Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Activity
    Rohan Jaswal
    @rohanjaswal2507
    I think there is some problem here. Let me dig little more
    Rohan Jaswal
    @rohanjaswal2507
    d3.js is available on a CDN at cloudflare: http://cdnjs.cloudflare.com/ajax/libs/d3/3.5.6/d3.js
    Is there any biojs library which which is also available through CDN. I tried the same with MSA(http://cdn.biojs.net/msa/0.4/msa.min.gz.js), but getting some error while loading the script in ipython.
    So, is there any other library which could be used in similar fashion to biojs?
    Should I go with this or try something else?
    Douglas Blank
    @dsblank
    @rohanjaswal2507 Let's get this code into github so that we can start to make progress, even drawing on some experts from either biojs, javascript, or ipython.
    Let's get the simplest example working of using biojs in ipython, whatever it is. And then see if you can get a jsobject interface working. Then, you should announce yourself to the biojs community, and identify what your plan is. Sound good?
    Tim Ruffles
    @timruffles
    @rohanjaswal2507 an easy way to get anything hosted is https://rawgit.com/. just get a reference to a specific version via a tag on gh, and you can use github as a CDN via rawgit
    @rohanjaswal2507 any sticking points on getting the first/hello world widget into iPython?
    Douglas Blank
    @dsblank
    @rohanjaswal2507 Did we lose you? We haven't heard from you for one week.
    Rohan Jaswal
    @rohanjaswal2507
    @timruffles, yes i have created the hello world widget. Will share the code in few hours. THE same widget with certain modifications can be used as a starting point.
    @dsblank no no. Actually I was traveling and could Not reply using the gitter Android app. The app isn't good.
    Just got back in room. Let me push the code to GitHub so that we can discuss further :smile:
    Rohan Jaswal
    @rohanjaswal2507
    @dsblank I pushed some basic code to github: https://github.com/rohanjaswal2507/biojsWidget
    and tell me if I am going wrong somewhere. biojs-io-fasta isn't being imported this way
    Rohan Jaswal
    @rohanjaswal2507
    I used browserify also. But that also didn't help in this case
    Rohan Jaswal
    @rohanjaswal2507
    @dsblank did you look into the code?
    Douglas Blank
    @dsblank
    @rohanjaswal2507 You should ask in the jupyter/notebook issues, stackoverflow, or on the jupyter mailing list. I'm going to be away from my development machines for awhile. But you should use the jupyter group to help solve issues like this.
    Rohan Jaswal
    @rohanjaswal2507
    Okay. I will ask people in jupyter notebook gitter room and then proceed further.
    thanks! :smile:
    Douglas Blank
    @dsblank
    Hopefully they can provide answers quickly and specifically.
    Rohan Jaswal
    @rohanjaswal2507
    Yeah, let's see
    Rohan Jaswal
    @rohanjaswal2507
    Created a ipython widget for MSA. Let me tidy my code and add a few examples and then I will upload the code to github.
    Further, I am thinking of creating such widgets for some more biojs components and then get them all together.
    Douglas Blank
    @dsblank
    Everything is working now? What was the issue?
    Rohan Jaswal
    @rohanjaswal2507
    @dsblank yes the problem is solved.
    And I pushed the initial code to https://github.com/rohanjaswal2507/msaWidget
    Actually, the script generated using browserify and the script available for MSA on cdn.biojs.sh didn't define MSA as module for requirejs.
    So, then I used webpack for the same.
    Now, I am working on addition of more features to MSA and then will wrap up some other biojs component in Ipython.
    Will add more examples to this repo very soon.
    Douglas Blank
    @dsblank
    Look forward to seeing this!
    Rohan Jaswal
    @rohanjaswal2507
    alt
    Rohan Jaswal
    @rohanjaswal2507
    Here is the link to repo where I will integrate all these widgets : https://github.com/rohanjaswal2507/biojsIPython
    Rohan Jaswal
    @rohanjaswal2507
    working on wrapping up of cytoscape.js in IPython
    Rohan Jaswal
    @rohanjaswal2507
    Added basic graph drawing using cytoscape.js:
    rohanjaswal2507/biojsIPython@a2fd22e
    Here is the screenshot:
    http://imgur.com/wVl6lId
    Rohan Jaswal
    @rohanjaswal2507
    Please give your reviews, comments and inputs so that I can make it better.
    A lot of work needs to be done to wrap up cytoscape completely. Therefore, In the beginning I will be focusing on the basic functionalities of the application.
    Tim Ruffles
    @timruffles
    Okay - looks great! So from these beginnings, how confident are you that we'll be able to achieve some of the project goals? The code we've written so far proves the APIs work. What more do you hope to learn from fully wrapping Cytoscape? What do we need to prove: data in/out, and UI interactions?
    for the project to be successful, we want to move towards a point where biojs authors can easily achieve and advertise iPython compatibility
    Rohan Jaswal
    @rohanjaswal2507
    Thanks @timruffles.
    I am quite confident that we will be able to achieve a BioJS specification which will enable the use of these components in Python.
    And yes, the most important thing to do is to manage data in/out and UI interactions for each component.
    For this specification to be fully compatible, we will need inputs from the people who are gonna use these components as well.
    For example, there might be some differences in the approach used by me and some other Person who wants to use a biojs component in Python.
    And as far as wrapping up of cytoscape is concerned, even I don't know what do I have to learn and achieve.
    Since cytoscape is a large library and has so many functions and features, So I would initially like to implement all the major and significant ones.
    And then I might ask for suggestions and inputs from the people who use cytoscape.
    Rohan Jaswal
    @rohanjaswal2507
    @timruffles Can we link this room to the git repo? So that we have notifications about updates on the repo here as well.