One of the often occuring task in my work is to present results of an analysis in some kind of table. I have used for such purpose quite a number of approaches, starting from generating simple HTML file, through fetching of SQL data into table stored in a wiki, up to using Rails. One of the dreams I have recently is a web-based spreadsheet that would allow me to apply some specific piece of code over every row/column and show resulting table.
A simple mockup is shown above. In this example, a code:
print " <img src="http://www.pdb.org/pdb/images/#{column_1}_bio_r_250.jpg>"
… iterated over first column containing PDB codes, would substitute these codes with an image of a protein from PDB server.
In other words I dream about simple (single file would be the best – I like the approach Sinatra framework is taking) web-based programmable spreadsheet. Something like Resolver One, but simpler. Is there anything like that available?
Freelancing science 
Marcin Cieslik
May 19, 2009 at 16:10
So data is in rows and columns are “transformations”. Why do you think this is superior to a flow-chart with vector(i.e. rows) input?
Burke Squires
May 20, 2009 at 18:18
I am not sure is this fits the bill…but some folks at the EBI have created a java-based platform for data storage and annotation. It is called ISAcreator and can be found here:
http://isatab.sourceforge.net/isacreator.html
Burke
Tyler
May 23, 2009 at 22:30
It seems like you could probably throw something together with dabbleDB that would fit the bill…
Bogdan
June 5, 2009 at 10:56
I’m mostly stuck with Python doing this kind of things. Each time I just copy over the older script, change the number of items parsed from a single line of data file, and then change print statements 🙂
That’s fairly easy, but I guess this could be extended to a more-or-less universal script, counting columns on its own, and accepting string parameters with $1, $2 … embedded to denote column contents.
Also, there’s awk (gawk), which I guess could do the job best, but my knowledge of gawk is limited to simple column extraction, like
gawk '{print $2"\t"$5}' datafile.tsvBogdan
June 5, 2009 at 10:57
oops, missed a closing ‘ after right curly brace above
Pawel Szczesny
June 22, 2009 at 13:28
Thank you all for the comments.
Marcin, it’s all about presentation to the non-programming colleagues and looking for possibility to avoid Excel files :).
Burke, thanks a lot, I wasn’t aware of ISAcreator. Need to have a look.
Tyler, duh!, DableDB 🙂 I’ve used it so long ago I forgot about its existence.
Bogdan, I have a similar workflow (but use Perl one-liners instead of gawk) however as I pointed to Marcin, it’s the “presentation” part that dictates other requirements :). I’ve corrected your gawk snippet.