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Mark Fortner
@phidias51
I'm curious if the bio-pv component supports the latest 1.0 version of the web components spec, and in general, if there's a way to see which components in the catalogue implement the spec?
Yo Yehudi
@yochannah
@phidias51 at the moment, most of them don't support web compontents particularly - especially older ones - but we're doing some work to make it easier for new components to implement the spec if desired, and/or provide a wrapper tool for older components so they can be used as webcomponents.
Mark Fortner
@phidias51
@yochannah do they currently support the version 0 spec?
Dennis Schwartz
@DennisSchwartz
@yochannah are we doing a community call today? It’s in my calendar. Maybe it would be worth just having a catch up in general, it’s been a while :see_no_evil: But in the evening would work much better for me haha
Yo Yehudi
@yochannah
I don't have one in the calendar (hmm) but YES PLEASE this evening
@sarthak-sehgal can you make it?
Dennis Schwartz
@DennisSchwartz
Ok sure. I’m free from 5pm BST. Not sure what time that is for @sarthak-sehgal though
Yo Yehudi
@yochannah
21:30 this time of year I think
that would be fabulous for me
Dennis Schwartz
@DennisSchwartz
Ok that sounds not too horrible.
Yo Yehudi
@yochannah
even if sarthak can't make it we should catch up
Dennis Schwartz
@DennisSchwartz
Yeah agreed
Dennis Schwartz
@DennisSchwartz
Ok so 5pm. I can probably create a zoom room
Yo Yehudi
@yochannah
we can use intermine zoom also if that's easier
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 Kr Dhandh
@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?