bioroebe (0.0.132)

This project is called BioRoebe. The name insinuates that it has to do with "bio"-sciences - biology, genetics, bioinformatics. In other words, this project tries to collect useful Bioruby-related code - in Ruby. It is thus similar in spirit to the BioRuby project, but deviates from it in that it attempts to provide convenient solutions for many of the problems faced by molecular biologists on a daily base - in other words, this is a "tool"-set project. The focus between the two projects is not completely identical. The primary goal of Bioroebe is to provide "finished" scripts that can be used, as much as that is possible. We will try to make - and gather - tools available that can be used and applied in order to solve LifeScience related problems. In Ruby code. Of course you may also add your own solutions, so this really is an attempt to have a larger set of tools brought together eventually. The project was released in early 2013, so bear with me as I will slowly improve it. It should eventually be sufficiently useful to solve bioinformatics-related problems. Additionally, it tries to work as a "trainer" to teach people how to learn more about datasets used in the life sciences in general. This is the second focus of this project - a tutorial. An additional focus of this project is to provide the core-functionality available through BioRuby so that the two projects could, in principle, be used interchangably. Note that this is "on-going", we are not quite at this point yet. But in principle, if you work with BioRuby then you also should be able to convenientrly map towards BioRoebe, in a very convenient and simple manner without requiring any big change to your projects. Cooperation is a laudable goal, is it not. If you have suggestions on how to make this project more useful, please feel free to write an email with the specific points to work on. Do note that eventually it will be hosted on github. Changelog Summary for the more important points: Version 0.0.7 added a simple frameshift module, in where we can apply a frameshift event on our target sequence. Version 0.0.11 up to version 0.025 improved the help-menu section, and added class Punnet, which attempts to calculate the Punnet frequencies. Version 0.0.28 up to Version 0.0.30 added a simple calculator for calculating the melting temperature of a given DNA string and improved the documentation of the project. In September 2014, we also added Readline completion support. As of August 2015 we have also included the Taxonomy module into this project. The Taxonomy project allows us to mirror the NCBI Taxonomy database, and interconnect this dataset with local data. If you have specific suggestions to make this gem more useful for others, please drop me an email at: shevegen@gmail.com Thank you.
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