Queries regaarding GSoC 2012

107 views
Skip to first unread message

Apoc

unread,
Mar 20, 2012, 8:13:54 PM3/20/12
to crow...@googlegroups.com
Hi,

I am Shivansh, pursuing Engineering at BITS Pilani, currently in my 3rd year.

I am well versed in Web Technologies, that include HTML5, JavaScripts (jQuery), 
CSS; with PHP & MySQL and App Development for Windows Phone 7.

I have worked in my college on several websites with the same knowledge. I had 
also given a talk at the 3rd WikiConference held at Mumbai on "Improving Wiki UI 
using AJAX & jQuery" & presented 4 ideas/projects with the Wiki community.

I am interested in pursuing/developing the Idea - 

Idea 5 - BioGPS: A web interface for webpage annotation
Idea 6 - An enhanced HTML5 canvas-based data-chart viewer.
Idea 7 - BioGPS:JQuery-based BioGPS gene-report layout canvas

as these are the ideas closest to my set of skills & expertise.

A couple of queries though-

I am unable to view the data chart plugin- http://plugins.biogps.org/data_chart/data_chart.cgi?id=1017 or anything I search for (https://biogps.org/#goto=genereport&id=12311)- either in Chrome or Firefox.
Kindly help me with this.

Also, in the Gene-Wiki portal (http://en.wikipedia.org/wiki/Portal:Gene_Wiki), whatever jquery/javascripts have to be implemented, would it be done through the user common.js, & subsequently be implemented as & when done; as done in MediaWiki?

Finally, I am not able to fork the repo. Could you send me a link so that I can get familiar with it. And the Jquery UI that has to be developed would be over the downloaded repo?

Waiting for a reply.

With Regards,
Shivansh

Chunlei Wu

unread,
Mar 20, 2012, 8:22:03 PM3/20/12
to crow...@googlegroups.com
Hi Shivansh, 

       To address your first question. I can access both links fine here. Are you able to test from another computer or maybe ask someone else in your area to see if they can access?

Chunlei

--
You received this message because you are subscribed to the Google
Groups "Crowdsourcing Biology" group.
To post to this group, send email to crow...@googlegroups.com
To unsubscribe from this group, send email to
crowdbio+u...@googlegroups.com
For more options, visit this group at
http://groups.google.com/group/crowdbio?hl=en?hl=en
 
GSoC Organization page: http://www.google-melange.com/gsoc/org/google/gsoc2012/scripps_crowdbio
GSoC Ideas page: http://sulab.org/gsoc/

Apoc

unread,
Mar 22, 2012, 2:28:52 PM3/22/12
to Crowdsourcing Biology
No, as I am behind a proxy server, it is blocking all the cgi files.

Could you give me the link to the svn, so that I can familiarize with
it & check the extent of the 3 ideas I want to work on.

Thanks,

On Mar 21, 5:22 am, Chunlei Wu <reill...@gmail.com> wrote:
> Hi Shivansh,
>
>        To address your first question. I can access both links fine here.
> Are you able to test from another computer or maybe ask someone else in
> your area to see if they can access?
>
> Chunlei
>
>
>
>
>
>
>
> On Tue, Mar 20, 2012 at 5:13 PM, Apoc <shivansh.b...@gmail.com> wrote:
> > Hi,
>
> > I am Shivansh, pursuing Engineering at BITS Pilani, currently in my 3rd
> > year.
>
> > I am well versed in Web Technologies, that include HTML5, JavaScripts
> > (jQuery),
> > CSS; with PHP & MySQL and App Development for Windows Phone 7.
>
> > I have worked in my college on several websites with the same knowledge. I
> > had
> > also given a talk at the 3rd WikiConference held at Mumbai on "Improving
> > Wiki UI
> > using AJAX & jQuery" & presented 4 ideas/projects with the Wiki community.
>
> > I am interested in pursuing/developing the Idea -
>
> > Idea 5 - BioGPS: A web interface for webpage annotation
> > Idea 6 - An enhanced HTML5 canvas-based data-chart viewer.
> > Idea 7 - BioGPS:JQuery-based BioGPS gene-report layout canvas
>
> > as these are the ideas closest to my set of skills & expertise.
>
> > A couple of queries though-
>
> > I am unable to view the data chart plugin-http://plugins.biogps.**
> > org/data_chart/data_chart.cgi?**id=1017<http://plugins.biogps.org/data_chart/data_chart.cgi?id=1017> or
> > anything I search for (https://biogps.org/#goto=**genereport&id=12311<https://biogps.org/#goto=genereport&id=12311>)-
> > either in Chrome or Firefox.
> > Kindly help me with this.
>
> > Also, in the Gene-Wiki portal (http://en.wikipedia.org/wiki/**
> > Portal:Gene_Wiki <http://en.wikipedia.org/wiki/Portal:Gene_Wiki>),

Apoc

unread,
Mar 23, 2012, 12:32:11 PM3/23/12
to crow...@googlegroups.com, c...@scripps.edu
Hi,

I am mainly interested in working on Idea 5 - A web Interface for webpage annotation and Idea 7 - a jQuery based BioGPS gene report layout canvas, as they are close & apt for my skills 7 expertise.

The queries I have for the respective Ideas are-

Web Interface - Could you please explain to me what all needs to be included in the RDFa with an example, as I couldnt understand from the description given on the Ideas page.

jQuery based BioGPS gene report layout canvas - Cant jQuery be implemented in the same, alongwith extjs, & add more attributes to it?
Also, am I correct that the layout of such a page like the report generated here - https://biogps.org/#goto=genereport&id=12311 - is to be changed/converted, using jQuery?

I am not very proficient with Python, but am confident with my Web development (mainly javascripting/jquery) skills. Could you tell me how much of python here would be used?

Regards,
Chunlei

Chunlei Wu

unread,
Mar 23, 2012, 1:39:23 PM3/23/12
to crow...@googlegroups.com
Hi Shivansh,

          Let me answer your question about idea 7 first (will address your question on idea 5 in a separate post). 

         1)  For a couple of reasons (e.g. limited licensing option for EXTJS), we are moving away from EXTJS, leaning toward to replace it with JQuery. JQuery is lightweighted and sufficient for our need.
         2) Yes, the page you see from the gene report link like (/gene/12311) is what we want to convert. The mostly important part is the layout canvas where multiple windows are rendered. Please note that user can select from the "current layout" dropdown menu to switch between different layout.
         3) the knowledge of Python for this task should be minimal. We should already have all data needed exposed as REST services with JSON output.

Chunlei
             

Chunlei Wu

unread,
Mar 23, 2012, 3:03:09 PM3/23/12
to crow...@googlegroups.com
Hi, Shivansh,

           Let me give you some examples to illustrate the basic workflow for idea 5:  A web Interface for webpage annotation.

   Example 1:

         1) User goes to this page:
             The big table there is the main content about a gene.
         2) We would like to enable users to select a DOM node, for example, "td" node containing text "Chr10:128134995-128142107 bp, - strand", and mark it as "genomic location". 
         3) Then we can put RDFa notation something like 'property="dc:genomic location"' to that "td" node.
         
   Example 2:
        1) User goes to this page:
            Again, the table in the middle is the main content of the page.

        2) User now can mark the each cell in the first row as, e.g., "Disease Term", "Total Publications", "Total meta-analysis", "Total GWAS studies", "Trend". 
        3) RDFa notations with above terms then can be added to the cells in the first row, just like in example 1.
        4) User indicates that the data in other rows are in the same structure, so that the same RDFa notations can be added to the rest of rows as well.

    Two examples above are for the end users to annotation one page (commonly, for one gene) with RDFa. The annotation "rules" established from this page then should be able to apply to the pages for other genes. In other words, the "rules" should work across a set of URLs with a template. For example:


     These rules are usually hard to define via a program, so we want to build an interface to allow human users with relevant knowledge to define these rules.

       Another background of "Idea 5" is that most of biological web resources are not semantic-ready. It's also hard to push all of developers to convert their websites. This project is to engage user community to contribute by helping annotate these web pages and making them semantic-friendly. 

Hope this helps, and let us know if any other question.

Chunlei

Shivansh Srivastava

unread,
Mar 24, 2012, 7:17:04 AM3/24/12
to crow...@googlegroups.com
Hi Chunlei,

Thank you for your detailed answer. That has helped me get a clearer picture.

A couple of more questions though- (I'll go Idea-by-idea)

- Idea 7 - a jQuery based BioGPS gene report layout canvas 

Regarding Python, I dont think I should worry much about it, & can be helped by the mentor during the period too.
I saw how the user can select the different layouts, & those would have to be converted to more efficient layouts in jQuery. Could you direct me to that part of your svn, so that I can browse through that code, & learn the working of it.

- Idea 5:  A web Interface for webpage annotation 

Am I right when I say - Regarding the annotations part, the description part has to be effectively implemented, and every property that a gene has, is to be merged in form of a an html page or a javascripted window/dialog box, something like-

<div itemscope itemtype="html page"?
<h1 property="dc:title">Name</h2>
<h2 property="dc:node">Property 1</h3>
</div>

It could further on be spanned & displayed.
So, for every gene, or a page opened by the user, I would have to take the td id of the table & corresponding to every gene, the description has to be shown in another html page/javascript window.

Am I going on with this in the right direction?

And, wouldnt it be better if this could be taken up with Microformats, or the reliance on RDFa is because the data dependencies lie with the xml sheets?

Also, the Rules which you sent me -
gave me an internal error.

Please direct me to the relevant code repo as I want to learn how it is built.

Regards,
--
Shivansh Srivastava | +91-955-243-5407 | http://in.linkedin.com/pub/shivansh-srivastava/17/a50/b18
Secretary, BITS Alumni Affairs Division | Web Expert, Newsletter, BITSAA International
3rd Year Undergraduate | B.E. (Hons.) - Electronics & Instrumentation
BITS-Pilani.

Chunlei Wu

unread,
Mar 24, 2012, 11:25:39 AM3/24/12
to crow...@googlegroups.com
Hi Shivansh,

       For your question on Idea #7:

            Given this page as an example: http://biogps.org/gene/1017

            * The code behide the overall page rendering is this code:

            (search for "case 'report_panel':'", that is the entry point for triggering gene report rendering)

           * Then the actually rendering of each gene report layout (those movable windows) is done in this code:
           

Chunlei

Chunlei Wu

unread,
Mar 24, 2012, 12:37:12 PM3/24/12
to crow...@googlegroups.com
Hi Shivansh,

       For you question on Idea #5:

           Ideally, RDFa properties should be added to the original html page, the display of the page should not change at all. I think it could work like a browser plugin or through some kind of server-side proxy, so that we can inject our own javascript to annotate page and insert RDFa properties (that is manipulate DOM directly). I think it's not a bad idea to have a separate window to display the html source and see how exactly RDFa properties are added.

           Microformats could be another option, given its popularity. But personally, I feel that RDFa should be the way to go in the future for semantic web.

          For these two lines:

               "rule 1" for URL template "http://www.informatics.jax.org/searches/accession_report.cgi?id={{MGI_ID}}"
           
         I probably did not state it clearly. What I mean is (for the first line):
              "rule 1" is the whatever user's annotation, could be something like:  next "td" after "td" with text of "Sequence Map" should be annotated as "genomic location".
                  then this rule should be able to apply to all pages with such URL template:
                       http://www.informatics.jax.org/searches/accession_report.cgi?id={{MGI_ID}}  (a template, not a real URL)
                 for example:

Let us know if any further question.

Chunlei

Shivansh Srivastava

unread,
Mar 29, 2012, 1:34:31 AM3/29/12
to crow...@googlegroups.com, reil...@gmail.com
Hi Chunlei,

Sorry for the late reply. I have my exams going on in my College.

I went through your specified javascripts -  https://bitbucket.org/sulab/biogps_core/src/45546b5e27a7/src/assets/js/biogps/mainApp/genereportpanel.js  for Idea #7 - Conversion from ExtJS4 to jQuery.

Am I correct in assuming that since this is the Window/Dialog box rendering code, these 2 would be the 2 js that would need all the conversion?

Also, I feel that I should also fill the GSoC application for the same.

From the conversation, I feel I am pretty confident about Ideas #6 - An enhanced HTML5 canvas based Chart viewer and #7 - jQuery based Gene Report Layout Canvas.
Although, I have got a hang of Idea #5- the RDFa properties, I feel I shouldnt delve into a project which I am not proficient in.

Hence, can I submit 2 proposals - 1 for each of the 2 ideas? Till 6th, I'd get time to get feedback on the proposal as well.

If not, which one according to you is more urgently needed. Then I may work on that & discuss on that idea henceforth.

Waiting for a reply.

With Regards,
Reply all
Reply to author
Forward
0 new messages