Navigating SPNS3D.org

[lirsveacba]

In the science project "Bioinformatics: The Perfect Marriage Between Computer Science and Medicine," all of the steps after seven become less and less descriptive until even the objective becomes blurry. (https://www.sciencebuddies.org/science- ... ?from=Home)

I have completed all of the steps before 7 successfully, but I have no idea how to get to the model in the example of step 7. (http://www.snps3d.org/cgi-bin/jmol?seq_ ... ymbol=CFTR)

In my project, I am studying the correlation between the SNPs (like rs29281 and rs2187601) on Fragile X Syndrome. How do I navigate the SNPS3D.com website, and what does ScienceBuddies.org say to do after that? I would appreciate any advice that you could give me. Thank you!

[deleted-71256]

Hi, I'm not an expert in this field, so I'm just offering some observations that might help. It appears from the link that you give that you've entered the search information but aren't seeing the model.

I clicked the link you gave in your note and when it first came up I saw a message in the box on the left that it was loading bleep. I gave up and did bleep else. When I tried the link a second time, there was no message, but the box was blank. I then waited a bit longer and it then showed me a model like the graphic in the box on Step 8.

So maybe all you need to do is to wait, particularly if you have a slow connection.

Bill

[deleted-71417]

Hi lirsveacba-

Sorry to hear you are getting a bit frustrated with the Bioinformatics :The perfect marriage between computer science and medicine. It seems to me to be a fantastic project, offering a glimpse into the world of a graduate student in this area. I hope this reply will help clarify things a little. First, as to the point of it all, maybe this article on SNPs3D and its intended utility will help:

http://www.biomedcentral.com/1471-2105/7/166

Second, as to how to get the model structure to display, I found the following formula by trial and error:

1) open the link:
http://www. SNPs3D.org

2)in the SNP Analysis search box, enter rs213950 and search

3)scroll down to the section labeled dbSNP

4) look under the column called model frequency. If you scroll down you will see on some entries one or two icons. One looks like three balls in a triangle, the other has a red dot and looks like Caspar the ghost, with two arms. If you click on the ghost icon you will get the annotated model displayed. I am afraid you cannot get the model displayed if the icon is not present. I was not able to display the model using the two SNPs you said you were interested in..

Third, some ideas on how to proceed:
1) I would suggest walking through the project using the example they used in the experiment write-up, then go back and attempt the snps and genes you are really interested in. If you can follow and understand the process in their example, you may gain a better understanding of the concept of the project.

2) Do not be afraid to experiment if you get stuck - as long as you do not attempt to hack their sites it is unlikely you will do any harm, and you can learn a whole lot by doing this.

3) You can also learn a whole lot by trying google searches on the name of the thing you are having trouble with, then reading several of the sites that are returned by the search. That is how I found the first link cited above. (I assume you know how to use google. Go to http://www.google.com and enter you r search term or phrase in the search box and click the search button.) I have been able to answer almost any question in this manner, though it sometimes requires trying to rephrase my question several times and looking through several pages of search results on each query.

4) Finally, persevere. This is a fantastic project that is right at the forefront of science today. If you can get into it and like it, it could be an outstanding career path. Any insight you can get now on this will put you way ahead as you start college and beyond.

I wish you great success!

Best regards,

Barrett Tomlinson

[lirsveacba]

Thank you so much, Mr. Tomlinson!! I'll follow the steps and try to get somewhere; this really cleared things up and can't thank you enough.