Bioinf @Bugaco

Bioinformatics section hosts tools that are useful to biologist. The Clusterer is a tool that does cluster analysis based on aligned sequences in Fasta format. More... The ChimeraBuster is a tool that finds putative chimeras in set of sequences. More ... The PhysioMapper is a dead project that attempted to allow mapping physiological properties on phylogenetic trees. Current database is at this location, but we are not updating it any more. If we find people interested in populating the database with significant data, we may find it interesting to restart the project. Sequence conversion utility is newest addition to Bioinf @Bugaco, and it features conversion between most popular sequence formats, including FASTA, GenBank, NEXUS, and less well known ones such as Stockholm. To find more about the tool visit Sequence conversion home page.

Analytics @Bugaco

Another one of the projects is analytics.bugaco.com. Google Analytics is a great tool, and I use it on all of web sites I have control over, but reporting using google analytics is non-trivial task for non-most-common reports. Analytics.bugaco.com will attempt to rectify this by providing set of reports that will augment reports provided by Google Analytics. After careful deliberation and reading ... article, I decided that analytics.bugaco.com should be GPL-ed library, with additional restriction that if you use analytics.bugaco.com source code to serve outside of your company firewall you must make source code available free of charge.

Documentation @Bugaco

To be able to find documentation for your favorite project may sometimes be a hassle, and given that Google is the ultimate search engine to find such things - a good question is - why not put them online and google for them? Well, some of my favorite projects don't have documentation online, so I posted it here.
7zip is an awesome compressor and decompressor. After I discovered it, I install it as soon as I get a new machine, but some command line options are less than intuitive and finding a help is not always trivial. So, 7zip documentation is available on this site.
worldwind is another great project, it is NASA project for exploration of terrains. I played with it, but I found it non-trivial to find their javadocs, so javadocs from the projects are available here.
GenePattern from Broad institute is a nice workflow/bioinformatics tool that is also lacking a public access to their javadocs, so I found it useful to place it on the site.

Games @Bugaco

There is a 2 simple java games written about a decade ago. They are also available here, and they are addictive fun to play. Click-o-mania and Cyclick-o-mania are applet clones of the same windows game, so that people can enjoy them on the web.

Java Flash Library @Bugaco

There are some other projects that I play with occasionally.
One of the projects is jflvlib, an library that allows you to generate Flash Movies from your java code. Reason for writting this library is to allow me to generate movies from scientific simulations. It is mildly popular, and it's hosted on SourceForge.net - check it out if you are interested in this type of the library, it has very simple API.