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Jean-Yves Sgro wrote a new post, Docker tutorials for Biologists 1 day, 10 hours 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 1 year, 9 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 1 year, 10 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, 1 month 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, 1 month 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, 1 month 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 2 years, 5 months 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 2 years, 5 months 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 2 years, 5 months agoThe slides are here (heavily truncated due to unpublished data)
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Oleg Moskvin uploaded the file: May 22, 2017 to
BioComP 2 years, 5 months agoSlides (truncated due to unpublished data) of the may 22 meeting
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Jean-Yves Sgro wrote a new post, asciinema: record commands in terminal 2 years, 6 months ago
RE: asciinema.org (Linux/MacOS)
It may be nice to share/show commands being typed on a Text Terminal and embed this simple “movie” within blog or HTML page.
It seems that the recording gets uploaded to […]
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Looks like an interesting idea. I’ll try it someday.
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Yury Bukhman started the topic Meeting notes – 22 May 2017 in the forum
BioComP 2 years, 6 months agoOleg gave an excellent presentation on single cell RNA-seq data analysis. It was interesting to hear about data quality issues that are specific to the single cell methodology, such as gene drop-outs, and about specialized normalization and clustering techniques used to deal with this kind of data.
The meetings will continue on 4’th Mondays of…[Read more]
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Jean-Yves Sgro wrote a new post, Omics Pipe: An Automated Framework for Next Generation Sequencing Analysis 2 years, 6 months ago
Re: pythonhosted.org/omics_pipe
Next Gen. data analysis requires many steps, that can be learned one by one, for example running an aligner such as bowtie, tophat or STAR, then handle the SAM/BAM file for […]
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Jean-Yves Sgro wrote a new post, alternativeto.net: finding alternate software 2 years, 6 months ago
Re:alternativeto.net
What software one uses may be the result of colleague recommendations, using “what others use in the lab,” or haphazardly found options online.
Or perhaps it is time to “upgrade” a […]
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Jean-Yves Sgro wrote a new post, omictools.com: Search engine for biological data analysis 2 years, 7 months ago
Re: omictools.com
Finding software that is relevant to any biological analysis can be inspired by reading a paper or perhaps searching within Google.
The web site https://omictools.com/ contains 16,971 s […]
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Thank you, that’s a well-organized and handy tool. I like the idea of a “3-dimensional” classification by Technology / Interpretation / Topic
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Thanks, Jean-Yves! This looks very useful to me. I am looking for QC tools for shotgun metagenomics in particular. Several are listed, along with a review paper.
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Oleg Moskvin replied to the topic Organizational in the forum
BioComP 2 years, 7 months agoCurrently, we have 3 parallel platforms on the site operating from the front end:
From top to bottom, the purpose shifts from more “static” and “serious” to more dynamic and interactive. At the bottom level, there is no more rich text formatting (for fast twitter-like or facebook-like updates). Those…[Read more]
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Oleg Moskvin replied to the topic Organizational in the forum
BioComP 2 years, 7 months agoCurrently, we have 3 parallel platforms on the site operating from the front end:
From top to bottom, the purpose shifts from more “static” and “serious” to more dynamic and interactive. At the bottom level, there is no more rich text formatting (for fast twitter-like or facebook-like updates).
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Yury Bukhman replied to the topic Meeting notes – 14 Apr 2017 in the forum
BioComP 2 years, 7 months agoNote from Yury Bukhman
The paper on using Docker and Continuous Integration to set up reproducible data analysis workflows that I have mentioned is here: http://www.nature.com.ezproxy.library.wisc.edu/nbt/journal/v35/n4/full/nbt.3780.html
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Yury Bukhman started the topic Meeting notes – 14 Apr 2017 in the forum
BioComP 2 years, 7 months agoNotes from Jean-Yves Sgro
FYI: I mentioned the dynamic small print web blog server based on MarkDown called “Jekyll”
I installed it and tried it on my Mac last year but eventually it was best to make my material available on the
Biochem web site.
Info about Jekyll: e.g. Building Static Sites with Je…[Read more]
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Yury Bukhman started the topic Meeting notes – 14 Apr 2017 in the forum
BioComP 2 years, 7 months ago<span style=”text-decoration: underline;”>Notes from Jean-Yves Sgro</span>
FYI: I mentioned the dynamic small print web blog server based on MarkDown called “Jekyll”
I installed it and tried it on my Mac last year but eventually it was best to make my material available on the
Biochem web site.
Info about Jekyll: e.g. Building Static Si…[Read more]
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