Is there an option in NetLogo to know in which link is located a citizen that is moving in a network or links at every tick?
I am not asking for the code or anyone solution for me. I want only a tip as I already check in the NetLogo dictionary the options available relate to turtles and links but I cannot find the way.
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I am mid-way through my university project, and I have run into an issue. I have a long list of around 1000 proteins that I wanted to analyse in STRING, however, my list is too large. I decided to try and utilise Cytoscape (and downloaded the stringApp), but the networks generated are still very messy. I've attached a screenshot here. Is there any way to improve the presentation of the network by downloading any Cytoscape apps or by tweaking the settings?
Thanks in advance
Well, the short answer is "no". A slightly longer answer is "it depends".
Showing a hairball really isn't helpful, usually, so you need to refine things somewhat. What is your data source (i.e. where did the 1000 proteins come from)? What do you hope to see in the network? If you are looking for particular groups of proteins (e.g. complexes), you would probably want to use MCL to cluster them first. If you have some other data you want to map, such as transcriptomic or proteomic data, you could refine your network based on fold change or abundance values.
All that being said, somethings you might try. First, you are seeing the "fast" version of the network. Try clicking on the show graphics details button (the diamond in the network view tool bar). That will give you the full graphics details. Second, you might try spreading the network out a bit by using the Layout->Layout Tools. Turn off the "Selected Only" and then adjust the scale. Finally, depending on your biological question, you might want to eliminate proteins that are only present in the nucleus or cytoplasm, or are only in lung tissue. This is all possible using the sliders provided by the stringApp's Results Panel.
-- scooter
I am making a grid based game which has "line of sight" targeting. Often times a game engine would use Raycast for this but I don't want to use an engine so I am trying to "roll my own" solution.
So basically, given P1,P2 pairs I want to find all those spaces between them (marked X).
I am having a big of a hard time figuring out how to do this. Somehow I have to find out which sides are closest together and use those as my starting points for "raycast". Then I guess I could take "samples" at cell-size increments and compare those with the indexes of the cells.
Unfortunately, I don't have any code yet ... I was hoping some could help with some pseudocode just to get the algorithm. I think if I could figure out how to get the start and end points for each of the pink lines then I could use that to find the orange squares.
Apparently, Bresenham algorithm is a good choice here.
I wish I could post some content in addition to the link but it wouldn't help me give a complete context. So, better to visit the link and use the information there. Don't miss out on the comments section. There are good insights there as well.
Please check this as well Elegant/Clean (special case) Straight-line Grid Traversal Algorithm?.
The description of my problem is simple, I fear that the problem isn't that simple. I would like to find the copied, duplicated part on an image. Which part of the image is copied and pasted back to the same image to another position(for example by using Photoshop)?
Please check the attached image. The red rectangle containing the value 20 is moved from the price field to the validity field. Please note that the rectangle size and position isn't fixed and unknown, it could vary, just the image is given, no other information.
Could you help me naming a theoretical method, idea, paper, people who are working on the problem above?
I posted my method to here(stackoverflow) instead of Computer Vision to reach as many people I can, because maybe the problem can be transformed. I could think a solution, like looking for the 2 largest rectangle which contain the same values inside a huge matrix(image).
Thanks for your help and time.
Note: I don't want to use the metadata to detect the forgery.
If you have access to the digital version of the forgery, and the forger (or the author of the forger-creation software) is a complete idiot, it can be as simple as looking at the image metadata for signs of 'shopping.
If digital files has been "washed" to remove said signs, or the forgery has been printed and then scanned back to you, it is a MUCH harder problem, again unless the forgers are complete idiots.
In the latter case you can only hope for making the forger's work harder, but there is no way to make it impossible - after all, banknotes can be forged, and they are much better protected than train tickets.
I'd start reading from here: http://www.cs.dartmouth.edu/farid/downloads/publications/spm09.pdf
SHIFT features can be used to identify "similar regions" that might have been copied from a different part of the image. A starting point can be to use OpenCV's SHIFT demo (included in the library) and use parts of the image as input, to see where a rough match is available. Detailed matching can follow to see if the region actually is a copy.
This question is in regards to Mike Bostock's very exciting d3.js library in general, and more specifically the treemap plot. Note: treemap seems to have two versions, the "talk version" and the "example version". My question relates to the "talk version," which has the zoom feature.
My question is more of a wish: How difficult would it be to extend treemap to accommodate and show multiple internal nodes, with multiple levels of zoom? For example, click to go down one level and option-click to go up one level. Perhaps to keep things tidy, only nodes one level deeper are painted -- as you zoom in, deeper levels are resolved.
This is my pie-in-the-sky wish -- I am not familiar with javascript and can't take this on right now -- but it seems do-able on a visual/UI level. I did notice that mbostock commented here that treemap only shows leaf nodes, but I don't know if this is a design constraint or just a SMOP.
Anyone with any interest in doing this? Possibly for a commission? Thanks.
It appears the author posted an nearly exact answer my question on his website the day after I posted this question. Whether or not this question prompted the adaptation, I am excited to try it out!
He is calling it "Zoomable Treemap". He also points out a couple other examples on the net.
Thanks, mbostock!
I'm a member of a small but fairly sociable online forum, and just for fun we've been plotting a chart of who's met who in real life. Here's what it looked like fairly recently.
(The colour is the "distance" from the currently-selected user, e.g., yellow is someone who's met someone who's met them. And no, I'm not Zak.) Apologies for the faded lines, they don't seem to have weathered the SO upload process very well.
It's generated as SVG, with a big block of JSON defining who's met who. The position (x,y) of each member on the chart is hard-coded into that JSON. Until now, it's been fairly easy to cope when someone meets someone else - at worst, maybe two or three people need to be shuffled around - but it does involve editing the co-ordinates manually. And now that the European and North American contingents are meeting up, and a few on the periphery are showing up at meets, all hell is breaking loose...
We can put some effort into making all the nodes draggable, which would make the job of re-arranging a bit less tiresome. But it seems more sensible to let the computer take care of positioning them, especially as the problem will only get harder with more members.
So, does anyone know of an algorithm for positioning these nodes on the chart, based on which other nodes they're linked with?
Ideally, it would
minimise or avoid long links
avoid having lines run underneath unrelated nodes
take account of the fact that well-connected nodes are bigger
do its best to show the wider "all these guys met each other" relationships (the big circle at the bottom is largely the result of one meet, for example, though the chart has no idea of when any two people met)
but if it gets us close enough to tweak it, that's progress.
And, what's the real name for these charts? I believe they're called "link charts", but I'm not getting good results from Google using that name or anything else I can think of.
We'll likely be implementing this in PHP or Javascript, but right now it's how to begin approaching the problem that's the bigger question.
Edit: Some great answers coming already. I would be very interested in the actual algorithm(s) used, though, as well as tools that do the job.
What you are looking for are f.e. force-based algorithms. There are quite a few libraries, and some have been named already, like prefuse, yWorks. Here a few more: jung, gvf, jGraph.
The real name for it is "graph". To generate graph, and have a good layout algorithm, the best is to use a software which will do the job.
I advise you to use Gephi.
This soft is able to do all the things you want to.
Have a look at the yWorks tools.
You can google for graph visualization. There are more libraries for this, including GraphViz, but probably not all your requirements will be met.
If you can deal w/ Java, take a look at prefuse.
Have a look at NodeXL
Also, this book may be relevant.