Benchling - New DNA & plasmid editor for DIYbio & Synbio

[Cory Li]

Hi all,

We didn't really get a chance to introduce ourselves properly the last time we were brought up in a DIYBio thread, so I want to formally show you all Benchling.

Benchling is a free web-based replacement for traditional vector & plasmid editors such as VectorNTI and ApE. You can jump straight to the demo here: https://benchling.com/demo. We'd love for you to check it out! We're actively developing a ton of new features, and we'd be happy to listen to any feedback you guys have.

We think Benchling is great in both DIYBio and educational contexts because it's both completely free and runs in the browser on any machine.

We also think this is pretty exciting from an open science perspective.  You can effortlessly share your sequence data with collaborators _as_ you're working on it by just sending a link.  AFAIK, there's no other tool that allows you to do this, short of getting an accession number and posting it on a database such as NCBI or the parts registry.  As an example, here's one of the sequences I've been working on: https://benchling.com/s/jqIFBG.

Anyways, check it out and let us know what you guys think. Our roadmap is also heavily influenced by feature requests, so we'd love to hear what tools you guys need that would make your lives easier.

Cheers,

Cory

[CodonAUG]

This is real cool, thanks for sharing and making it.

Is there a public database of sequences in Benchling already or do we have to add this stuff ourselves?

[Cory Li]

We're in the process of adding a large number of common cloning vectors to a shared database, so you'll hopefully be able to browse those soon.

But in the meantime, we do have automatic import from large existing databases: NCBI Entrez, The Biobricks Parts Registry, and the JBEI Public Registry.

Just type in the accession number and it'll automatically pull in the sequence for you: https://benchling.com/import

Let me know if that works for you!

[Richard Nyuk]

I'm currently using VectorNTI for most things - it's not amazing, but it works. What's particularly new/different about Benchling that'll make switching "worth it," and is there a non-tortuous way of getting my tens of thousands of plasmids integrated?

[Meredith L. Patterson]

Hi Cory,

Importing the following plasmids by accession number fails:

http://www.ncbi.nlm.nih.gov/nuccore/NC_008502.1

http://www.ncbi.nlm.nih.gov/nuccore/CP000424.1

Any idea what's wrong?

Cheers,

--mlp

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[Cory Li]

@mlp: sorry about that!  Looks like there was a small bug in the NCBI importer that we've now fixed.  CP000424.1 should now import without error. (NC_008502.1 won't work though, since there's technically no sequence data in it -- it's more or less a pointer to CP000424.1).  Let us know if you run into any more issues!

@richard: we do have VectorNTI archive import, so it should be a pretty seamless process if you go into your VectorNTI database and export the entire thing as an *.ma4 archive.  We'll even correctly parse out all the vnti annotation types and stuff.

The biggest advantage of benchling over vectorNTI imho is the ability to rapidly and easily collaborate on sequence data -- a huge issue in one of my old labs was keeping track of all the vnti plasmid files that were being emailed back and forth.  With Benchling, it's much easier since everything is instantly shared with collaborators, and all accessible from the same place.  Also, I'd say our interface is strictly easier to use than VectorNTI (or at least the last version that I used which was admittedly a while ago).  A lot of operations in vnti are quite annoying / a much bigger hassle to do than they should be, ex: editing bases and editing annotations.

Cheers,

Cory

[Meredith L. Patterson]

Hi Cory,

The import widget does find CP000424.1 now, but when I click "Import" it redirects me to https://benchling.com/undefined. The sequence does show up in my library, though. :) Thanks!

Cheers,

--mlp

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[Cory Li]

@mlp -- sorry about the bug! looks like we were handling redirects from database imports incorrectly.  It's just been fixed and pushed live. Let us know if you run into any additional bugs or have any feature requests :)