DJ,

    Thanks for the URL to the book. It looks like a nice resource. Perl 
was originally used in early years of bioinformatics because of its 
regular expression capabilities which allowed for searching patterns, 
and its ease of use for dealing with text which were two important 
aspects when dealing with DNA and proteins. I think python came along 
later. A lot of code is still written in Perl, such as BioPerl, so Perl 
has some advantage there, but Python is really coming up very quickly. 
There is a BioPython and people entering into Bioinformatics now seem to 
work with Python.

    Your project sounds very interesting. It seems like you could do for 
the Catechism something similar to what Bible Word Locator, 
http://www.openbible.info/labs/word-locator/, does for the Bible ?  or 
maybe to use for cross-references ?   Getting word positions from texts 
sounds like it was extremely tedious.

    I have been trying to think of possibilities for how what you are 
trying to do could be of use in a Bioinformatics world. Visualization 
programs are very important, but there are now a fair amount of them. In 
this case, sequences anywhere from 10-100 letters are 'aligned' to 
nearly the exact or the exact sequence occurring in a genome, which is 
itself a very, very large sequence, or groups of sequences.

   I think a desktop application would be my ideal. Just how far I get 
into it will depend on how much I am doing at work. :-)

Matthew

On 10/15/2010 6:36 PM, DJ Ortley wrote:
> Matthew,
>
> Regarding Python, it seems to be growing as the go to language in many 
> areas of science.  I think a lot of this has to do with the fact that 
> its a fairly easy language to learn and libraries such as numpy and 
> matplotlib (which produces some beautiful plots) are getting fairly 
> mature.  If you haven't checked it out, you should check out Dive Into 
> Python (http://diveintopython.org/), which you can read through for free.
>
> I honestly don't have experience with zoomable applications.  I can 
> guess at what they're like to work with, which is why I told you about 
> what I was working on.  While not 'zoomable' per se, the technology 
> that I'm developing might be helpful.  One of the things that I have 
> in the database is a vector of word positions for every unique word 
> (after being normalized, made to be upper case, punctuation removed, 
> etc..)  So, the database can be queried for the phrase 'The Eucharist' 
> in the Catechism and it will return two vectors of word positions 
> which can be used in visualization and whatnot.  This is all in 
> PostgreSQL at the moment.  I assume you're thinking of building a 
> desktop application, or are you thinking of a web app?  Or do you 
> know? (btw, my background isn't in software either, I've just been 
> doing it for a long time, I'm actually an Electrical Engineer.)
>
> -DJ
>
> On Fri, Oct 15, 2010 at 3:47 PM, Matthew McCormack 
> <mccormack@... 
> <mailto:mccormack@...>> wrote:
>
>      Hi DJ,
>
>        Thanks for your e-mail.  I don't know if I could be of much
>     help. To me it looks quite complicated. My training is in
>     biochemistry and I have learned a little Perl (and some HTML, SQL,
>     and a tiny bit of Java) to write simple perl scripts.  Even though
>     Python use is growing rapidly in my field, I am not very familiar
>     with it and have never really used it.  I basically program to get
>     some simple thing done such as processing a very large text file
>     list, and am not a very eloquent programmer. As long as it works
>     it is all right with me, and my scripts most likely use many more
>     lines than a 'real' programmer would use. I do get a fair amount
>     of 'stuff' done with Perl scripts, though.
>
>       I put up the project at Cathnet to see if anyone who had a
>     greater programming expertise could steer me in a direction in
>     which they though would be helpful. Zoomable applications are out
>     there, and in my naivete I thought it may be easy to zoom on text
>     files. However, it seems that all the zoomable apps use images to
>     zoom on and so that would make interaction such as typing a
>     command that would highlight a particular section of the text
>     impossible.?  Right now, I am thinking of trying to make image
>     files from a pdf and then using Microsoft's DeepZoom. I would have
>     to make a separate Deep Zoom file for everything I wanted
>     highlighted though, but it may get some done that I could use.
>
>     Matthew
>
>
>
>
>     On 10/13/2010 10:04 AM, DJ wrote:
>
>         Hey, welcome to Cathnet.
>
>         I saw your project and it makes me think somewhat of a project
>         that I've been working on behind the scenes for the past few
>         months.  The reason I haven't created a Cathnet project for it
>         is because I've been wanting to actually produce an alpha
>         version of my idea before publishing what I've been doing.  I
>         didn't want to start a project for something that I might
>         never get past the basic level of producing.
>
>         My idea was to produce a search engine that did fuzzy
>         searching and produced a list of ranked documents according to
>         the search.  Once you selected a document from the search
>         results, you would be navigating the document with a
>         persistent bar across the top or side of the screen that shows
>         the search results using a dispersion plot (see
>         http://nltk.googlecode.com/svn/trunk/doc/book/ch01.html and
>         look at figure 1.2, but imagine it being fixed in height and
>         with a bit of massaging of how the information is presented.)
>
>         Let me know if you wanted to collaborate.
>
>         -DJ
>
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