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Will open science change chemistry?

chemistryworld.com

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Re: Will open science change chemistry?

#11

Post by slashdave »

0cf8612b2e1e wrote: post #7

This article conflates a lot of different “open” ideas. Open access journals, machine readable datasets, standardized data representation, open community engagement, etc. Each of which is challenging on its own, let alone hoping to tackle all at once. Chemistry has the blessing and the curse of being an older disciple. Fundamentals have not changed in decades. If you grab an organic chemistry text from the 70s, I gue…

We already have standardized, digital chemistry reaction libraries (reaxys, scifinder). They cost money, but are heavily used by organic chemists.

Re: Will open science change chemistry?

#12

Post by 0cf8612b2e1e »

slashdave wrote: post #11
0cf8612b2e1e wrote: post #7

This article conflates a lot of different “open” ideas. Open access journals, machine readable datasets, standardized data representation, open community engagement, etc. Each of which is challenging on its own, let alone hoping to tackle all at once. Chemistry has the blessing and the curse of being an older disciple. Fundamentals have not changed in decades. If you grab an organic chemistry text from the 70s, I gue…

We already have standardized, digital chemistry reaction libraries (reaxys, scifinder). They cost money, but are heavily used by organic chemists.

More the focus on open libraries. I am not aware of anything of significant size, but I have not been in the space for a while.

Re: Will open science change chemistry?

#13

Post by slashdave »

0cf8612b2e1e wrote: post #12
slashdave wrote: post #11

Earlier quoted context omitted.

We already have standardized, digital chemistry reaction libraries (reaxys, scifinder). They cost money, but are heavily used by organic chemists.

More the focus on open libraries. I am not aware of anything of significant size, but I have not been in the space for a while.

There are attempts.

https://open-reaction-database.org

Re: Will open science change chemistry?

#15

Post by adastra22 »

slashdave wrote: post #13
0cf8612b2e1e wrote: post #12

Earlier quoted context omitted.

More the focus on open libraries. I am not aware of anything of significant size, but I have not been in the space for a while.

There are attempts. https://open-reaction-database.org

Is there any open-source structure-based search?

Re: Will open science change chemistry?

#16

Post by Qem »

Unfortunately computational quantum chemistry still dominated by proprietary software, like the infamous Gaussian. It seems physicists have better open source tools and culture,by comparison.

Re: Will open science change chemistry?

#17

Post by ekianjo »

ahaucnx wrote: post #9

I'm a strong proponent of open data but I think it needs to go beyond science. Companies should also be incentivized or even required for keeping designs, data, interfaces etc. open. Because often scientists are reliant on devices and data platforms that restrict ownership. So even if the scientist wants to keep his data open, a product or a service that the scientist uses for his research might prevent this.

> Companies should also be incentivized or even required

required sounds bad because you make the costs higher and prevents small companies from entering the market once its too much. as for incentives any idea on how that could work?

Re: Will open science change chemistry?

#18

Post by StableAlkyne »

Qem wrote: post #16

Unfortunately computational quantum chemistry still dominated by proprietary software, like the infamous Gaussian. It seems physicists have better open source tools and culture,by comparison.

Gaussian's main advantage is the GUI!

If you need a gaussian basis set code, nwchem exists! Orca is another one.

If you need a plane wave code but don't want to shell for VASP, Quantum Espresso is awesome, and easy to compile.

Then there's CP2k, whose gaussian basis with planewave auxiliaries are pretty decent at molecular dynamics boxes.

And to set up structures in a GUI, Avogadro is very useful for molecules. VESTA is great at crystals if you are willing to do a little math. And in Python, ASE and Pymatgen will do everything else that the GUI can't.

Don't get me wrong, Gaussian is a fantastic program, and their developers deserve every penny - but there's no scientific reason you can't use free codes!

IMO, the big limiter to open science in computational chemistry isn't the codes. It's the lack of computer power the average consumer has.

Re: Will open science change chemistry?

#20

Post by VygmraMGVl »

galleywest200 wrote: post #10
gorpy7 wrote: post #8

I think it’s okay if people take responsibility for their actions, to take risks known or unknown. It’s okay to live in a world where we’re not entirely insulated from negative consequences. Ive always been bummed by how inaccessible chemistry is.

Back when I ran a maker-space in Seattle we interviewed this dude who had a full bio-safety rated lab in his garage. I wish to see more of that stuff!

SoundBio is a bio + chemistry makerspace in Seattle. Not BSL, though.
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