Posts tagged open source

TIde – systematic identification of optimal drug targets


TIde is developed to systematically run an automated scan and identify drug targets from a kinetic network SBML model. It is still under development but if it does all that they say it will, we will have another addition to the list of the few breakthroughs that has brought more answers than questions. Oh, don’t get me wrong, I am a good fan of the inquisitive mind and all these unanswered questions is what that keeps this field as cutting-edge as it is.

But, it cannot be denied that amidst all this complexity, it is only simplicity that everyone finds interesting.

Anyway, back to TIde, an open source, platform independent tool to investigate ordinary differential equation models; a systematic approach could not only accelerate the drug research, but also save valuable of the time and money (resources that could be used elsewhere).

Good open source software  are the best things that have happened to the programming world.




Untill recently, I was vaguely aware of how powerful a tool Biomart is, but after my lectures and tutorials on Biomart, I have to say, I have become a big fan. The documentation to install the tool and create the database is pretty good, and the huge community to support new programmers is impressive. Plus the plugins and APIs…

This object-oriented data mining system that lets one build complex queries from the underlying databases, and it’s web interface aids non-programmers (biologists) query for data with lesser effort; plus once one has defined what he wants to download using Biomart, he can simply generate an XML file.

I have to accept that the tools isn’t flawless, but hey, it’s open source, we can clean it up ourself. Plus, it should not be overlooked that Biomart has just being around for 6 years and there is still so much work being put into it – most of the mojor issues will be dealt with in their next major release, which they are now re-writing in Java.

I am quiet excited to start some real work on Biomart…

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