Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Repo info
Activity
  • Oct 19 05:36
  • Oct 15 07:15
    CavalierSpirit starred biojs/biojs
  • Oct 11 22:47

    udp on master

    Change URL to biojs.net (compare)

  • Oct 11 22:42

    udp on master

    add gitlab config file.... will… migrate to gitlab style yml con… requires javascript runtime and 18 more (compare)

  • Oct 11 22:41

    udp on moved-notice

    (compare)

  • Oct 11 22:32
    udp closed #167
  • Oct 11 22:32
    udp commented #167
  • Oct 11 21:28
    udp commented #168
  • Oct 10 17:02
    udp commented #168
  • Oct 10 14:30
    yochannah commented #168
  • Oct 10 14:17
    udp commented #168
  • Oct 08 16:47
    cycle20 commented #168
  • Oct 08 16:47
    cycle20 commented #168
  • Oct 08 16:28
    cycle20 commented #168
  • Oct 08 16:10
    yochannah commented #168
  • Oct 08 15:43
    cycle20 commented #168
  • Oct 06 09:47
    alifahriander starred biojs/biojs
  • Aug 25 10:30
  • Aug 25 10:30
    Fuad9 starred biojs/biojs
  • Aug 02 23:36
    rpark37 starred biojs/biojs
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?
tyomach
@tyomach
Is the registry at http://biojs.net still alive?
Sarthak Sehgal
@sarthak-sehgal
Hi, thank you for your interest in the BioJS registry. Unfortunately, the registry is no longer maintained. We had to take the difficult decision as we could not identify potential maintainers.
prachitej
@prachitej
Hi, I am a college student and I wanted to ask whether we could contribute to your project as part of our curriculum?