1. Open Source does not preclude commercialization. You need to choose the appropriate license. The reason companies buy software is to get support, custom patches, more input into the dev cycle etc. There is an entire, well established model on how you can make this work.

2. The one problem with niche software is that it requires you to have licensing fees, the kind no one is willing to pay which is why scientific software companies do not usually make money for most algorithmic software (you can make money on platforms, data management solutions, etc). This makes open source even more attractive really as it broadens out development and results in better code. Think of CHARMM. I think one reason the software has not evolved in quality (it has had oodles of algorithms thrown in) is because it's not open source. IMO the benevolent dictator model works really well in these cases

It is also an unfortunate by-product of closed to non academics cases that “hobbyists” and non-profit users get caught in the crossfire , there is nothing worse than alienating the motivated.

But my point still is that , to demand or even expect academics to adopt open source because of funds coming from the public is unrealistic and impractical.

From my own experience , the best crystallography software I use happens to be split down the middle, 50% of them are closed source and non-free for non academics and the rest of them are free and open source. The going is equally good for both of them and I cannot live without either. I would never expect the non-free software to adopt the model of the free, because what they have going just works! If I have to stop using the non-free version because I move to a non-academic setting , then so be it! , I still have the free version to fall back on.

I think the best way to persuade academics to adopt open source is to adopt a “Gandhian” attitude to persuasion. Contribute selflessly and hope they see the point. If you are a hobbyist, I would email the author and request him to allow you to use it. If the email works great, if not just sit back and hope the software gets liberated sometime soon, or better yet fund an open source alternative.

Okay realistically this is not going to happen but given that the interest of the researchers is in having the software used, and in finding a way of keeping it supported surely it would be preferable to allow it to be available for any non-profit use? The more people using it the more likely it is for them to come up with something that might turn a profit – limiting use to people who have neither the time nor the inclination to actually make it useful seems farcical.

And of course, open sourcing it would be be even better in this regard

1. Open Source does not preclude commercialization. You need to choose the appropriate license. The reason companies buy software is to get support, custom patches, more input into the dev cycle etc. There is an entire, well established model on how you can make this work.

2. The one problem with niche software is that it requires you to have licensing fees, the kind no one is willing to pay which is why scientific software companies do not usually make money for most algorithmic software (you can make money on platforms, data management solutions, etc). This makes open source even more attractive really as it broadens out development and results in better code. Think of CHARMM. I think one reason the software has not evolved in quality (it has had oodles of algorithms thrown in) is because it's not open source. IMO the benevolent dictator model works really well in these cases

It is also an unfortunate by-product of closed to non academics cases that “hobbyists” and non-profit users get caught in the crossfire , there is nothing worse than alienating the motivated.

But my point still is that , to demand or even expect academics to adopt open source because of funds coming from the public is unrealistic and impractical.

From my own experience , the best crystallography software I use happens to be split down the middle, 50% of them are closed source and non-free for non academics and the rest of them are free and open source. The going is equally good for both of them and I cannot live without either. I would never expect the non-free software to adopt the model of the free, because what they have going just works! If I have to stop using the non-free version because I move to a non-academic setting , then so be it! , I still have the free version to fall back on.

I think the best way to persuade academics to adopt open source is to adopt a “Gandhian” attitude to persuasion. Contribute selflessly and hope they see the point. If you are a hobbyist, I would email the author and request him to allow you to use it. If the email works great, if not just sit back and hope the software gets liberated sometime soon, or better yet fund an open source alternative.

Okay realistically this is not going to happen but given that the interest of the researchers is in having the software used, and in finding a way of keeping it supported surely it would be preferable to allow it to be available for any non-profit use? The more people using it the more likely it is for them to come up with something that might turn a profit – limiting use to people who have neither the time nor the inclination to actually make it useful seems farcical.

And of course, open sourcing it would be be even better in this regard

* since he had no interest in further academic work — only in the knowledge gained and the signaling mechanism thereto — grad school is vastly expensive for that purpose
* interesting parts of the field are so immature that huge chunks are accessible to the motivated amateur: eg hadoop, command of the baseline machine learning toolkit
* armed with those tools, he can get a job to fill out his toolbox at a bioinformaticist's salary rather than at a grad student's salary
* much of the interesting research done on the computer-engineering end of bioinformatics is done in a commercial and not academic setting

It's frustrating to be reminded of the many petty obstacles to amateur science — not only academic-only software with no carve-out for the amateur scientist, but lack of access to journals and all the rest.

Imagine if we had to prove our bonafides to contribute to Linux or view its mailing lists?

That said open source works and works very well, there is no denying it. Numpy/Python, R , Ruby on Rails etc succeed because they are open source and quite universally applicable. Its a different matter to open source a niche application that which is used by a small group of people. I dont think its fair to expect the same model to translate to other platforms or software.

Although I can see your point that setting things free guarantees their long term survival , helps keep quality up etc etc , it rarely pays the bills! Accordingly, I think the biggest way to encourage open source is to start contributing to projects , and hit those paypal buttons everytime an open source projects makes your work easier. I would rather do that than expect academics or government funded projects to give things away everytime.

This half-way model is the one I have always had problems with and more now than ever. It also results in academics not appreciating open source.