bioroebe (0.0.396)

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, BioRuby and BioRoebe, is not completely identical. The primary goal of Bioroebe is to provide "finished" scripts that can be used, as much as that is possible. Users should not require to write new code - or, in the case that this can not be avoided, they should be able to make it a simple as possible to write said code, if it taps into the problem domain of "Life Sciences". The scripts which are part of the Bioroebe project, should also ideally be decently well documented and explain what they do. That way, a user can find out why something has been written in that way. The Bioroebe project will try to make - and gather - scripts that that can be used and applied in order to solve LifeScience related problems. In Ruby code, primarily. C may also be an option at a later time. 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, for the whole ruby ecosystem. The Bioroebe-project was first released in early 2013, so bear with me as I will slowly improve on it. As you can see from the releases, it has been steadily growing in size. And hopefully, it has also grown in regards to usability, quality and usefulness. 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. Teaching other human beings. Yet another, 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 conveniently map your scripts towards BioRoebe, in a very simple manner, without requiring any big change to your project. After all, cooperation is a laudable goal. Do note that eventually the whole project will be hosted on github as well, but until that happens, bear with me here on "good old rubygems.org". In the past two or three years, there used to be a changelog summary, but I feel that most people will not really care about a changelog, so this is no longer shown here. Readline completion support is available since as of September 2014. As of August 2015, the Taxonomy project was included into this project. The Taxonomy project allows us to mirror the NCBI Taxonomy database, and interconnect this dataset with local data. This still requires some changes, which I assume will be finished in the course of 2016 or early 2017. As of Jan 2016, the "EMBOSS compseq tool" has been partially copied. You can invoke this by doing "compseq" in the interactive menu. For more help options, run "help" in the BioShell. If you have specific suggestions to make this project more useful, please feel free to write an email to me with the specific points to work on. shevegen@gmail.com Thank you.
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