Bioinformatics

I've been pushing capabilities of javascript mapping frameworks. There's a real limit on the number of markers a browser can display without getting bogged down. 500 is a good limit, and that's probably too high for internet explorer. You can put as many markers as you like via WMS tiles. You can even take map clicks, send them back as AJAX queries and open an info window. I recently helped my friend do this, and we have a pretty snappy map displaying 5,000+ clickable "markers" no problem. It's actually not markers, just tiles, but it works quite well: That's a snapshot of the google maps application, with an info window that appears when a marker is clicked. It sends a GetFeatureInfo request back to a mapserver WMS. Vector drawing in the browser is limited. The amazing efforts of the OpenLayers , featureserver projects make this difficult to assert, as they abstract away all of the browser incompatibilities and give a nice platform to do real vector edit...

There's a new article out in BMC Bioinformatics with a comparison of the speed and length of programs from various languages. This article was sent to the biology in python ( BIP ) mailing list. Looking at the code, it's not that bad, but it is clear that the authors are not pythonistas, and that the reviewers have done a great job on the actual paper, but likely there was no thorough review of the code. The authors define their own max() function that needlessly overrides python's built-in, and they use the code: line.rstrip('/n') that indicates there was not a thorough understanding of python, or a complete code review. Even a non-python programmer should have seen the intent was to strip a newline '\n', but the operation is not inplace, so the desired behavior could be achieved by: line = line.rstrip('\n') Syntactical mistakes aside, python was given a poor review on speed. Andrew Dalke, of wide-finder (and general python-bio) fame ran the alig...