Chris May

This week I received a notification that I had been awarded a letter of commendation from the University of Chicago.

I realized that I never posted anything on here about my graduation.  I graduated this summer with the degree of Master of Science in Computer Science.

I'm obviously proud to have been able to graduate from such a well regarded school. 

I know that I learned a lot of valuable things while I was going to class, in areas that I probably would not have entered otherwise.

Best news is, I paid it all as I went.  So I have no debt!  :)

 

Awk is a tool for processing text files, or data that is treated as text.

For some stuff I have been working on, I tend to use Awk a lot to filter down text being returned from another program (like a ls command).

Here is a nice tutorial on Awk.

Also, when using regular expressions (regexp, or regex) with Awk, here are a few helpful reminders and links.

.	matches any character
*	zero or more repetitions of the previous character or expression
?	zero or one occurrence of the previous expression
+	one or more occurrences of the previous expression

Regexp cheat sheet.

Test regular expressions.

Regexp website (tutorials and more)

Another Regexp tutorial

This is the paper I wrote for my Bioinformatics course at the University Of Chicago, discussing some of the methods available to sequencing DNA of complex organisms, and how Myers was able to use the whole genome shotgun method to sequence the human genome.

TermPaper.pdf (793.88 KB)

 

I am writing a paper for where I am supposed to defend the claim that Whole Genome Shotgun Sequencing was successful at mapping the human genome.

In the research I have done, I have come across a bunch of papers from the late 90s from people on both sides (e.g. Venter/Myers PRO, Green
AGAINST).

It seem then after the release of the human genome, there again a number of papers looking at the results, kind of doing a post mortem on the whole debate.

However, these articles seem to indicate that WGS would NOT have worked in the human genome, where such a large portion of the genome is a duplicate, if not for the IHGP teams work.  Some papers seemed to suggest that this hybrid method would be the standard way to sequence genes.

I have not found much on the subject from recent months.  Almost all
my references are from 2002 or earlier.

I tried posting to some newsgroups for some opinions and got back nada.

I must not be looking in the right spots, but it sure is frustrating.

UPDATE: After more research, it appears that the reason I was finding so many articles complaining about the WGS method was due to the massive egos that were seeing their Nobel prize dreams going up in smoke.  Venter and Myers successfully used WGS on the mouse genome, and then later applied it again to human, without any data from GenBank, validating the results, and the technique.

For my most recent project at U of C, I had to write some script to find places where DNA and RNA might bind.

DNA (and RNA) will bind when 2 strands have a complementary sequence.  A binds with T, T bind with A, G binds with C and C binds with G. 

Basically the same thing happens with RNA.

Here are 2 functions that will quickly find the complementary sequence for DNA and RNA:

Public Function FlipRnaCode(ByVal sEnd As String) As String
    sEnd = Replace(sEnd, "U", "a", 1, -1, CompareMethod.Binary)
    sEnd = Replace(sEnd, "A", "u", 1, -1, CompareMethod.Binary)
    sEnd = Replace(sEnd, "G", "c", 1, -1, CompareMethod.Binary)
    sEnd = Replace(sEnd, "C", "g", 1, -1, CompareMethod.Binary)
    sEnd = UCase(sEnd)
    Return sEnd
End Function

Public Function FlipDnaCode(ByVal sEnd As String) As String
    sEnd = Replace(sEnd, "T", "a", 1, -1, CompareMethod.Binary)
    sEnd = Replace(sEnd, "A", "t", 1, -1, CompareMethod.Binary)
    sEnd = Replace(sEnd, "G", "c", 1, -1, CompareMethod.Binary)
    sEnd = Replace(sEnd, "C", "g", 1, -1, CompareMethod.Binary)
    sEnd = UCase(sEnd)
    Return sEnd
End Function

 

 

I find myself frequently trying to find the dates on this calendar, and I can never find any links to this site.

http://academic-calendar.uchicago.edu/future/index.html

It has all the dates of academic interest (days off, starting and ending days of each quater).

This quater I am planning on taking Bioinformatics.

I saw a presentation on Bioinformatics at Fermi Lab.  They have searching programs to look at, I believe, the genome sequence, to find similar patterns.  Pretty interesting.

Hopefully the course will be good too!

I found this article that talks about some of the classes used in the .net framework v2.0 when doing XSLT.

http://www.15seconds.com/issue/060608.htm

I am taking a course on XML / XSLT at UofC that I am planning on doing in .Net.  I have written xml schamas xml stylesheets and xml transforms before, but not using .net 2.0, so it should be interesting.

I just got my first set of grades from University of Chicago.  I got an A in OO Architecture and Design Patterns, and a B in Software Construction.

I think I couldn't have done any better than a B in Software Construction.  The work was very challenging, in a good way, but the time requirement was so great that week after week I wasn't able to complete the weeks assignment, or if I was able to complete it, my code wasn't as strong as it could have been.

I am taking this quater off to focus on work, and I am not sure if I will be taking anything in the summer as they usually do the really basic classes then.  We will see. 

I probably still need to take some kind of discrete math class, but I don't want to pay the $3600 bucks to take it at UofC if I can take it elsewhere for less.