scaffoldhunter-users

[Scaffoldhunter-users] GSoC-2013

[shruti g. <shr...@gm...>]

Hello everyone,

I am a third year undergraduate student pursuing a degree in Information
Systems. I am interested to work with Scaffold for GSoC 2013. I am aware
that it is too late to apply for a project now, but I had been busy with my
exams, and so, could not get here earlier.


I have worked on Probabilistic Graphical Models with RooStats(CERN), for
Google Summer of Code - 2012. The project consisted of construction and
sampling of Bayesian Belief Networks. The code is written in C++.

As a semester course, I have studied basic propositional logic, data
structures and algorithms (including graph algorithms). I have also done a
course in Object Oriented Programming and Design focused on Java. I have
also completed a basic in Graphs and Networks.

I am interested in the following projects:

   - Scaffold Tree Layout


I am already working on my proposal. It would be great if a mentor could
tell me if applying now is encouraged. And, if it is okay to apply now.

Looking forward to working with you,
Thank you

Shruti Gupta.

Re: [Scaffoldhunter-users] GSoC-2013

[Karsten K. <ka...@us...>]

Hi Shruti,

thanks for your interest. It is not too late until the deadline is over ;-).
You can apply any time till then. If you have any further questions, feel
free to send them to this list.

Looking forward to your proposal,
kind regards,
    Karsten

On 2/05/2013 3:13 PM, shruti gupta wrote:
> Hello everyone, 
>
> I am a third year undergraduate student pursuing a degree in
> Information Systems. I am interested to work with Scaffold for GSoC
> 2013. I am aware that it is too late to apply for a project now, but I
> had been busy with my exams, and so, could not get here earlier.
>
>
> I have worked on Probabilistic Graphical Models with RooStats(CERN),
> for Google Summer of Code - 2012. The project consisted of
> construction and sampling of Bayesian Belief Networks. The code is
> written in C++.
>  
> As a semester course, I have studied basic propositional logic, data
> structures and algorithms (including graph algorithms). I have also
> done a course in Object Oriented Programming and Design focused on
> Java. I have also completed a basic in Graphs and Networks.
>
> I am interested in the following projects:
>
>   * Scaffold Tree Layout
>
>
> I am already working on my proposal. It would be great if a mentor
> could tell me if applying now is encouraged. And, if it is okay to
> apply now.
>
> Looking forward to working with you,
>
> Thank you
>
> Shruti Gupta.
>
>
>
> ------------------------------------------------------------------------------
> Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET
> Get 100% visibility into your production application - at no cost.
> Code-level diagnostics for performance bottlenecks with <2% overhead
> Download for free and get started troubleshooting in minutes.
> http://p.sf.net/sfu/appdyn_d2d_ap1
>
>
> _______________________________________________
> Scaffoldhunter-users mailing list
> Sca...@li...
> https://lists.sourceforge.net/lists/listinfo/scaffoldhunter-users

Re: [Scaffoldhunter-users] GSoC-2013

[shruti g. <shr...@gm...>]

Dear Sir,

Thank you for your reply. As far as I have understood, here we are trying
to reduce the area covered by the graph without affecting the information
conveyed by it. Are you intending to look at some Force-directed algorithms
to reduce this?
Or you have something else in mind? Or this question forms a part of the
Literature Survey for the project?

Hope to hear from you soon,

Shruti


On Thu, May 2, 2013 at 10:55 AM, Karsten Klein
<ka...@us...>wrote:

> Hi Shruti,
>
> thanks for your interest. It is not too late until the deadline is over
> ;-).
> You can apply any time till then. If you have any further questions, feel
> free to send them to this list.
>
> Looking forward to your proposal,
> kind regards,
>     Karsten
>
> On 2/05/2013 3:13 PM, shruti gupta wrote:
> > Hello everyone,
> >
> > I am a third year undergraduate student pursuing a degree in
> > Information Systems. I am interested to work with Scaffold for GSoC
> > 2013. I am aware that it is too late to apply for a project now, but I
> > had been busy with my exams, and so, could not get here earlier.
> >
> >
> > I have worked on Probabilistic Graphical Models with RooStats(CERN),
> > for Google Summer of Code - 2012. The project consisted of
> > construction and sampling of Bayesian Belief Networks. The code is
> > written in C++.
> >
> > As a semester course, I have studied basic propositional logic, data
> > structures and algorithms (including graph algorithms). I have also
> > done a course in Object Oriented Programming and Design focused on
> > Java. I have also completed a basic in Graphs and Networks.
> >
> > I am interested in the following projects:
> >
> >   * Scaffold Tree Layout
> >
> >
> > I am already working on my proposal. It would be great if a mentor
> > could tell me if applying now is encouraged. And, if it is okay to
> > apply now.
> >
> > Looking forward to working with you,
> >
> > Thank you
> >
> > Shruti Gupta.
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> > Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET
> > Get 100% visibility into your production application - at no cost.
> > Code-level diagnostics for performance bottlenecks with <2% overhead
> > Download for free and get started troubleshooting in minutes.
> > http://p.sf.net/sfu/appdyn_d2d_ap1
> >
> >
> > _______________________________________________
> > Scaffoldhunter-users mailing list
> > Sca...@li...
> > https://lists.sourceforge.net/lists/listinfo/scaffoldhunter-users
>
>

Re: [Scaffoldhunter-users] GSoC-2013

[Karsten K. <ka...@us...>]

The problem is to extend a layout algorithm to adhere to the
requirements we have in Scaffold Hunter.
The graph here is not just an abstract mathematical structure, but the
nodes have prescribed sizes (due to
the scaffold images) that need to be respected, there is a layering
given by the depth level of scaffolds within
the scaffold tree inclusion hierarchy, and the user can sort the
scaffolds according to some criteria, which has
to be clearly reflected in the layout.

As long as the layout method scales to several thousand objects,  and
supports those constraints, the type does
not matter much, it could e.g. be a distance based method. There is for
example a paper by Brandes and Pich (More
flexible radial layout) that describes how the radial layout style can
be resembled using Stress Majorization, but
it is not trivial to model the system correctly in order to respect the
above constraints in addition.

So there is a couple of options, but no preselection of a method for
this project.

    Karsten

On 2/05/2013 3:38 PM, shruti gupta wrote:
> Dear Sir,
>
> Thank you for your reply. As far as I have understood, here we are
> trying to reduce the area covered by the graph without affecting the
> information conveyed by it. Are you intending to look at some
> Force-directed algorithms to reduce this?
> Or you have something else in mind? Or this question forms a part of
> the Literature Survey for the project?
>
> Hope to hear from you soon,
>
> Shruti
>
>
> On Thu, May 2, 2013 at 10:55 AM, Karsten Klein
> <ka...@us... <mailto:ka...@us...>> wrote:
>
>     Hi Shruti,
>
>     thanks for your interest. It is not too late until the deadline is
>     over ;-).
>     You can apply any time till then. If you have any further
>     questions, feel
>     free to send them to this list.
>
>     Looking forward to your proposal,
>     kind regards,
>         Karsten
>
>     On 2/05/2013 3:13 PM, shruti gupta wrote:
>     > Hello everyone,
>     >
>     > I am a third year undergraduate student pursuing a degree in
>     > Information Systems. I am interested to work with Scaffold for GSoC
>     > 2013. I am aware that it is too late to apply for a project now,
>     but I
>     > had been busy with my exams, and so, could not get here earlier.
>     >
>     >
>     > I have worked on Probabilistic Graphical Models with RooStats(CERN),
>     > for Google Summer of Code - 2012. The project consisted of
>     > construction and sampling of Bayesian Belief Networks. The code is
>     > written in C++.
>     >
>     > As a semester course, I have studied basic propositional logic, data
>     > structures and algorithms (including graph algorithms). I have also
>     > done a course in Object Oriented Programming and Design focused on
>     > Java. I have also completed a basic in Graphs and Networks.
>     >
>     > I am interested in the following projects:
>     >
>     >   * Scaffold Tree Layout
>     >
>     >
>     > I am already working on my proposal. It would be great if a mentor
>     > could tell me if applying now is encouraged. And, if it is okay to
>     > apply now.
>     >
>     > Looking forward to working with you,
>     >
>     > Thank you
>     >
>     > Shruti Gupta.
>     >
>     >
>     >
>     >
>     ------------------------------------------------------------------------------
>     > Introducing AppDynamics Lite, a free troubleshooting tool for
>     Java/.NET
>     > Get 100% visibility into your production application - at no cost.
>     > Code-level diagnostics for performance bottlenecks with <2% overhead
>     > Download for free and get started troubleshooting in minutes.
>     > http://p.sf.net/sfu/appdyn_d2d_ap1
>     >
>     >
>     > _______________________________________________
>     > Scaffoldhunter-users mailing list
>     > Sca...@li...
>     <mailto:Sca...@li...>
>     > https://lists.sourceforge.net/lists/listinfo/scaffoldhunter-users
>
>

Re: [Scaffoldhunter-users] GSoC-2013

[shruti g. <shr...@gm...>]

Dear Sir,

Thank you for your reply. I will go through the paper, and  mention it in
the proposal. Given finite size of the nodes, reducing area of the graph
might also lead to overlaps, which also will have to be taken care of,
right? Further discussion for the Layout algorithm to be used, can be left
off to the Community Bonding Period if I am lucky enough to be selected! Is
it okay with you ?


On Thu, May 2, 2013 at 11:30 AM, Karsten Klein
<ka...@us...>wrote:

> The problem is to extend a layout algorithm to adhere to the
> requirements we have in Scaffold Hunter.
> The graph here is not just an abstract mathematical structure, but the
> nodes have prescribed sizes (due to
> the scaffold images) that need to be respected, there is a layering
> given by the depth level of scaffolds within
> the scaffold tree inclusion hierarchy, and the user can sort the
> scaffolds according to some criteria, which has
> to be clearly reflected in the layout.
>
> As long as the layout method scales to several thousand objects,  and
> supports those constraints, the type does
> not matter much, it could e.g. be a distance based method. There is for
> example a paper by Brandes and Pich (More
> flexible radial layout) that describes how the radial layout style can
> be resembled using Stress Majorization, but
> it is not trivial to model the system correctly in order to respect the
> above constraints in addition.
>
> So there is a couple of options, but no preselection of a method for
> this project.
>
>     Karsten
>
> On 2/05/2013 3:38 PM, shruti gupta wrote:
> > Dear Sir,
> >
> > Thank you for your reply. As far as I have understood, here we are
> > trying to reduce the area covered by the graph without affecting the
> > information conveyed by it. Are you intending to look at some
> > Force-directed algorithms to reduce this?
> > Or you have something else in mind? Or this question forms a part of
> > the Literature Survey for the project?
> >
> > Hope to hear from you soon,
> >
> > Shruti
> >
> >
> > On Thu, May 2, 2013 at 10:55 AM, Karsten Klein
> > <ka...@us... <mailto:ka...@us...>> wrote:
> >
> >     Hi Shruti,
> >
> >     thanks for your interest. It is not too late until the deadline is
> >     over ;-).
> >     You can apply any time till then. If you have any further
> >     questions, feel
> >     free to send them to this list.
> >
> >     Looking forward to your proposal,
> >     kind regards,
> >         Karsten
> >
> >     On 2/05/2013 3:13 PM, shruti gupta wrote:
> >     > Hello everyone,
> >     >
> >     > I am a third year undergraduate student pursuing a degree in
> >     > Information Systems. I am interested to work with Scaffold for GSoC
> >     > 2013. I am aware that it is too late to apply for a project now,
> >     but I
> >     > had been busy with my exams, and so, could not get here earlier.
> >     >
> >     >
> >     > I have worked on Probabilistic Graphical Models with
> RooStats(CERN),
> >     > for Google Summer of Code - 2012. The project consisted of
> >     > construction and sampling of Bayesian Belief Networks. The code is
> >     > written in C++.
> >     >
> >     > As a semester course, I have studied basic propositional logic,
> data
> >     > structures and algorithms (including graph algorithms). I have also
> >     > done a course in Object Oriented Programming and Design focused on
> >     > Java. I have also completed a basic in Graphs and Networks.
> >     >
> >     > I am interested in the following projects:
> >     >
> >     >   * Scaffold Tree Layout
> >     >
> >     >
> >     > I am already working on my proposal. It would be great if a mentor
> >     > could tell me if applying now is encouraged. And, if it is okay to
> >     > apply now.
> >     >
> >     > Looking forward to working with you,
> >     >
> >     > Thank you
> >     >
> >     > Shruti Gupta.
> >     >
> >     >
> >     >
> >     >
> >
> ------------------------------------------------------------------------------
> >     > Introducing AppDynamics Lite, a free troubleshooting tool for
> >     Java/.NET
> >     > Get 100% visibility into your production application - at no cost.
> >     > Code-level diagnostics for performance bottlenecks with <2%
> overhead
> >     > Download for free and get started troubleshooting in minutes.
> >     > http://p.sf.net/sfu/appdyn_d2d_ap1
> >     >
> >     >
> >     > _______________________________________________
> >     > Scaffoldhunter-users mailing list
> >     > Sca...@li...
> >     <mailto:Sca...@li...>
> >     > https://lists.sourceforge.net/lists/listinfo/scaffoldhunter-users
> >
> >
>
>

Re: [Scaffoldhunter-users] GSoC-2013

[shruti g. <shr...@gm...>]

Dear Sir,

On Thu, May 2, 2013 at 12:05 PM, Karsten Klein
<ka...@us...>wrote:

> Sure, that needs a bit of discussion.
> Regarding the node overlap, the layout (or the method applied) has to
> guarantee that the visualization is overlap free
> for the scaffold tree view. For a similarity map etc non-overlap might
> not be such a strict requirement, but for this view
> it is.
>

I have uploaded the draft proposal on the melange site, it would be great
if you could have a look and provide some feedback regarding the same. I
would be glad to incorporate the same. I have tried to base my proposal
upon your suggestions.

Hope to hear from you soon,

Shruti.

On 2/05/2013 4:05 PM, shruti gupta wrote:
> Dear Sir,
>

> > Thank you for your reply. I will go through the paper, and  mention it
> > in the proposal. Given finite size of the nodes, reducing area of the
> > graph might also lead to overlaps, which also will have to be taken
> > care of, right? Further discussion for the Layout algorithm to be
> > used, can be left off to the Community Bonding Period if I am lucky
> > enough to be selected! Is it okay with you ?
> >
> >
> > On Thu, May 2, 2013 at 11:30 AM, Karsten Klein
> > <ka...@us... <mailto:ka...@us...>> wrote:
> >
> >     The problem is to extend a layout algorithm to adhere to the
> >     requirements we have in Scaffold Hunter.
> >     The graph here is not just an abstract mathematical structure, but
> the
> >     nodes have prescribed sizes (due to
> >     the scaffold images) that need to be respected, there is a layering
> >     given by the depth level of scaffolds within
> >     the scaffold tree inclusion hierarchy, and the user can sort the
> >     scaffolds according to some criteria, which has
> >     to be clearly reflected in the layout.
> >
> >     As long as the layout method scales to several thousand objects,  and
> >     supports those constraints, the type does
> >     not matter much, it could e.g. be a distance based method. There
> >     is for
> >     example a paper by Brandes and Pich (More
> >     flexible radial layout) that describes how the radial layout style
> can
> >     be resembled using Stress Majorization, but
> >     it is not trivial to model the system correctly in order to
> >     respect the
> >     above constraints in addition.
> >
> >     So there is a couple of options, but no preselection of a method for
> >     this project.
> >
> >         Karsten
> >
> >     On 2/05/2013 3:38 PM, shruti gupta wrote:
> >     > Dear Sir,
> >     >
> >     > Thank you for your reply. As far as I have understood, here we are
> >     > trying to reduce the area covered by the graph without affecting
> the
> >     > information conveyed by it. Are you intending to look at some
> >     > Force-directed algorithms to reduce this?
> >     > Or you have something else in mind? Or this question forms a part
> of
> >     > the Literature Survey for the project?
> >     >
> >     > Hope to hear from you soon,
> >     >
> >     > Shruti
> >     >
> >     >
> >     > On Thu, May 2, 2013 at 10:55 AM, Karsten Klein
> >     > <ka...@us... <mailto:ka...@us...>
> >     <mailto:ka...@us...
> >     <mailto:ka...@us...>>> wrote:
> >     >
> >     >     Hi Shruti,
> >     >
> >     >     thanks for your interest. It is not too late until the
> >     deadline is
> >     >     over ;-).
> >     >     You can apply any time till then. If you have any further
> >     >     questions, feel
> >     >     free to send them to this list.
> >     >
> >     >     Looking forward to your proposal,
> >     >     kind regards,
> >     >         Karsten
> >     >
> >     >     On 2/05/2013 3:13 PM, shruti gupta wrote:
> >     >     > Hello everyone,
> >     >     >
> >     >     > I am a third year undergraduate student pursuing a degree in
> >     >     > Information Systems. I am interested to work with Scaffold
> >     for GSoC
> >     >     > 2013. I am aware that it is too late to apply for a
> >     project now,
> >     >     but I
> >     >     > had been busy with my exams, and so, could not get here
> >     earlier.
> >     >     >
> >     >     >
> >     >     > I have worked on Probabilistic Graphical Models with
> >     RooStats(CERN),
> >     >     > for Google Summer of Code - 2012. The project consisted of
> >     >     > construction and sampling of Bayesian Belief Networks. The
> >     code is
> >     >     > written in C++.
> >     >     >
> >     >     > As a semester course, I have studied basic propositional
> >     logic, data
> >     >     > structures and algorithms (including graph algorithms). I
> >     have also
> >     >     > done a course in Object Oriented Programming and Design
> >     focused on
> >     >     > Java. I have also completed a basic in Graphs and Networks.
> >     >     >
> >     >     > I am interested in the following projects:
> >     >     >
> >     >     >   * Scaffold Tree Layout
> >     >     >
> >     >     >
> >     >     > I am already working on my proposal. It would be great if
> >     a mentor
> >     >     > could tell me if applying now is encouraged. And, if it is
> >     okay to
> >     >     > apply now.
> >     >     >
> >     >     > Looking forward to working with you,
> >     >     >
> >     >     > Thank you
> >     >     >
> >     >     > Shruti Gupta.
> >     >     >
> >     >     >
> >     >     >
> >     >     >
> >     >
> >
> ------------------------------------------------------------------------------
> >     >     > Introducing AppDynamics Lite, a free troubleshooting tool for
> >     >     Java/.NET
> >     >     > Get 100% visibility into your production application - at
> >     no cost.
> >     >     > Code-level diagnostics for performance bottlenecks with
> >     <2% overhead
> >     >     > Download for free and get started troubleshooting in minutes.
> >     >     > http://p.sf.net/sfu/appdyn_d2d_ap1
> >     >     >
> >     >     >
> >     >     > _______________________________________________
> >     >     > Scaffoldhunter-users mailing list
> >     >     > Sca...@li...
> >     <mailto:Sca...@li...>
> >     >     <mailto:Sca...@li...
> >     <mailto:Sca...@li...>>
> >     >     >
> >     https://lists.sourceforge.net/lists/listinfo/scaffoldhunter-users
> >     >
> >     >
> >
> >
>
>