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Dennis Schwartz
@DennisSchwartz
yeah sure, if that’s easy for you :) I would have to find the credentials haha
Yo Yehudi
@yochannah
Dennis Schwartz
@DennisSchwartz
Awesome :)
Sarthak Sehgal
@sarthak-sehgal
So sorry I couldn’t make it! :( Hope you’re doing good Dennis, long time! :smiley:
Goutam
@goutamdh
Hi I want to contribute in biojs. How can I start ?
Nikhil Vats
@Nikhil-Vats
Hi Goutam, you can have a look at the projects of BioJS here - GitHub.com/biojs
Thanks for showing interest. :smile:
Yo Yehudi
@yochannah
@sarthak-sehgal and @Nikhil-Vats mentioned at BOSC2019 :heart_eyes_cat: https://twitter.com/yoyehudi/status/1153948323340017669
Saber Soleymani
@noghte
Hello, is bioJS still an active project? The GitHub link on biojs.net points to https://github.com/biasmv/pv that seems not updated for a few years. I am quite new to the bioinformatics, so maybe I am checking a different source code!
Sarthak Sehgal
@sarthak-sehgal
Hey Saber, bio-pv is one of the many components hosted by the BioJS registry. You can find a the projects here: github.com/biojs
Right now we are working on a Yeoman generator (https://github.com/biojs/generator-biojs-webcomponents)
Mark Fortner
@phidias51
Are there any plans to list the version of the web component spec supported by each component? This would make it easier to figure out which components could be used in various projects.
Mark Fortner
@phidias51
@yochannah I was wondering if you were planning on creating any components for InterMine's Target Mine application? It would be useful to be able to reuse them in other applications.
Yo Yehudi
@yochannah
hey @phidias51 - anything particular you had in mind?
and the versioning suggestion is a great idea - I think we could add it to 3.0 and assume anything that doesn't list itself as 3.0 compatible is older
Mark Fortner
@phidias51
It would be nice to have some list components. You pass in a gene or a protein, and it gives you a list of drugs. You click on a drug and it shows you the chembl or drugbank record for that drug including a structure. You might have something similar for gene -> pathway, where you get a list of pathways, and then click on a pathway name to view the pathway diagram. For proteins, you might show the structure of the protein and/or a domain cartoon.
Most of the components that I've clicked on in the component list don't have previews so it's difficult for me to figure out if they'd be of any use in any of the projects that I'm working on. Even just a screenshot would be useful. Ultimately though, it's the version number that dictates its usability.
I've noticed a couple of components were React wrappers of older components. Most of the work that we do is framework agnostic, so if the components were w3c compliant we would be able to use them in React, Vue, or straight HTML projects.
Ino de Bruijn
@inodb
hey all! My apologies in advance if this is in the docs somewhere. I was wondering if anyone has experience distributing nodejs command line apps. Wasn't sure sure if biojs is limited to browser based components only. Is there some documentation on how to add a nodejs command line app?
Yo Yehudi
@yochannah
hey @inodb! I think I'd recommend packaging it for npm, same as I would for a browser based app
https://docs.npmjs.com/packages-and-modules/contributing-packages-to-the-registry probably has what you need, but the most recent biojs tool that @Nikhil-Vats worked on was a pure CLI tool -
so we might be able to help if you have specific questions?
Ino de Bruijn
@inodb

Hey @yochannah :wave: ! Thank you! The generator-biojs-webcomponents package is not on https://biojs.net/. Is that on purpose?

Btw: I love your tweets! Sad I missed my chance to say hi at the GSoC Mentor Summit - hopefully next time

Yo Yehudi
@yochannah
Thanks! :)
(Re the tweets 😁)
and yes, hopefully next time! The GSoC summit is one of my favourite conferences so I'll surely be back :)
you raisea good point about the generator not being on bios.net :facepalm: it's not a biojs tool in itself, but it should be there to help people get started. @Nikhil-Vats, @sarthak-sehgal - do either of you two have time to add it?
Ino de Bruijn
@inodb
sounds good! Thanks! What defines a biojs tool? Do you think a command line variant annotator in JS could be considered? I saw there’s bionode as well: https://www.bionode.io/, but that doesn’t seem to be actively maintained atm.
Sarthak Sehgal
@sarthak-sehgal
A bit packed atm but should be able to do it by the weekend. Can you ping me the server details @yochannah?
Dennis Schwartz
@DennisSchwartz
@yochannah @sarthak-sehgal do you guys remember where we keep our logins for stuff? I need to log into namecheap, because our domain is about to expire :see_no_evil:
Sarthak Sehgal
@sarthak-sehgal
I don't have them :(
Yo Yehudi
@yochannah
we need to fix this - do either of you use keybase?
(I'd suggest registering now if you don't)
as our keepass strategy is problematic
Nikhil Vats
@Nikhil-Vats
@inodb Let me know if you have any questions regarding the generator -https://www.npmjs.com/package/generator-biojs-webcomponents?
Shubham Awasthi
@awasthishubh
Hey @yochannah @DennisSchwartz
This is Shubham a 3rd-year undergrad in Information Technology. Does BioJS have any plan for this year's GSoC?
Yo Yehudi
@yochannah
Hey @awasthishubh - lovely to see you here again!
we're definitely thinking about it, yes - watch this space, we'll add more info soon!
Shubham Awasthi
@awasthishubh
Sure! Thanks for the information. :)
Tianyi Shi
@TianyiShi2001
Hello everyone. I’m a newbie in Javascript and biojs. I am an intermediate Python programmer and I know a bit about BioPython ( https://biopython.org ).
I think web technologies (in which JS plays an important role) are valuable to informatics.
However, it seems to me that biojs is not as good as BioPython in terms of functionality, organisation and popularity.
I want to build a JS library that would mirror BioPython.
Anyone having the same idea?
Today, I have created scripts which have a Protein class. Passing a protein sequence to it, and an object containing the sequence, amino acid composition, molecular weight and isoelectric point ,is returned. ( https://github.com/TianyiShi2001/biojs/blob/master/Protein.mjs )
Sarthak Sehgal
@sarthak-sehgal
Hi Tianyi, thank you for considering contributing to open science and Bio* projects. Appreciate your concern towards making the process easier for JS components. Please give me a day to get back to you.
Sarthak Sehgal
@sarthak-sehgal
@TianyiShi2001 I'm getting a 404 on the GitHub URL you mentioned although I do understand your intent and appreciate you working towards the project. Currently BioJS as an organisation is not taking up new projects but feel free to update us on the progress as members of the community might be interested to contribute in their capacity. Cheers.
Tianyi Shi
@TianyiShi2001
Sorry I was developing on more features and I changed the directory structure, so the original link is broken
5371581509261_.pic_hd.jpg
Here’s what it looks like (see terminal at the bottom). It reads a FASTA file containing a protein sequence and gives the parameters of the protein, similar to the ExPASy ProtParam tool (https://web.expasy.org/protparam/) (not fully functional as I only have a simple FASTA parser and a simple protein sequence parser)
What I intend to do is to recreate all ExPASy tools in open-sourced code
Tianyi Shi
@TianyiShi2001
Most tools on ExPASy are not open-sourced, and they are poorly organised (compared to, say, BioPython) and sometimes obsolete (it seems that the ExPASy ProtParam tool hasn't been updated since its publication in 2005, and the source data (e.g. pKas of amino acids) they used are even based on older literature).
Mark Fortner
@phidias51
I’m looking for recommendations for a network/pathway viewer component. I’d like to be able to use it to render networks from a variety of databases. I’d like to simply pass it the database and id and have it render the network. Is there such a thing?