[BiO BB] Advanced web query interfaces for biological databases

Keith Callenberg keithcallenberg at gmail.com
Tue Apr 15 00:49:54 EDT 2008


I completely agree that there are significant limitations to user
interfaces, but there is a reason why at least half of NCBI's users
use their web-based tools when they are applicable, and it is that
doing so is often simpler and saves time from installing BLAST, ORF
Finder, etc on your machine, having to download the data, and making
sure you are using the correct command-line options.

I do not disagree with your assertion that the half that use the
web-based tools are likely doing simpler queries with smaller amounts
of data, but this just illustrates that there are tasks that are
suitable for a web interface and there are tasks that must be done
programmatically.

I guess my point of disagreement with Mike is the order or priority in
development, because I do not claim that having an API and/or publicly
available database is not important. It is just that it would not make
sense, at least for our project, to focus on a minority of power users
without first accommodating the base of users who are biologists not
bioinformaticians.

Keith

On Mon, Apr 14, 2008 at 8:19 PM, Ryan Golhar <golharam at umdnj.edu> wrote:
> I support this view.  "Programmatically" means allowing outside users
> developing their own software interfacing with your database/website via an
> API.
>
>  Although NCBI has a fairly well developed website, there is a lot I can't
> do from a GUI because of the amount of data we work with.  It easier for us
> to use NCBI's API (E-utilities) to access their live database and extract
> information in a way we need.
>
>  Anyone who works with lots of data will know a GUI interface will never be
> sufficient.  Its much easier to accomplish the work with a script or
> program.
>
>
>  Mike Marchywka wrote:
>
> >
> >
> >
> >
> > > our database as it will be some time before we have a sizable pool of
> > > users, letalone developers.
> > >
> >
> > And what kind of interface will your few developers use? I guess my point
> is that if you have
> > a compelling data set, developers will come out of the wood work to
> support it.
> >
> >
> > > Also, I might not be clear on what you mean by "programmatically," but
> > > I think it is a bit short-sighted to limit the scope of web-based
> > > interfaces to only casual queries.
> > >
> >
> > I'm not advocating intentional limitations, just expressing the problem
> with a GUI. You
> > end up guessing how a user wants to work ( or you are omniscient). For
> examples
> > or introductory material that is great and even important for proof of
> concept if
> > nothing else. To let motivated users exploit the full capabilities of most
> data sources,
> > however, you need to let them ( or their machines ) interact with existing
> tools.
> >
> > Further, if you define a machine usable interface (API) you better
> document your features
> > without having to worry about modal dialogs and button colors.
> >
> >
> >
> > Mike Marchywka
> > 586 Saint James Walk
> > Marietta GA 30067-7165
> > 404-788-1216 (C)<- leave message
> > 989-348-4796 (P)<- emergency only
> > marchywka at hotmail.com
> > Note: If I am asking for free stuff, I normally use for hobby/non-profit
> > information but may use in investment forums, public and private.
> > Please indicate any concerns if applicable.
> > Note: Hotmail is possibly blocking my mom's entire
> > ISP - try  me on marchywka at yahoo.com if no reply
> > here. Thanks.
> >
> >
> >
> > > Date: Sun, 13 Apr 2008 17:23:30 -0700
> > > From: keithcallenberg at gmail.com
> > > To: bbb at bioinformatics.org
> > > Subject: Re: [BiO BB] Advanced web query interfaces for biological
> databases
> > >
> > > Thanks for your suggestion, Mike. As a developer I also value the
> > > concept of an open and freely available API, and I wish that more
> > > sites would provide these, but I am not sure it is yet appropriate for
> > > our database as it will be some time before we have a sizable pool of
> > > users, letalone developers.
> > >
> > > Also, I might not be clear on what you mean by "programmatically," but
> > > I think it is a bit short-sighted to limit the scope of web-based
> > > interfaces to only casual queries. I am not usually a supporter of the
> > > term "Web 2.0" because I think it has lately signified little more
> > > than colorful buttons, but I do believe more and more tasks can be
> > > accomplished from within the browser. I believe energy should be put
> > > into moving more advanced tasks online because it removes learning
> > > curves and hardware restrictions, thereby increasing your base of
> > > users.
> > >
> > > I think it is not easy to develop an intuitive web-based UI that is
> > > not fairly restrictive, but that does not mean it should not be
> > > pursued.
> > >
> > > Keith
> > >
> > >
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