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Canvasmol?

 

 

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magnusmanske at googlemail

Sep 6, 2011, 1:09 AM

Post #1 of 6 (606 views)
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Canvasmol?

Support for 3D-rendered molecules on Wikipedia has been on the
wishlist since ... forever. This was never done due to security
concerns, IIRC.

I just found this site : http://alteredqualia.com/canvasmol/#Penicillin

3D molecule rendering completely in JavaScript using canvas. Since it
only runs in the user's browser, Wikipedia servers are not at risk;
we'd probably have to check the code for potential XSS problems etc.,
and add a wrapper with a fallback to our normal PNG for non-JavaScript
browsers and, yes, old IE. But so what.

Any takers? Or should I give it a go?

Magnus

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tstarling at wikimedia

Sep 6, 2011, 4:42 AM

Post #2 of 6 (589 views)
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Re: Canvasmol? [In reply to]

On 06/09/11 18:09, Magnus Manske wrote:
> Support for 3D-rendered molecules on Wikipedia has been on the
> wishlist since ... forever. This was never done due to security
> concerns, IIRC.

The security issues were just normal XSS, easily fixed with an hour or
two of work.

> I just found this site : http://alteredqualia.com/canvasmol/#Penicillin
>
> 3D molecule rendering completely in JavaScript using canvas. Since it
> only runs in the user's browser, Wikipedia servers are not at risk;
> we'd probably have to check the code for potential XSS problems etc.,
> and add a wrapper with a fallback to our normal PNG for non-JavaScript
> browsers and, yes, old IE. But so what.

I think we should go with Jmol, which has many excellent features (not
just ball and stick rendering like this canvasmol), a substantial
community behind it, and a large content base already hosted on
MediaWiki wikis, most notably Proteopedia.

http://proteopedia.org/wiki/index.php/Main_Page

-- Tim Starling


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magnusmanske at googlemail

Sep 6, 2011, 7:05 AM

Post #3 of 6 (591 views)
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Re: Canvasmol? [In reply to]

On Tue, Sep 6, 2011 at 12:42 PM, Tim Starling <tstarling [at] wikimedia> wrote:
> On 06/09/11 18:09, Magnus Manske wrote:
>> Support for 3D-rendered molecules on Wikipedia has been on the
>> wishlist since ... forever. This was never done due to security
>> concerns, IIRC.
>
> The security issues were just normal XSS, easily fixed with an hour or
> two of work.
>
>> I just found this site : http://alteredqualia.com/canvasmol/#Penicillin
>>
>> 3D molecule rendering completely in JavaScript using canvas. Since it
>> only runs in the user's browser, Wikipedia servers are not at risk;
>> we'd probably have to check the code for potential XSS problems etc.,
>> and add a wrapper with a fallback to our normal PNG for non-JavaScript
>> browsers and, yes, old IE. But so what.
>
> I think we should go with Jmol, which has many excellent features (not
> just ball and stick rendering like this canvasmol), a substantial
> community behind it, and a large content base already hosted on
> MediaWiki wikis, most notably Proteopedia.
>
> http://proteopedia.org/wiki/index.php/Main_Page

Jmol is fine with me. My point was that, since we can't seem to get
the "traditional" stuff deployed, pure JavaScript might be a workable
shortcut.


Magnus

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mhershberger at wikimedia

Sep 6, 2011, 10:26 AM

Post #4 of 6 (585 views)
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Re: Canvasmol? [In reply to]

Tim Starling <tstarling [at] wikimedia> writes:

> On 06/09/11 18:09, Magnus Manske wrote:
>> Support for 3D-rendered molecules on Wikipedia has been on the
>> wishlist since ... forever. This was never done due to security
>> concerns, IIRC.
>
> The security issues were just normal XSS, easily fixed with an hour or
> two of work.
[...]
> I think we should go with Jmol, which has many excellent features (not
> just ball and stick rendering like this canvasmol), a substantial
> community behind it, and a large content base already hosted on
> MediaWiki wikis, most notably Proteopedia.

Since there are obviously MW users for Jmol, I'd like to think there are
interested MW developers for Jmol. Maybe I can find someone on
Proteopedia.

Mark.

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nvervelle at gmail

Sep 12, 2011, 10:57 AM

Post #5 of 6 (575 views)
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Re: Canvasmol? [In reply to]

On Tue, Sep 6, 2011 at 7:26 PM, Mark A. Hershberger <
mhershberger [at] wikimedia> wrote:

> Tim Starling <tstarling [at] wikimedia> writes:
>
> > On 06/09/11 18:09, Magnus Manske wrote:
> >> Support for 3D-rendered molecules on Wikipedia has been on the
> >> wishlist since ... forever. This was never done due to security
> >> concerns, IIRC.
> >
> > The security issues were just normal XSS, easily fixed with an hour or
> > two of work.
> [...]
> > I think we should go with Jmol, which has many excellent features (not
> > just ball and stick rendering like this canvasmol), a substantial
> > community behind it, and a large content base already hosted on
> > MediaWiki wikis, most notably Proteopedia.
>
> Since there are obviously MW users for Jmol, I'd like to think there are
> interested MW developers for Jmol. Maybe I can find someone on
> Proteopedia.
>
>
Hi,

I wrote a good part of the Jmol extension for MW.
I'm still interested in developing it if there's a chance of seeing it used
on MW.
I don't have much free time in the following weeks, but I hope this will
change before November.

Nico
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sumanah at wikimedia

Oct 10, 2011, 2:40 PM

Post #6 of 6 (517 views)
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Re: Canvasmol? [In reply to]

On 09/12/2011 10:57 AM, Nicolas Vervelle wrote:
> On Tue, Sep 6, 2011 at 7:26 PM, Mark A. Hershberger <
> mhershberger [at] wikimedia> wrote:
>
>> Tim Starling <tstarling [at] wikimedia> writes:
>>
>>> On 06/09/11 18:09, Magnus Manske wrote:
>>>> Support for 3D-rendered molecules on Wikipedia has been on the
>>>> wishlist since ... forever. This was never done due to security
>>>> concerns, IIRC.
>>>
>>> The security issues were just normal XSS, easily fixed with an hour or
>>> two of work.
>> [...]
>>> I think we should go with Jmol, which has many excellent features (not
>>> just ball and stick rendering like this canvasmol), a substantial
>>> community behind it, and a large content base already hosted on
>>> MediaWiki wikis, most notably Proteopedia.
>>
>> Since there are obviously MW users for Jmol, I'd like to think there are
>> interested MW developers for Jmol. Maybe I can find someone on
>> Proteopedia.
>>
>>
> Hi,
>
> I wrote a good part of the Jmol extension for MW.
> I'm still interested in developing it if there's a chance of seeing it used
> on MW.
> I don't have much free time in the following weeks, but I hope this will
> change before November.
>
> Nico

Nico asks:

> I'm quite busy right now, being abroad for my work until the beginning
of November.
> After that, I should have more free time to work on things like Jmol
> extension.
>
> If anyone can pinpoint what has to be done in the extension, it would
> help me to see what I still have to do on it.

So, Tim, could you point to an assessment of the security issues to fix
in Jmol? And anyone else, please put any other requests/concerns in
https://www.mediawiki.org/wiki/Extension_talk:Jmol so Nico can address
them in November.

--
Sumana Harihareswara
Volunteer Development Coordinator
Wikimedia Foundation

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