I think that equating "It just pastes sequences together" to "I just extracted teh DNA" to be flawed logic. Saying "the cloning was simulated with snapgene 3.1.2" is just about as good as saying "the DNA was extracted with the Qiagen miniprep kit", in which the latter is sufficient for a user to go and find out how the protocol was done (and vice versa). When a miniprep is done with 2 different kits, the outcome can be very different. When I paste sequences together, it doesn't matter if I did it in snapgene, GENtle2, notepad, or vim. All give the same outcome. To replicate my work, you can even do the cloning by hand for all I care, all I need to give is primers and sequence, which are both in text format. Putting DNA through proprietary software won't change the inherent text in anyway so that I couldn't replicate them in free open source software. It's just quicker.
On Sunday, April 17, 2016 at 4:54:36 AM UTC-7, Cathal (Phone) wrote:
-- I love open source software, and would jump to using it if there was a good alternative. Both the above open source softwares mentioned either 404ed or haven't been updated in months. Meanwhile, if I find a pragmatic issue in above mentioned proprietary software, I can email the support team, get a reply back in an hour, and get the fix within a week. This allows me to focus on experiments rather than coding software.
It's not worth my time to figure out software to efficiently simulate cloning of DNA because the outcome is the same. I fully agree, if the outcome is changed by math involved, it ought to be open. But cloning with snapgene, benchling, genomecompiler, ApE, or any other proprietary software doesn't do anything different than cloning with GENtle2, AngularPlasmid, or DNApy. I care more about doing science than I care about the license of my software that does one thing. Is that really a bad thing?
-Koeng
On Sunday, April 17, 2016 at 4:54:36 AM UTC-7, Cathal (Phone) wrote:
More like "Should scientists be allowed to redact portions of their materials/methods chapters".
This isn't about the license, though asa separate issue I firmly believe that proprietary software is harmful to users' freedom and self-determination. Ignoring the liberty of scientists, is a piece of software were proprietary but the source code were available to all for inspection (which is *not* considered "open"), that would still be barely, slightly acceptable to the scientific process.
When the source code remains secret, then an entire section of the scientific process is sliced out of peer and piblic review, effectively a black box we're all supposed to trust. And, to replicate work, downstream scientists are also supposed to trust it, too.
Even when the workings of that black box are supposedly transparent ("It just pastes the sequences together!") it's as unacceptable to a scientific ethic as saying "I just extracted teh DNA": the methods matter to the scientific process and legacy.
So, yes: secret processes and methods have no place in science. Whether a crappy secret miniprep protocol or a crappy secret software platform.
...and if it's not secret, I still say reject if if it's proprietary, but that is a separate disussion riddled with human rights and general ethics questions, not a pure scientific process question.On 17 April 2016 05:05:43 IST, Bryan Jones <bryan...@gmail.com> wrote:While I like open source as much as anyone, I have to agree that it's kind of silly to say that closed source software has no place in science. Should scientists be disallowed from using Windows? If you are doing processing of the sequence (e.g. A multiple sequence alignment) then it's important to know the math that goes into it, but it doesn't really matter if they don't tell you the way that they render the graphical drawings of a plasmid.
On Sat, Apr 16, 2016, 5:20 PM Jake <jake...@mail.com> wrote:> Open is crucial. Secret-innards software has no value to me and has no place in the scientific process.--I'd counter that an exaggerated sense of entitlement and open bigotry like this have no place in science.When someone takes the time and effort to create something for you to use for free, you have no business criticizing the author's choice of license to release it under. Nobody's forcing you to use it. To go so far as to then insult them by saying they have no place in science is really offensive. Having such poor manners is what really has no place in science, and you will go nowhere in it with that attitude.
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