gmod-ajax

[Gmod-ajax] Article: Using game design to build the next Digg or Flickr

[Ian H. <ih...@be...>]

So I keep posting this sort of thing even though I really don't know how 
relevant these things are, and of course we do have a long list of more 
practical immediate things to do (like, um, getting something that we 
can seamlessly use in place of an existing GBrowse instantiation, 
ideally before modENCODE is history...)

However I do think it's good to stay on top of this trend of thought. 
People are increasingly realizing that there is not that much difference 
between a social web application and a casual game. And what we are 
building is not all that far from a social web app.

This article stresses the following five game-like aspects of a 
successful social app:

- Collecting
- Points
- Feedback
- Exchanges
- Customization

http://blogs.business2.com/startups/2007/08/five-ways-to-bu.html

Raph Koster posts a lot of links like this on his blog. It's a fun site 
to dip into occasionally. See also Amy Jo Kim.

I.

Re: [Gmod-ajax] Article: Using game design to build the next Digg or Flickr

[Mitch S. <mit...@be...>]

Ian Holmes wrote:
> So I keep posting this sort of thing even though I really don't know how 
> relevant these things are, and of course we do have a long list of more 
> practical immediate things to do (like, um, getting something that we 
> can seamlessly use in place of an existing GBrowse instantiation, 
> ideally before modENCODE is history...)
>   

I like the game angle; it seems like it could be a pretty rich vein of 
new UI ideas, which I get a big kick out of.

However, if at all possible I'd like to start moving things in a more 
concrete/applied direction.

Like collecting, for example.  We've talked about collecting things like 
tracks, but I think a lot of biologists would also be interested in 
collecting individual features (genes).  That's something that the 
biologists that I've worked with liked to do a lot (then they'd send me 
Excel files full of gene symbols that weren't necessarily the 
standardized symbols). Then I can also imagine them wanting to see SNPs 
near their genes, regulatory elements near their genes, etc.

I've been thinking that I'd like to make track definitions just be 
queries on a genomic data source (plus some information on how to render 
the result).  That's pretty much how the gbrowse config works right now; 
each track is defined in terms of the type of the feature to be 
displayed in it.  But I'd like to also allow for queries that are more 
general than just by type, for tracks like "the genes I'm interested in" 
or "SNPs near the genes I'm interested in", "SNPs near the genes that 
are active during development phase foo", "genes that are under GO term 
such-and-such", etc.

Mitch

Re: [Gmod-ajax] Article: Using game design to build the next Digg or Flickr

[Ian H. <ih...@be...>]

How would this compare with existing systems e.g. Ensembl MART?


Mitch Skinner wrote:
> Ian Holmes wrote:
>> So I keep posting this sort of thing even though I really don't know how 
>> relevant these things are, and of course we do have a long list of more 
>> practical immediate things to do (like, um, getting something that we 
>> can seamlessly use in place of an existing GBrowse instantiation, 
>> ideally before modENCODE is history...)
>>   
> 
> I like the game angle; it seems like it could be a pretty rich vein of 
> new UI ideas, which I get a big kick out of.
> 
> However, if at all possible I'd like to start moving things in a more 
> concrete/applied direction.
> 
> Like collecting, for example.  We've talked about collecting things like 
> tracks, but I think a lot of biologists would also be interested in 
> collecting individual features (genes).  That's something that the 
> biologists that I've worked with liked to do a lot (then they'd send me 
> Excel files full of gene symbols that weren't necessarily the 
> standardized symbols). Then I can also imagine them wanting to see SNPs 
> near their genes, regulatory elements near their genes, etc.
> 
> I've been thinking that I'd like to make track definitions just be 
> queries on a genomic data source (plus some information on how to render 
> the result).  That's pretty much how the gbrowse config works right now; 
> each track is defined in terms of the type of the feature to be 
> displayed in it.  But I'd like to also allow for queries that are more 
> general than just by type, for tracks like "the genes I'm interested in" 
> or "SNPs near the genes I'm interested in", "SNPs near the genes that 
> are active during development phase foo", "genes that are under GO term 
> such-and-such", etc.
> 
> Mitch
> 
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Re: [Gmod-ajax] Article: Using game design to build the next Digg or Flickr

[Mitch S. <mit...@be...>]

Ian Holmes wrote:
> How would this compare with existing systems e.g. Ensembl MART?
>

I've only spent a bit of time with it, but I don't see a way to view the 
results of a biomart query in the genome browser, which is what I was 
thinking.  In addition to creating new tracks by uploading, we could 
allow people to create tracks by defining queries.  It should be easy 
for us to track how popular these are, so there's a natural connection 
to the points and feedback/recognition items from the game/webapp article.

Also, while you can specify a list of IDs to biomart, that requires the 
user to manage their own collection.  We could certainly make collection 
management a lot easier (e.g., an "add this to my collection" button on 
feature popups).  Centralizing collections also makes them easier to 
share (like the "post your hotlist" thing, with individual features 
instead of tracks).

In addition to having a nice query building UI like biomart does, I 
think it makes sense to expose something lower level, like (say) raw 
SPARQL.  Most biologists won't use it, but if we make it easy for more 
advanced users to share their queries with other people then it's still 
pretty useful IMO.

But these are all just random ideas.  Mainly, I wanted to ask for help 
translating game ideas into stuff that relates more concretely to what 
we're doing.

Mitch

Re: [Gmod-ajax] Article: Using game design to build the next Digg or Flickr

[Chris M. <cj...@fr...>]

On Aug 24, 2007, at 5:41 PM, Mitch Skinner wrote:

> Ian Holmes wrote:
>> How would this compare with existing systems e.g. Ensembl MART?
>>
>
> I've only spent a bit of time with it, but I don't see a way to  
> view the
> results of a biomart query in the genome browser, which is what I was
> thinking.  In addition to creating new tracks by uploading, we could
> allow people to create tracks by defining queries.  It should be easy
> for us to track how popular these are, so there's a natural connection
> to the points and feedback/recognition items from the game/webapp  
> article.
>
> Also, while you can specify a list of IDs to biomart, that requires  
> the
> user to manage their own collection.  We could certainly make  
> collection
> management a lot easier (e.g., an "add this to my collection"  
> button on
> feature popups).  Centralizing collections also makes them easier to
> share (like the "post your hotlist" thing, with individual features
> instead of tracks).

I like this idea, but in the interests of not seeing us diverge too  
far from the core plan I'd like to place this in the context of a  
wider architecture.

I think GBrowse-ajax should make the assumption that we will soon  
live in an ideal bioinformatics nation where data sources will expose  
powerful query interfaces - MART, InterMine, or more ontology-based  
schemes - through some appropriate HTTP API or RESTful architecture.

GBrowse should provide a way of slurping a bunch of feature IDs and  
showing them in an appropriate way. Or, conversely, a way of  
exporting a bunch of IDs, perhaps from a ROI.

So long as gbrowse is mashup/plugin friendly then it should be  
possible to wrap this functionality in the way you describe.

> In addition to having a nice query building UI like biomart does, I
> think it makes sense to expose something lower level, like (say) raw
> SPARQL.  Most biologists won't use it, but if we make it easy for more
> advanced users to share their queries with other people then it's  
> still
> pretty useful IMO.

SPARQL is fairly limited. However, it is the standard query language  
for RDF.

You can assume that a SPARQL wrapper for Chado will be available  
sometime in the next half of year or so. We've already done this for  
the GO database[1]. Again, I think GBrowse should just worry about  
accepting lists of IDs and/or regions - this would be the main point  
of contact. Some enterprising semweb fan will then hopefully cobble  
together a non-horrible SPARQL interface that pipes the results into  
a GBrowse display.

> But these are all just random ideas.  Mainly, I wanted to ask for help
> translating game ideas into stuff that relates more concretely to what
> we're doing.
>
> Mitch
>
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Re: [Gmod-ajax] Article: Using game design to build the next Digg or Flickr

[Ian H. <ih...@be...>]

Yes, I think that if you provide the ability to represent arbitrary sets 
of features (which the divbrowser was clearly born to do) and an API 
that is mashup/plugin friendly, then we could inch our way towards 
something like this without forgetting that the G in GBrowse stands for 
Generic -- i.e. without doing something that is too specific to one 
particular database.

And yes, I am guiltier than anyone of tossing random ideas into the mix 
  -- really this is blue-sky discussion and should not be confused with 
the more modest, concrete & well-defined goals that we have put in 
writing elsewhere (in our proposal to NIH, on the wiki, etc.)




Chris Mungall wrote:
> On Aug 24, 2007, at 5:41 PM, Mitch Skinner wrote:
> 
>> Ian Holmes wrote:
>>> How would this compare with existing systems e.g. Ensembl MART?
>>>
>> I've only spent a bit of time with it, but I don't see a way to  
>> view the
>> results of a biomart query in the genome browser, which is what I was
>> thinking.  In addition to creating new tracks by uploading, we could
>> allow people to create tracks by defining queries.  It should be easy
>> for us to track how popular these are, so there's a natural connection
>> to the points and feedback/recognition items from the game/webapp  
>> article.
>>
>> Also, while you can specify a list of IDs to biomart, that requires  
>> the
>> user to manage their own collection.  We could certainly make  
>> collection
>> management a lot easier (e.g., an "add this to my collection"  
>> button on
>> feature popups).  Centralizing collections also makes them easier to
>> share (like the "post your hotlist" thing, with individual features
>> instead of tracks).
> 
> I like this idea, but in the interests of not seeing us diverge too  
> far from the core plan I'd like to place this in the context of a  
> wider architecture.
> 
> I think GBrowse-ajax should make the assumption that we will soon  
> live in an ideal bioinformatics nation where data sources will expose  
> powerful query interfaces - MART, InterMine, or more ontology-based  
> schemes - through some appropriate HTTP API or RESTful architecture.
> 
> GBrowse should provide a way of slurping a bunch of feature IDs and  
> showing them in an appropriate way. Or, conversely, a way of  
> exporting a bunch of IDs, perhaps from a ROI.
> 
> So long as gbrowse is mashup/plugin friendly then it should be  
> possible to wrap this functionality in the way you describe.
> 
>> In addition to having a nice query building UI like biomart does, I
>> think it makes sense to expose something lower level, like (say) raw
>> SPARQL.  Most biologists won't use it, but if we make it easy for more
>> advanced users to share their queries with other people then it's  
>> still
>> pretty useful IMO.
> 
> SPARQL is fairly limited. However, it is the standard query language  
> for RDF.
> 
> You can assume that a SPARQL wrapper for Chado will be available  
> sometime in the next half of year or so. We've already done this for  
> the GO database[1]. Again, I think GBrowse should just worry about  
> accepting lists of IDs and/or regions - this would be the main point  
> of contact. Some enterprising semweb fan will then hopefully cobble  
> together a non-horrible SPARQL interface that pipes the results into  
> a GBrowse display.
> 
>> But these are all just random ideas.  Mainly, I wanted to ask for help
>> translating game ideas into stuff that relates more concretely to what
>> we're doing.
>>
>> Mitch
>>
>> ---------------------------------------------------------------------- 
>> ---
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>> Still grepping through log files to find problems?  Stop.
>> Now Search log events and configuration files using AJAX and a  
>> browser.
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>>
> 
> 
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> Still grepping through log files to find problems?  Stop.
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