Monthly Archives: December 2008

Resolver one – Pythonic spreadsheets

Everytime  I have struggled with syntax in Excel  I have always longed to break free from the tyranny of its visual basic syntax. Although very powerful, excels formulae and their complex mix of parenthesis , square brackets , dollar signs and brackets always had me wishing that spreasheets spoke a language with a more readable syntax.  When I first heard of Resolver One a pythonic spreadsheet on Jon Udels blog I couldn’t wait to try it out. I finally did just that .

This is kinda like my hello world of Resolver One spreadsheets . In this spreadsheet I play around with a few things I have struggled with in Excel. String manipulation: the bread and butter of Bioinformatics analysis , formatting and column formulae involving regular expressions  and finally  conditional formatting . Although resolver one exists mainly for windows platforms , I do run  it with both Parallels on my mac and on Windows Vista computers i have access to . The spreadsheet is fairly snappy , but does slow down if you have a large number of cells ( when I had a 2000 sequences and 9 columns , it did take almost a minute to recalculate )

Resolver one I feel could potentially provide the user interface I always needed when interacting with data produced by my python programs. Since most data is very amenable to the spreadsheet setup , I see this being a very nifty tool in my informatics aresenal.

For now you can find my spreadsheet at this URL and watch the screencast at its full resolution on bioscreencast.com at this URL.

The video embed below does not seem to work, only has audio , please check out the video URL and on the bioscreencast.com URL

Why does the java plugin installation have to be so convoluted

I have written in the past on my frustrations with the mess that is 32bit browsers and 64 bit plugins. I was desperately trying to get a java web start application to play on my 64bit ubuntu linux box. I of course imagined that upgrading java to java 6 update 11 would be the way to go to get java installed on my computer . 

So I navigated to the extremely “streamlined and user friendly”  ( please I am being sarcastic) sun java download site and proceeded to download that update . Now despite having done this many times before , it amazed me as to how convoluted the whole experience was.  First there was the whole java , java EE ,jre , java sdk mess ..but since I knew all I wanted was the jre I went ahead and installed the java 6 update 11 package. You would think , that would include the java plugin , but as far as I could tell there was no plugin. No where in the docs was there any mention of the plugin . No where on their site was there a link or indication that I could get a package with the plugin and jre.

So I went about trolling through the many pages at Sun and elsewhere  on the web , looking for the plugin. Finally I found a site outside of sun that seemed liked something out of a phishing exploit , as far as its colors and overall look and feel . The site called java tester offered to check my plugin version and install the plugin. Of course I was desperate and I clicked yes . Lo and behold , java got installed fine and I was happy to have the few test applets on that page and other sun pages work fine after that. So thanks to java tester a non sun site , I could actually get a working plugin on my browser . You would think Sun would design a more user focused java site to push its plugin out . But I guess we may have to wait for another few years. So with a working plugin I thought I should be there.. Nah not really.

So now onto the webstart application . I clicked on the link , saw the java process startup ..and then nothing happened . I did see the jnlp “download”  and try to get started ..but then all activity ceased and  the starting message vanished into bitspace . So I assumed it must be the whole 32bit browser , 64 bit plugin mess again and decided to switch machines and try the webstart application on Safari in OSX on a new Mac Pro which I knew was 64bit all the way. This time the java webstart application did start and install an icon on the dock telling me that it was running. 

Of course the famous java application incompatibility/bug with putting menu items on the OSX dock prevented me from actually using the application. 

This whole experience has soured me enough to write this post. I really think java gets  lot of un-warranted bad PR , but trust me for a 12 year old platform I would expect to see more streamlined user experience that the mess that is currently java plugins , webstart and applets. And amidst the rumblings of sun bleeding engineers to Adobes Flex/Flash RIAA platform I wonder if java fx is the messiah that we all await.