These are chat archives for biojs/biojs

22nd
Jun 2016
Faye Li
@fayeli
Jun 22 2016 02:18
@daviddao hi there! (: I haven't really been blogging so far but I've been sharing my progress with the other GSoC students in videos due to the nature of my project. If anyone is interested feel free to have a look! https://www.youtube.com/watch?v=uWDkqoFHr_g
Sebastian Wilzbach
@wilzbach
Jun 22 2016 02:21
nice video, but ... ehm stupid question, but what is the relation to BioJS?
Sebastian Wilzbach
@wilzbach
Jun 22 2016 02:27
last time i checked biojs was described as "BioJS is an open source project for bioinformatics data on the web. Its goal is to develop an open-source library of JavaScript components to visualise biological data"
Faye Li
@fayeli
Jun 22 2016 02:36
and while we're at it I actually do have some questions about making my code into a BioJS component. I've started managing my project dependencies with RequireJS. My code calls a number of js libraries, mostly implementation of computer vision algorithms. I'm quite new to writing library so I'm not so sure if I'm doing it right. I believe the way I'm handling modules now is the AMD way. But as I'm reading up on the BioJS documentation I realised BioJS components are built through the npm way. Does it sound like I have a lot of refactoring to do? Does anybody have experience doing so? I'd love some guidance on this! Thanks!
@wilzbach um excuse me? this is a visualisation component for DICOM images. they are medical scans used for clinical diagnosis and biological research
Sebastian Wilzbach
@wilzbach
Jun 22 2016 04:01
@fayeli maybe you misunderstood my question. BioJS = (1) "reusable" (2) web components. So when I asked how your project is related to BioJS - my question was about those two points
Faye Li
@fayeli
Jun 22 2016 04:39
Well, it's currently not a BioJS component yet. As I was saying, I'm developing my project in javascript but I'm still working on correctly porting it so that its consistent with the BioJS component standard. I've written reusable functions and tools which allow you to create visualisation on another DICOM image. But let's stop spamming the chat and bring this discussion back to my question regarding the two ways of writing modular Javascript.
Jessica Jordan
@jessica-jordan
Jun 22 2016 07:17
@wilzbach so far we haven't setup a specific requirement to deliver your BioJS component as a web component
Jessica Jordan
@jessica-jordan
Jun 22 2016 07:22
The only requirement we ask users in our docs, tutorials and even on workshops so far is, that they deliver their functionality that is related to any biological context as part of an npm package that is tagged with the keyword "BioJS" in its package.json. Because of that none of our GSoC projects require our students to deliver their code as part of a web component and even if students hadn't published their component to the npm registry yet either, this would also be completely fine for now (as we just reached the project mid term) as long as this happens in agreement with their mentors and previously discussed milestones
Jessica Jordan
@jessica-jordan
Jun 22 2016 07:39
@fayeli Although I don't have my own experience with requirejs in node / npm, this might be worth looking into: https://www.npmjs.com/package/requirejs and http://requirejs.org/docs/node.html
Jessica Jordan
@jessica-jordan
Jun 22 2016 09:11
@fayeli And also thanks for sharing your great update so far. Looking forward to your upcoming progress soon - keep up the good work! :-)
Sebastian Wilzbach
@wilzbach
Jun 22 2016 09:26

The only requirement we ask users in our docs, tutorials and even on workshops so far is, that they deliver their functionality that is related to any biological context as part of an npm package that is tagged with the keyword "BioJS" in its package.json.

Yes, that was my idea and a huge mistake.

this would also be completely fine for now

@fayeli My comment wasn't meant in a negative way (sorry if it sounded like this). I was just curious how it will end up being a BioJS component ;-)