These are chat archives for biojs/biojs

16th
Mar 2016
remii
@01remi
Mar 16 2016 03:05
Hello everyone, my name is obia remmy from Cameroon.A 3rd year computer engineering student at the university of Buea.I am interested in working on the project "Web Components integration in BioJS".I have good skills java,javascript and C.I have worked before on an application that required me to make use of facebook,youtube and an sms api, alongside google polymer. I will be honoured to be accepted for gsoc to work on this project.
Gaston Che
@gastonche
Mar 16 2016 03:19
Pls can anyone direct me on how to start contributing to biojs
I have taken out time to acquaint myself with the code
@Remmy welcome Remmy.
remii
@01remi
Mar 16 2016 03:21
thank you @gastonche
@gastonche pls did you go through the basics tutorials??I had some issues setting up.maybe you could help.
tyreek
@tyreek
Mar 16 2016 03:26
(shizle via irc) Hi my name is Gaston che, i am a third year software engineering student from the unibersity of buea, cameroon.
(shizle via irc) I am quite interested in the GSOC BIOJS Generic protein expression view for Human Body project, and would like some one to pls help direct me on how to start contributing to the biojs community now. I ahve taken out time to get myself acquainted with biojs
Gaston Che
@gastonche
Mar 16 2016 03:28
Yeah Remmy I did
@remmy What was your issue
remii
@01remi
Mar 16 2016 03:33
node reuse.js throw back error message reuse is not a function.It indicates the preoblem is from console.log(reuse(3,6))
remii
@01remi
Mar 16 2016 03:39
Don't mind, i had a mistake in my syntax.just found it.Thanks
Gaston Che
@gastonche
Mar 16 2016 03:43
That's cool
@Remmy
tyreek
@tyreek
Mar 16 2016 04:09
(greenify via irc) great to see that you start to help each other!
(greenify via irc) @01remi: your message is too long for irc, but let us know your questions!
(greenify via irc) @gastonche: did you read https://github.com/biojs/biojs/blob/master/CONTRIBUTING.md already?
remii
@01remi
Mar 16 2016 04:12
understood @tyreek.
Gaston Che
@gastonche
Mar 16 2016 04:45
Thanks tyreek
Rohan Jaswal
@rohanjaswal2507
Mar 16 2016 10:42
@timruffles I am getting this error while working with widgets in IPython. What can I do to troubleshoot the problem?
Doug Blank
@dsblank
Mar 16 2016 10:44
@rohanjaswal2507 How did you install IPython?
Rohan Jaswal
@rohanjaswal2507
Mar 16 2016 10:46
I guess I used the package manager of Fedora to do that.
I installed IPython long time back.
Is there any problem with this method of installation?
Doug Blank
@dsblank
Mar 16 2016 10:46
Then that is probably too old. Try using pip, to upgrade the whole set of packages.
IPython is moving very fast
Rohan Jaswal
@rohanjaswal2507
Mar 16 2016 10:47
okay. Let me do that.
Doug Blank
@dsblank
Mar 16 2016 10:47
But it also looks like you have mixtures of old and new
Also, if you are going to develop code for IPython, you probably want to target Python3, right?
Rohan Jaswal
@rohanjaswal2507
Mar 16 2016 10:47
Yes
Actually, all the packages are up-to-date
Doug Blank
@dsblank
Mar 16 2016 10:49
What version of ipython do you have?
Rohan Jaswal
@rohanjaswal2507
Mar 16 2016 10:49
4.1.2
Doug Blank
@dsblank
Mar 16 2016 10:50
Did you install ipywidgets?
Rohan Jaswal
@rohanjaswal2507
Mar 16 2016 10:50
Yes I didi
*did
Doug Blank
@dsblank
Mar 16 2016 10:51
I just tested on mine (same version) and it works. So it must be an installation issue.
Rohan Jaswal
@rohanjaswal2507
Mar 16 2016 10:51
ok
So, what should I do get things working on my machine?
Should I do the installation again?
Doug Blank
@dsblank
Mar 16 2016 10:53
I would uninstall all of the IPython code (IPython, Jupyter, ipywidgets) and check to make sure all are gone ("locate IPython")
Then once clean, reinstall via the recommended method (pip install ... )
Rohan Jaswal
@rohanjaswal2507
Mar 16 2016 10:55
ok
Rohan Jaswal
@rohanjaswal2507
Mar 16 2016 11:04
@dsblank I did it. But still not working.
Doug Blank
@dsblank
Mar 16 2016 11:04
You get the same error?
Rohan Jaswal
@rohanjaswal2507
Mar 16 2016 11:07
Yes
Doug Blank
@dsblank
Mar 16 2016 11:08
I guess you'll have to ask the IPython people... they have a gitter chat here under ipython/ipython
Rohan Jaswal
@rohanjaswal2507
Mar 16 2016 11:10
okay. I ll do that
Doug Blank
@dsblank
Mar 16 2016 11:10
You can also do your work via mybinder.org, or try.jupyter.org
Also, mathsagecloud support free IPython use
Rohan Jaswal
@rohanjaswal2507
Mar 16 2016 12:20
@dsblank I figured out something.
Doug Blank
@dsblank
Mar 16 2016 12:21
Good... what dis you do?
did
Rohan Jaswal
@rohanjaswal2507
Mar 16 2016 12:21
names of some modules have been changed in IPython with time.
Doug Blank
@dsblank
Mar 16 2016 12:21
Do you know what the problem was?
Rohan Jaswal
@rohanjaswal2507
Mar 16 2016 12:22
I was referring to a tutorial which was little old and tried to import some modules which do not exist now.
Doug Blank
@dsblank
Mar 16 2016 12:22
Now, you are up and running?
Rohan Jaswal
@rohanjaswal2507
Mar 16 2016 12:23
So, now I will try getting some help from the updated examples in ipywidgets repository.
Yeah, almost all the notebook examples are working fine.
Doug Blank
@dsblank
Mar 16 2016 12:24
Great! Note that a BioJS widget will be useful, but still has limitations.
Have you looked at the biojs webcomponents work?
Rohan Jaswal
@rohanjaswal2507
Mar 16 2016 12:26
I haven't gone deeper in web components yet. I just had a look 2 days ago.
Rohan Jaswal
@rohanjaswal2507
Mar 16 2016 17:44
@dsblank @timruffles I went through biojs2galaxy and tried to analyse how the components are integrated with galaxy. Will try to think of ways to wrap up a simple biojs component in IPython.
Could you me any suggestions/guidance for my approach?
tyreek
@tyreek
Mar 16 2016 19:04
(greenify via irc) some discussion is going on at biojs/biojs#111
(greenify via irc) I wrote biojs2galaxy - so feel free to ping me about that https://github.com/biojs/biojs2galaxy
(greenify via irc) short summary: think about biojs components as web components (=biojs3) e.g. <biojs-msa><biojs-seq name="aa">AAA</biojs-seq></biojs-msa> - now you only need to bind the html with the data from IPython/Jupyter
(greenify via irc) for galaxy we inject the data with a special mako file - https://github.com/greenify/msa/blob/master/galaxy.mako
tyreek
@tyreek
Mar 16 2016 19:10
(greenify via irc) we had to go this approach as currently the components are quite different, however it would be nice to have a unified api
Abhishek Shrivastava
@abstatic
Mar 16 2016 19:18
@greenify - seems like a very workable approach .. i will also look into it!
epipi237
@epipi237
Mar 16 2016 22:38
hello i went through the ideas list for biojs and i was really happy to have stumbled on this opensource project cuz almost all of them are interesting.I am more interested on the Visualisation of standard types in life science with BioSchemas, schema.org and BioJS.I will be very happy to recieve some work to get started with the biojs code base thanks
epipi237
@epipi237
Mar 16 2016 23:11
wow.I love this.currently reading some articles on bioschema and i have my environment setup.I am ready for the task.for a formal presentation,i am vaumi vaumi ezechiel from the faculty of engineering and technology of the university of Buea currently a third year student.I have worked on many projects like afrimode.com halflucky.com/public rhicam.com and many more. thanks