Open Source version of VectorNTI

[Marshall Louis Reaves]

So, Invitrogen did this rather sleazy thing where they got everyone
using VectorNTI because it was free for a long time, and now its not
free, even for academic users.

Does anyone know about any reliable freeware for organizing and
analyzing plasmid sequence data?

Thanks!

MLR

[Mackenzie Cowell]

APE - a plasmid editor

http://www.biology.utah.edu/jorgensen/wayned/ape/

Clotho - iGEM project partially by APE, but with additional features for engineering biobricks.

http://chess.eecs.berkeley.edu/clotho/

EnzymeX from MekenTosj

http://mekentosj.com/science/enzymex/

I personally recommend clotho: http://vimeo.com/2218118

Cheers,

Mac

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[Tom Randall]

On Feb 13, 12:43 pm, Marshall Louis Reaves <marshallrea...@gmail.com>
wrote:

Gentle
http://gentle.magnusmanske.de/
very VNTI-like

BioEdit
http://www.mbio.ncsu.edu/BioEdit/bioedit.html
old, but still functional, even on Windows 7

[J. S. John]

On Sat, Feb 13, 2010 at 12:43 PM, Marshall Louis Reaves
<marshal...@gmail.com> wrote:

Whats the specific nature of the project? I got the older version of
vectorNTI and I wanted to learn how to use it. The lack of a problems
and/or exercises has hindered me.

Is there anything you can outsource to DIYbio members, etc?

Thanks

[Eric]

I just happened to run into your question and must say that this is
one of the primary reasons I started work on my own analysis software.
VectorNTI is simply far too expensive and unnecessarily complicated to
use, illustrated by the fact that training courses are offered at over
$1000 per person. I was never happy with the user friendliness or
capabilities of alternatives, including free ones, so I decided that I
would step out of the lab to start full-time work on my own and get it
right, resulting in QuickGene.

Unfortunately, setting all this up, working on it full-time and
recruiting programmers has cost me quite a bit of money, so it's cheap
but not free. The goal is to make the first decent, modern, affordable
software for molecular biologists and by using a plug-in model, anyone
with Java know-how can contribute. (The documentation and SDK are
still being developed)

I just launched the first version last month, so many capabilities are
still in the works (such as alignments, database support, project
organization, and automated in silico cloning) but it already saves a
lot of time and solves a lot of project planning headaches. In
particular, I'm proud of the very intuitive search capabilities,
sequence statistics, and very extensive restriction enzyme data. I
also wanted to make it extremely easy to use, so that no one needs to
waste time with manuals or training, and you can better spend time
with students teaching science instead of how to use software.

I can understand that this might be construed as a sales-pitch, but I
can only assure you that my heart is in the right place. I'm a
biologist with a passion for genetics who simply got tired of all the
crap we have to work with on the software front. The DIYbio community
is teaming with great ideas on how to improve, and I would love to
hear your opinions and ideas for the solution I'm building.

You can easily download it for PC or Mac (with a Linux beta coming
soon) from the website: http://www.crimsonbase.com/download

Best,
Eric Lammertsma

On Feb 13, 6:43 pm, Marshall Louis Reaves <marshallrea...@gmail.com>
wrote:

[JonathanCline]

On Feb 24, 3:35 am, Eric <e.lammert...@gmail.com> wrote:
> resulting in QuickGene.
> Unfortunately, setting all this up, working on it full-time and
> recruiting programmers has cost me quite a bit of money, so it's cheap
> but not free. The goal is to make the first decent, modern, affordable
> software for molecular biologists and by using a plug-in model, anyone
> with Java know-how can contribute. (The documentation and SDK are
> still being developed)

Can you comment on developing this as an Eclipse SDK/plugin? Or is
it?

--
## Jonathan Cline
## jcl...@ieee.org
## Mobile: +1-805-617-0223
########################

[Eric Lammertsma]

>
> Can you comment on developing this as an Eclipse SDK/plugin?  Or is
> it?
>
> --
> ## Jonathan Cline
> ## jcl...@ieee.org
> ## Mobile: +1-805-617-0223
> ########################

QuickGene is developed in SWT, which is what Eclipse is based on, so
development is somewhat similar. However, it has its own easy-to-use
plug-in system rather than the Eclipse RCP approach. Internally,
QuickGene is already pretty massive, so it's still going to take a bit
of time to put together a clear, robust SDK with documentation. If
there's some genuine interest on getting to work on a plug-in, I could
put some of the currently developing features on ice to kick that into
gear and lay out something usable to get started on. Of course, that
would be absolutely great!

[Dunqiang Liao]

VectorFriends, free for academic researchers. It combines various types of cloning simulations, sequence analysis and data management into one application.

http://www.vectorfriends.com 

[Cory Li]

Benchling (https://benchling.com) is free, pure HTML5 app so there's no installation required. You can check out the demo directly here.

We posted about it just a bit earlier on the DIYBio mailing list. It'll support your plasmid editing needs, as well as sangar sequence trace viewing, basic sequence alignment, primer searching, etc.
Best thing is that it's all online, so you can share sequences with friends and colleagues just via links.

[Cathal Garvey (Phone)]

Hi all,
Bearing in mind the original post's account of being screwed by the originally-free-of-charge VectorNTI, I strongly recommend rejecting software that isn't free-as-in-freedom. Particularly ones using nonstandard formats or which store your data 'in the cloud', meaning they can be taken from you at any time, or spied upon, or simply are difficult to transfer elsewhere with annotations intact.

GENtle 1/2 (which seemingly bear no relation) are good bets. The former is old, unmaintained, and unstable, but quite feature-rich. The latter is a newer webapp, it's true, but it's either Open Source or Free Software (Can't recall), meaning you can host your own for you and your friends and keep your autonomy.

Personally I no longer find these (vector programs) very useful for engineering, preferring a scripted approach, but I'll grant you options in this regard are very limited right now. I'll happily castigate even my own attempt, fastac, as being truly dishusting, but that's what happens when you splice Multi-FASTA with bash scripting..

--
Sent from my Android device with K-9 Mail. Please excuse my brevity.

[Sebastian Cocioba]

SnapGene Viewer works fine for me.

Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC
Plant Biotech R&D

---

From: Dunqiang Liao
Sent: 10/1/2013 12:04 AM
To: diy...@googlegroups.com
Cc: m...@diybio.org
Subject: [DIYbio] Re: Open Source version of VectorNTI

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[DIYBIO Groningen]

I suggest you to take a look to Serial Cloner. It is multi platform and works well.

http://serialbasics.free.fr/Serial_Cloner.html

To view this discussion on the web visit https://groups.google.com/d/msgid/diybio/-3508845007909131620%40unknownmsgid.

[Koeng]

If you use snapgene viewer, believe me get SnapGene, it is so so so so worth the price. I absolutely love it