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
or if you don't have
jq installed: bionode-ncbi urls sra PRJNA183192 | sed 's|.*url":"\(.*\)","uid.*|\1|' | xargs wget
bionode-watermill
As a simple first feature i'm thinking an SBML/JSON parser might be interesting
nice!
- 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
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
European Student Council Symposium 2018
May I guess
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.
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.
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.
- i mean help me integrate it with Bionode. and .zip file support
im working on it giving it std in support now, but currently you can pass .fa or .gbk files to it via arguments like "aminosee Chimp_Clint_chrY.gbk" which will generate the reports seen at https://www.funk.co.nz/aminosee/output/ , if anybody would like to send a pull request, i am the maintainer of the thing on github at https://github.com/tomachinz/AminoSee it has some nutty race conditions im hoping to refactor (my first big Node project) as it was first done without callbacks. I use bash scripts to get around that but soon it will handle * as input better (it works though, but im rendering each of the 23 amino acids again so could be 23 x faster etc).
Hello everyone I am willing to put some effort to maintain the project : I saw to things that can be damaging to the project
1) On the website : https://www.bionode.io/
http://afra.sbcs.qmul.ac.uk/ for example is going to a dead website same for https://genevalidator.sbcs.qmul.ac.uk/
2) http://try.bionode.io/ is not secured
1) On the website : https://www.bionode.io/
http://afra.sbcs.qmul.ac.uk/ for example is going to a dead website same for https://genevalidator.sbcs.qmul.ac.uk/
2) http://try.bionode.io/ is not secured
3) There is a socket error on the first tutorial of http://try.bionode.io/ hence the tutorial is not working
So if anyone here is willing to do some pair programming on discord this week (no more than two hours just to give me an overview of the project) I am willing to help!!
Hi sorry to pile on, the try.bionode.io
docker terminal plugin windows don't work on chrome.
'ws://docker.bionode.io/mouvzqhodrh' failed:
I guess this might be because it is running on http and the web socker (ws) is not secure (wss). Came into that issue once. If the front end makes the connection to a ws: chrome will kill it. Will only work for localhost.
