Bioinformatics library + Name Origins?

[Tyler Backman]

Are you guys fans of the author Neal Stephenson? In his novel Anathem, an Incanter is a person who can alter reality at will because they understand the timeless mathematical nature of the universe. Might this be the reason for this softwares name?

I just discovered Incanter today and am very excited.... I am a graduate student developing software for drug discovery in R, and think Incanter has great potential as a bioinformatics and cheminformatics language. I may experiment with developing some simple bioinformatics libraries for Incanter- first for the import and export of common file types.

I think it would be good to replicate many of the features of Bioconductor, but I need to think about how best to do this in a lisp-like way. Any suggestions?

[Mike Anderson]

On Friday, 12 April 2013 06:14:50 UTC+8, Tyler Backman wrote:

Are you guys fans of the author Neal Stephenson? In his novel Anathem, an Incanter is a person who can alter reality at will because they understand the timeless mathematical nature of the universe. Might this be the reason for this softwares name?

I always though it was a play on the word "Incantation", meaning a magical spell made with words - http://en.wikipedia.org/wiki/Incantation

 

But if it has more meanings and allusions then I'm delighted to hear!

I just discovered Incanter today and am very excited.... I am a graduate student developing software for drug discovery in R, and think Incanter has great potential as a bioinformatics and cheminformatics language. I may experiment with developing some simple bioinformatics libraries for Incanter- first for the import and export of common file types.

Go for it! I'd encourage you to check out core.matrix as well, which is an emerging high performance back-end matrix library. I hope at some point soon it will be possible to run Incanter on top of core.matrix.

 

If you see specific features that would be useful in core.matrix for bioinformatics, I'd be very interested to know so that we can consider them for addition.

I think it would be good to replicate many of the features of Bioconductor, but I need to think about how best to do this in a lisp-like way. Any suggestions?

My suggestion would be to think hard about how to break down the features into the simplest possible operations. The "Clojure way" is often about composing simple functions in powerful ways. Obligatory viewing: http://www.infoq.com/presentations/Simple-Made-Easy

[Ben Mabey]

On 4/12/13 7:42 PM, Mike Anderson wrote:

On Friday, 12 April 2013 06:14:50 UTC+8, Tyler Backman wrote:

Are you guys fans of the author Neal Stephenson? In his novel Anathem, an Incanter is a person who can alter reality at will because they understand the timeless mathematical nature of the universe. Might this be the reason for this softwares name?

I always though it was a play on the word "Incantation", meaning a magical spell made with words - http://en.wikipedia.org/wiki/Incantation

 

But if it has more meanings and allusions then I'm delighted to hear!

It is indeed a nod to Anathem.  In the early days of clojure there was an Anathem meme going around and a number of libraries were named after things and characters in the book. (Avout seems to be one of the only ones remaining http://avout.io/.. there was at one point an Orolo and an extramural.)  The Neal Stephenson influence doesn't stop with just Anathem though: http://blog.fogus.me/2011/11/15/the-macronomicon-slides/

I haven't been to a ClojureConj since the first one but there were plenty of Anathem references then at it as well. :)

-Ben

[Tyler Backman]

On Friday, April 12, 2013 6:42:15 PM UTC-7, Mike Anderson wrote:

My suggestion would be to think hard about how to break down the features into the simplest possible operations. The "Clojure way" is often about composing simple functions in powerful ways. Obligatory viewing: http://www.infoq.com/presentations/Simple-Made-Easy

Thanks, That's very helpful information. I can see how some of the existing bioconductor packages already have interfaces which work with this paradigm and some do not.

I am really excited to write data analysis libraries entirely in the same language we do the analysis itself in. I really love R, but I think having to write many of the packages themselves in C for sufficient performance makes it take much longer to develop new R packages.

I can see that writing functions to handle large sequencing data efficiently will be one of the most challenging issues, but I'm more in need of functions which can handle small molecules, and biochemical pathway data.

On Friday, April 12, 2013 7:31:24 PM UTC-7, Ben Mabey wrote:

In the early days of clojure there was an Anathem meme going around and a number of libraries were named after things and characters in the book. 

Well I think I've found the right place then, this is one of my favorite books! I've heard that Neal Stephenson is himself a LISP programmer.