Re: [DIYbio] Re: Open source web sequence/plasmid viewer/editor components?

Blackboxing is fine if there is no alternative, but I would say there should be effort to actively try and 'unbox' these items/processes. The mini-prep might have been discovered by academics, published on, then improved by commercial industry... only to later be dissected by academics again when they were trying to improve/reverse-engineer things. (the reverse-engineering effort is supposed to be saved by patent disclosure... but... well... we all know those have their issues in practice and in society)

Science is definitely about being open and well documented, so things can be reproduced. Good, well quality-controlled black boxes can still fit in to this pipeline and accelerate the time-to-success of an experiment.

 

Which can be a MAJOR problem if the company that produced a closed-source/blackbox kit goes bankrupt or gets bought by another company that then discontinues that kit with no alternative. For all we know, the magic "spells" in children's cartoons that call for "frog extract" could have actually worked, at some historical time with some historical and specific frog and a specific extract technique. For the present-day though, this is just a junk recipe that we all "know" is fake/fictitious. (will the biochemists who did their PhD dissertations on magic frog-guts extract please stand up!)

I think the big difference, as a scientist/engineer is whether the solutions available meet my needs. As a decent programmer (and so called software engineer, by day, these days) I can tweak software to add new features sometimes within minutes of getting the source code. This is not happening with any decent commercial software tool through feature requests unless you've got thousands of dollars on the line and are willing to make it well worth their time. Pretty much the same thing about new features that are specific to your workflow, or maybe are experimental ideas. Another issue which I can attest to is, what if you have some technique which doesn't integrate with existing closed-source tools, and which you cannot even PAY the closed-source company to help you with, because you don't want to risk leaking ANY details about your own Intellectual Property.

I was just tweaking some open-source scientific simulator GUI code last night, it felt really good.