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Does anyone know if it is possible to convert SNP coordinates from Hapmap database to the new reference genome GRCh38. UCSC doesn't have the liftover yet ready. Any suggestions?
As was linked in the BioStars answer, NCBI offers a remapping tool that will translate positions from one reference genome to another. UCSC also offers a similar tool, LiftOver, which has a downloadable version as well.
However, as I discovered years ago, these tools do not always succeed in remapping your coordinates, and sometimes produce incorrect results. You should take all output from these tools with a grain of salt. Bottom line, you should only assume your original coordinates are the correct ones, and try to work with the corresponding reference genome build.
The UCSC liftover tool as mentioned above can work most of the time https://genome.ucsc.edu/cgi-bin/hgLiftOver
However, there might be repetitive pieces which may make the liftover tool confused.
An alternative way is to map the sequences (fasta/fastq) onto the new hg38 genome using bowtie to get coordinates.
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I'm looking to create shapes like this :
https://www.lucegallard.com/?lightbox=dataItem-isiz1h39
But they have to be generated at random and never overlap. It would be too easy to just use beginShape() and curveVErtex(x,y), etc.
Plus the result would we static, it needs to be changed easily and randomly. My question is "is there a function to create 'weird' ellipses?" or "Could anyone help me with an algorithm to achieve this?"
Thanks allot in advance!
Stack Overflow isn't really designed for general "how do I do this" type questions. It's for specific "I tried X, expected Y, but got Z instead" type questions. But I'll try to help in a general sense:
You need to break your problem down into smaller pieces and take those pieces on one at a time. Try to create a program that just generates a single random shape. Then try to add a second randomly-generated shape that doesn't intersect with the first shape.
Think about how you would describe this program to somebody who can't see the website you've linked in your post. Try to describe it in as much detail as you can. Pretend you have a friend who has never seen what you're talking about. Can you write down a set of steps that this friend could follow to draw what you're talking about? When you have those steps written down, that's an algorithm that you can start thinking about implementing with code.
A simple check would be for each new point you generate, check whether it's inside any previous shapes. If so, go back and pick a different new point. That will at least get you started going in a direction.
If you get stuck, please post a MCVE along with a more specific technical question. Good luck.
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Like the title says.
I have an image on my PC and want to find out where it was taken.
Is there a possibility to find the place by google maps ?
Thanks
What you are asking might be possible. But the scope of what you are asking is near impossible, if not impossible. It also seems unlikely that such a search would find a result you are looking for.
If you are just trying to place where a picture was taken, you would likely have far more luck, in much shorter time, posting the picture, as well as your best guess to narrow down the area, to a site such as Reddit.
Try running jhead on the image and see if it contains GPS coordinates. It is free here.
Or, if you don't mind uploading your image to a web-service to view the GPS data, you can upload it to here.
If you get the GPS cooridnates, you can type them in to maps.google.com, like this
52.785,-2.012
and hit enter and the map will centre on your location.
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I should to prepare myself for upcoming task which consist of a lot of graphs.
I need some data (available in free domain) to train myself.
Bigger - is better...
could you suggest some open data resource?
I'll appreciate this.
You can visit http://snap.stanford.edu/data/ . It contains many different kind of network or graph data.
Here is an answer for your could you suggest some open data resource? and not for which consist of a lot of graphs. So, plz, keep it in mind.
Here (data.gov.au) you can find a huge datasets (864!) of a different types in a different formats (txt, csv, xml, ). You will find a Finance, Industry, Geography, etc. datasets.
In other case, if you want some special (and meaningful data, for example, global population density) you can see this (a bit outdated, but usefull) source from readwriteweb.com.
And one more source: "Open Governmental Datasets" - it's worth to see it indeed.
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Does any one have an idea regarding what sort of algorithm might Google be using to find similar images ?
No, but they could be using SIFT.
I'm not sure this has much to do with image processing. When I ask for "similar images" of the Eiffel tower, I get a bunch of photos of Paris Hilton, and street maps from Paris. Curiously, all of these images have the word "Paris" in the file name.
Currently the Google Image Search provides these filtering options:
Image size
Face detection
Continuous-tone ("Photo") vs. Smooth shading ("Clipart") vs. bitonal("Line drawing")
Color histogram
These options can be seen in its Image Search Result page.
I don't know about faces, but see at least:
http://www.incm.cnrs-mrs.fr/LaurentPerrinet/Publications/Perrinet08spie
Compare two images the python/linux way
I have heard, that one should use this when comparing images
(I mean: make the prob model, calc. the probs, use this):
http://en.wikipedia.org/wiki/Kullback%E2%80%93Leibler_divergence
Or then it might even be one of those PCFG things that MIT people tend to use with robotics stuff. One I read used some sort of PCFG model made of basic shapes (that you can rotate magically) and searched the best match with
http://en.wikipedia.org/wiki/Inside-outside_algorithm
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Hi I need to graph some arrays to analyse signals, I have a cocoa project going. Can anyone tell me where I can find tools to simplify this task?
Basically i want to display my arrays like on a graphing calculator.
Even though it's a young library, I'd suggest looking at the open source Core Plot framework. It works on Mac and iPhone and can currently plot line and bar charts. As I said, it's young and a lot of the core functionality is still being written, but it might work right now for your case.
Take a look at this post to the Apple mailing lists. http://lists.apple.com/archives/scitech/2007/Jun/msg00022.html
It mentions 3 potential graphing packages that you can try. I have not had personal experience with them, so buyer beware, but it will at least give you a start on where to look.
XCode allows you to create data formatters to present object data in the debugger, but it doesn't provide any way to graphically represent the data using charts or graphs. (At least, not that I know of!) I think that's beyond the scope of XCode. You might consider dumping the data from your array to a file using a bit of code or the console, and then loading it into Excel or MATLAB. Then you can create a graph of your signal with no problem.
Just out of curiosity, are you familiar with another IDE that provides graphs of array data? I know tools like MATLAB and Mathematica do it pretty nicely, but I've never seen it in an IDE.