4 ms·

About ten years ago I started down this path myself, it just seemed overwhelming though to recreate all the functionality of the desktop systems like Vector NTI

About ten years ago I started down this path myself, it just seemed overwhelming though to recreate all the functionality of the desktop systems like Vector NTI on the web. With today's tools it is likely much better. It does seem as you're alluding to though that a Jupyter like format would work really well. I wonder what the state of the art is today at least on desktop.

jfarlow 10y ago
Unfortunately, software has not much advanced beyond where it was ten years ago. There have been a lot of attempts, but the fact is that it's very difficult to see returns on mass-market scientific software - the market is relatively small compared to the likes of Snapchat. The software tooling certainly makes it easier to make the scientific tools - but you still have to earn enough to support a company (and compete against 'decent' freeware). Desktop software - outside of very custom huge pharma-style companies, or free-ware academic python libraries is a non-starter - as no one will download it. The nicest Desktop software I know of is SnapGene: http://www.snapgene.com/ http://www.snapgene.com/ which has to compete against the ancient (and pretty good) freeware, APE: http://biologylabs.utah.edu/jorgensen/wayned/ape/ http://biologylabs.utah.edu/jorgensen/wayned/ape/ On the web there is YC's own Benchling: https://benchling.com/ https://benchling.com/ Twist (Startup DNA synthesizer) just bought Genome Compiler: http://www.genomecompiler.com/ http://www.genomecompiler.com/ Teselagen for those hardcore genetic engineers: https://www.teselagen.com/ https://www.teselagen.com/ Our own Pinecone: https://serotiny.bio/ https://serotiny.bio/ (styled to be a 'simple' abstraction above the DNA to produce functional proteins while bypassing cloning) And Desktop Genetics (for CRISPR design): https://www.deskgen.com/ https://www.deskgen.com/ The older players (VectorNTI, and-the-rest-I-can't-rememeber) are never updated and likely yet exist to service contracts from huge institutional customers. It's a relatively small (and dispersed) community of users right now. We need a place that scientists actually go to to show off all of our nice shiny new toys. Each comes with their own style and with their own strengths - it'd be fun to showcase them all together.
- jfarlow 10y ago
  Just because it's funny - direclty from Vector NTI's FAQ on their webpage, today, in April 2017: 1. When is Vector NTI Advance™ 11.5 available? Version 11.5 was launched on October 15, 2010. 2. Is Vector NTI Advance® 11.5 compatible with Microsoft® Windows 7? Yes. Version 11.5 is compatible with Windows 7 on 32-Bit Systems - 64-Bit compatibility is currently in development. 3. Is Vector NTI Advance® 11.5 compatible with Mac OS? Yes, this requires Mac OS® X running Windows® under Parallels Desktop® 5 or Boot Camp. https://www.thermofisher.com/us/en/home/life-science/cloning/vector-nti-software/vector-nti-advance-software/vector-nti-frequently-asked-questions.html https://www.thermofisher.com/us/en/home/life-science/cloning...
  - kevinwuhoo 10y ago
    That's absurd! Still the same version I was using when I was in grad school. I've heard that Benchling is a decent alternative. Although few, if any, companies have the marketing and sales resources as Thermo.
- sndean 10y ago
  > The nicest Desktop software I know of is SnapGene: http://www.snapgene.com/ http://www.snapgene.com/ Have to agree with that, though it's a bit expensive.
  - toufka 10y ago
    You're (not even you, your lab is) paying for niche, specialized, professional software - it's not "accounting software" or "photo software" or "chat software". Out of curiosity, how much do you expect professional "genetic engineering software" to cost? Between $270-700 for a permanent license seems like a pretty good deal to me.
    - sndean 10y ago
      > (not even you, your lab is) Well, I had to pay for it out of pocket. Got an annual license. But yeah, I get your point.

jfarlow 10y ago

Unfortunately, software has not much advanced beyond where it was ten years ago. There have been a lot of attempts, but the fact is that it's very difficult to see returns on mass-market scientific software - the market is relatively small compared to the likes of Snapchat. The software tooling certainly makes it easier to make the scientific tools - but you still have to earn enough to support a company (and compete against 'decent' freeware). Desktop software - outside of very custom huge pharma-style companies, or free-ware academic python libraries is a non-starter - as no one will download it. The nicest Desktop software I know of is SnapGene: http://www.snapgene.com/ http://www.snapgene.com/ which has to compete against the ancient (and pretty good) freeware, APE: http://biologylabs.utah.edu/jorgensen/wayned/ape/ http://biologylabs.utah.edu/jorgensen/wayned/ape/ On the web there is YC's own Benchling: https://benchling.com/ https://benchling.com/ Twist (Startup DNA synthesizer) just bought Genome Compiler: http://www.genomecompiler.com/ http://www.genomecompiler.com/ Teselagen for those hardcore genetic engineers: https://www.teselagen.com/ https://www.teselagen.com/ Our own Pinecone: https://serotiny.bio/ https://serotiny.bio/ (styled to be a 'simple' abstraction above the DNA to produce functional proteins while bypassing cloning) And Desktop Genetics (for CRISPR design): https://www.deskgen.com/ https://www.deskgen.com/ The older players (VectorNTI, and-the-rest-I-can't-rememeber) are never updated and likely yet exist to service contracts from huge institutional customers. It's a relatively small (and dispersed) community of users right now. We need a place that scientists actually go to to show off all of our nice shiny new toys. Each comes with their own style and with their own strengths - it'd be fun to showcase them all together.

jfarlow 10y ago
Just because it's funny - direclty from Vector NTI's FAQ on their webpage, today, in April 2017: 1. When is Vector NTI Advance™ 11.5 available? Version 11.5 was launched on October 15, 2010. 2. Is Vector NTI Advance® 11.5 compatible with Microsoft® Windows 7? Yes. Version 11.5 is compatible with Windows 7 on 32-Bit Systems - 64-Bit compatibility is currently in development. 3. Is Vector NTI Advance® 11.5 compatible with Mac OS? Yes, this requires Mac OS® X running Windows® under Parallels Desktop® 5 or Boot Camp. https://www.thermofisher.com/us/en/home/life-science/cloning/vector-nti-software/vector-nti-advance-software/vector-nti-frequently-asked-questions.html https://www.thermofisher.com/us/en/home/life-science/cloning...
- kevinwuhoo 10y ago
  That's absurd! Still the same version I was using when I was in grad school. I've heard that Benchling is a decent alternative. Although few, if any, companies have the marketing and sales resources as Thermo.
sndean 10y ago
> The nicest Desktop software I know of is SnapGene: http://www.snapgene.com/ http://www.snapgene.com/ Have to agree with that, though it's a bit expensive.
- toufka 10y ago
  You're (not even you, your lab is) paying for niche, specialized, professional software - it's not "accounting software" or "photo software" or "chat software". Out of curiosity, how much do you expect professional "genetic engineering software" to cost? Between $270-700 for a permanent license seems like a pretty good deal to me.
  - sndean 10y ago
    > (not even you, your lab is) Well, I had to pay for it out of pocket. Got an annual license. But yeah, I get your point.