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  • Nov 20 18:04

    bmpvieira on master

    Refactor to add CLI 3.0.0 (compare)

  • Nov 20 18:04

    bmpvieira on master

    Refactor to add CLI 3.0.0 (compare)

  • Sep 02 15:27
    dependabot[bot] labeled #6
  • Sep 02 15:27
    dependabot[bot] labeled #6
  • Sep 02 15:27
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    dependabot[bot] on npm_and_yarn

    Bump bl from 1.2.2 to 4.0.3 Bu… (compare)

  • Sep 02 15:27
    dependabot[bot] opened #6
  • Sep 02 15:27

    dependabot[bot] on npm_and_yarn

    Bump bl from 1.2.2 to 4.0.3 Bu… (compare)

  • Jul 27 16:44
    JWhoops closed #5
  • Jul 27 16:44
    JWhoops closed #5
  • Apr 16 04:31
    JorgeFelixc opened #44
  • Apr 16 04:31
    JorgeFelixc opened #44
  • Nov 19 2019 17:27
    katrinleinweber commented #43
  • Nov 19 2019 17:27
    katrinleinweber commented #43
  • Nov 19 2019 17:27
    katrinleinweber commented #43
  • Nov 19 2019 17:27
    katrinleinweber commented #43
  • Nov 19 2019 13:28

    bmpvieira on master

    Hyperlink DOIs to preferred res… Merge pull request #5 from katr… (compare)

  • Nov 19 2019 13:28

    bmpvieira on master

    Hyperlink DOIs to preferred res… Merge pull request #5 from katr… (compare)

  • Nov 19 2019 13:28
    bmpvieira closed #5
  • Nov 19 2019 13:28
    bmpvieira closed #5
Hitesh Joshi
@evoxtorm
My professors are loving this library
Bruno Vieira
@bmpvieira
Hey @evoxtorm ! Super happy to read that! :smile:
Thanks for using it! Would love to see those slides and know more about how you are using bionode-ncbi in your work
Hitesh Joshi
@evoxtorm
ok sure sure I'll share with you
Hitesh Joshi
@evoxtorm
Hey guyz,
Does anyone have data flow diagram of bionode-ncbi because I have to show how this library actually works
Julian Mazzitelli
@thejmazz
its mostly filtering/wrapping ncbi API calls, making a stream out of paginated response s, etc, there is no diagram I am aware of. is this use case being able to explain underlying technicalities so that others feel more comfortable with the software?
Hitesh Joshi
@evoxtorm
Ok Thanks @thejmazz
Olga Botvinnik
@olgabot
hello! I'm trying to download FASTQ files from this bioproject: PRJNA183192
But bionode-ncbi download sra PRJNA183192 repeats the first SRA file, SRR629557.sra until infinity
Bruno Vieira
@bmpvieira
Hey @olgabot ! What do you get if you just do bionode-ncbi urls sra PRJNA183192
also, bionode-ncbi download is very verbose by default (to pipe into other tools)
you can try bionode-ncbi download sra --pretty PRJNA183192 to display a progress bar instead
Bruno Vieira
@bmpvieira
if for some reasonbionode-ncbi urls gives you the right urls, but bionode-ncbi download keeps downloading the same file, please open an issue on GitHub and try this as a workaround: bionode-ncbi urls sra PRJNA183192 | jq .url | xargs wget
or if you don't have jq installed: bionode-ncbi urls sra PRJNA183192 | sed 's|.*url":"\(.*\)","uid.*|\1|' | xargs wget
Hitesh Joshi
@evoxtorm
Hey this year also bionode has same project
bionode-watermill
Hitesh Joshi
@evoxtorm
In GSOC
Julian Mazzitelli
@thejmazz
yes! i will try to make a more detailed project description soon!
Hitesh Joshi
@evoxtorm
ok
Maximilien Rothier Bautzer
@cachemoi
Hi,
Does bionode already have a module focused on systems biology? I can't seem to find one. If it hasn't been done already and if it's a feature you're looking for i'd like to start working on it.
As a simple first feature i'm thinking an SBML/JSON parser might be interesting
Julian Mazzitelli
@thejmazz
everything we have is a repo on bionode organization. no SBML parser atm
nice!
Sarthak Sehgal
@sarthak-sehgal
Hello @all
I'm Sarthak from India
I'm interested in the "Bionode workflow engine for streamed data analysis (bionode-watermill)" project for GSoC 2018
How do I get started? :smiley:
Julian Mazzitelli
@thejmazz
Hi Sarthak! These are some points of interest:
  • playing with bioinformatics pipelines using shell scripts which clearly demonstrates difficulty (see my ngs-worklfows blog post on jmazz.me)
  • taking a look at the CWL project, and corresponding ecosystem (rabix team on GitHub for example), similarly WDL (workflow standard the Broad institute made)
  • reading some review literature on variant calling perhaps (the majority of pipelines are this, producing variant calling files (VCF) as output, for human genomics) (I would not expect students to fully understand these papers but I should look for a good introduction one)
  • the biological intuition probably would take a while to really get (but not the technical implementation of tools as much perhaps, which isn't required to run them...), at a superficial level you are calling a bunch of command line tools, each with their own set of parameters (understanding how these parameters affect the final output and the biological implications of such is the crux of being informed technically as well as biologically). in this way a pipeline tool would benefit from being able to assign a matrix of commands/parameters and then compare outputs (goal of fork() in watermill)
Let me know if anything unclear
Sarthak Sehgal
@sarthak-sehgal
Thanks a lot @thejmazz! I will start looking into them. :smiley:
Hitesh Joshi
@evoxtorm
Hey anyone have a sample for proposal
Julian Mazzitelli
@thejmazz

heres mine from 2016 Bionode workflow engine for streamed data analysis

note the timeline ended up very different from what proposed. but its good to get an idea if student can organize a plan

Hitesh Joshi
@evoxtorm
thanks
Hitesh Joshi
@evoxtorm
European Student Council Symposium 2018
Julian Mazzitelli
@thejmazz
thanks! abstract due June 23
Hitesh Joshi
@evoxtorm
You can still submit
May I guess
Akash Singh
@akashzcoder
does bionode has a metric to measure the accuracy of a multiple sequence alignment?
Julian Mazzitelli
@thejmazz
I don't think so, do you mean like a count of number of spots which are aligned to the most sequences?
you could use fork() from watermill to run a bunch of MSA's with different parameters, and then visualize with biojs MSA viewer (which is nice for its zoom out feature)
mohmaed7777
@mohmaed7777
hello ,,
Hitesh Joshi
@evoxtorm
Hii @mohmaed7777
Thakur Karthik
@ThakurKarthik
Hello is this project still in progress?I came here after seeing the project in GSOC 2019 ideas page("Bionode workflow engine for streamed data analysis (bionode-watermill)").I want to work on this.I have been working on Reactjs in new ES6 syntax and used Reduxjs for state management.So if someone guide me in right direction iam confident i will take this to live version.
Berk Sözer
@sozerberk
I guess this community is dead now?
Bruno Vieira
@bmpvieira
Hi all, the project isn't dead, just sleeping. The main contributors have been busy with other things. I've started working for http://www.resurgo.com mid January and we have plans to use and improve some of bionode tools. Bionode did not apply for GSoC 2019 due to lack of time but we hope to be in a position to apply next year.
Thakur Karthik
@ThakurKarthik
Hey thanks for informing :)
Berk Sözer
@sozerberk
@bmpvieira Thanks for the update!
Tom Atkinson
@tomachinz
Hiya, I'm the creator of AminoSee DNA viewer! aminosee.funk.nz
it converts an infinite stream of ascii into PNG files! using a colour lookup table for the amino acids
can someone show me how i can make this thing (its a node CLI app you type "aminosee *" to convert all .fa .txt files etc). currently adding std in support eg pipes. it just eats raw ascii throwing out anything that is not one of: ACGTU since it work with RNA as well white paper is over at https://www.funk.co.nz/blog/news/aminosee-dna-visualisation as you can see its possible to visualise the telomeres, centromeres ,repeat and genes.