing, a way to test an existing “pipeline” on the first published study of the effect of the Zika virus. […]
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Jean-Yves Sgro wrote a new post, Down-sampling FASTQ.gz paired ends 6 months, 2 weeks ago
Downsampling
I have performed a search for creating a set of down-sampled data from an actual large dataset, and while there are many creative information on BioStar and other forums, I find that the most […] -
Jean-Yves Sgro wrote a new post, Hunting for SRA sequence archives 6 months, 3 weeks ago
SRA: Sequence Read Archive
The Sequence Read Archive (SRA) makes biological sequence data available to the research community to enhance reproducibility and allow for new discoveries by comparing data sets. The S […]
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It seems quite handy. Thanks, Jean-Yves!
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Jean-Yves Sgro wrote a new post, Docker tutorials for Biologists 6 months, 3 weeks ago
I have started a series of tutorials that I am writing from the perspective of a biologist wanting to use a Docker container for a specific application.
An easy example could be using EMBOSS, the molecular […]
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Yury Bukhman uploaded the file: PAG XXVI notes to
BioComP 2 years, 3 months agoI have presented these notes at the BioComP meeting on 22 Jan 2018. They have been modified, mostly by rearranging the slides and adding hyperlinks to papers and software.
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Oleg Moskvin wrote a new post, Enterotypes-2018 2 years, 5 months ago
The recent update on enterotypes1 was an important read.
Yes, we desperately need to reduce the dimensionality of the gut microbiome data and discover the stable “archetypes” of the microbiome functional […]
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Oleg Moskvin started the topic Meeting notes – 23 Oct 2017 in the forum
BioComP 2 years, 8 months agoThis was the first meeting of the BioComP group in the new location – WID.
Presentation slides – “Deep Learning for Biological Data Analysis”
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Oleg Moskvin uploaded the file: October 23, 2017 to
BioComP 2 years, 8 months agoSlides from the October 23, 2017 meeting on Deep Learning in bioinformatics
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Yury Bukhman posted an update in the group
BioComP 2 years, 8 months agoOctober 23 meeting – O. Moskvin, Deep Learning for Biological Data Analysis.
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Oleg Moskvin will present “Deep Learning for Biological Data Analysis” on Monday Oct 23 at 3:30 PM at WID 4330. Note the location change from pre…[Read more] -
Oleg Moskvin replied to the topic Organizational in the forum
BioComP 3 years agoAfter analysis of what users actually tend to use and in order to de-clutter the interface, the “Collaborative Wiki” has been removed (it was not sufficiently customizable to add any functionality that is beyond what we already have in forums)
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Oleg Moskvin wrote a new post, Review on Deep Learning in Biology and Medicine 3 years ago
Deep neural networks are everywhere. They are revolutionizing our day-to-day lives, and this phenomenon no longer needs any introduction or description.
Deep learning is especially suitable to find structures […]
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Oleg Moskvin replied to the topic Meeting notes – 22 May 2017 in the forum
BioComP 3 years agoThe slides are here (heavily truncated due to unpublished data)
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