Dreaming of a free VectorNTI alternative…

It’s a pitty. Nearly every piece of software you can get free (as in beer) and open source and esspecially in science the idea of open and free software was always strong.

However, despite the huge success of public open-source projects (firefox, linux, libreoffice) there is still a good bioinformatic suite missing for scientist.

There are a very good commercial solutions (VectorNTI), which are very expensive and others which are less sophisticated but still expensive (Geneious, CLC Bio etc).  A few attempts are respectively were made to make free solutions (ApE and pDRAW32) but they often lack the “suite”-approach and tackle only a few problems a scientist has to work with everyday. So having named all this software choices, some might ask “What the hell is he asking for?”.

Well in principle I’d like to have a simple, open and expandable swiss army knife for cloning, sequencing, annotating and managing of protein and DNA sequences. Perhaps on the basis of Bioclipse or perhaps based on it’s on framework. The suite would access its data from a database which might be locally or remote. It would draw plasmid maps and proteins sketches and synchronize selections with a sequence view. It would help cloning fragments from one vector into another, and it would keep track of its actions (probably even able to recreate them). It would compare sequencing data with the newly generated constructs and store them together. It would be easy to expand by plug-ins or extensions to do fancy analysis like phylogeny or PFAM searches. … and it would be all free and maintained by us – the scientific community.

Some well-informed fellows might now say “Wait! There is Gentle which ticks (nearly) all of you boxes!” and I only have to disagree slightly. Gentle is definitely very close to my dream, and as much as I appreciate Magnus work (he invested a lot of time) I have to say it’s unfortunately not very modular and it got a little bit cluttered with stuff which would be better in an extension or an external module. But sure it would make a great starting point.

So how could this dream become true? Well firstly of course I hope many people read this post, secondly a few might add their idea to the comments, and maybe at some time we get the critical mass to actually start such a project… hope springs eternal …