Menu
▾
▴
Re: [Scaffoldhunter-users] GSoC-2013
|
From: shruti g. <shr...@gm...> - 2013-05-02 15:27:42
|
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 > > > > > > > > > > > > |
