Even Better Free Molecular Biology Software: Serial Cloner |
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Nick Oswald |
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In 2007, I wrote a couple of articles on the best free software for molecular biologists on Mac and PC. One of the highlights of those lists was a fantastic cross-platform for in silico DNA cloning, sequence analysis and visualization, called Serial Cloner (move over VectorNTI!).
The creator of Serial Cloner, Franck Perez, contacted me recently to tell me that he had just released an excellent new version of the software and asked if I would relay this to our readers. Well, as a big fan of Serial Cloner I am only too happy to oblige.
If you do molecular biology and you haven’t tried our Serial Cloner, I’d urge you to give it a go. It is very intuitive and is packed with features; from basics like constructing importing sequences, constructing plasmid maps and restriction mapping, through more complex things like sequence alignment, Gateway cloning and siRNA design.
Among the many improvements Franck has made in this new version are:
Check it out at http://serialbasics.free.fr/Serial_Cloner.html
10 links: Free Mac Software for Molecular Biologists
10 links: Free PC Software for Molecular Biologists
Free, Publication Quality Plasmid Annotation
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Kurt
It seems quit unstable, and crashes frequently. I’ll stick to PlasmaDNA, it’s not perfect, but it does the job
http://research.med.helsinki.fi/plasmadna/
Franck
@ Kurt
That’s a pretty harsh comment. A nice review from Nick and then, with only one short comment, you cleanly destroy it ! Unless you are using the Linux version which is not officially maintained, I am really surprised by your comment. Being the developer of Serial Cloner, I can tell you that I always answer to email of people reporting bugs or asking for new functions, so please, do not hesitate to contact me.
What I can just tell people is that me and my lab are the primary users of Serial Cloner and that I would not accept, like you, that my lab use an unstable soft, even if I were the developer. Serial Cloner has been downloaded several tens of thousands of time and is used as the main program by many labs of friends and colleagues.
What I can only tell people is : try by yourself; I hope you will like it !
Do not hesitate to contact me if you need help or which to see additional or better implemented functions,
best,
Franck
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Reef Koh
I’m an undergraduate research student. Just downloaded the software. It’s great.
bala
I’ve used an older version of Serial cloner, glad to see that it has been updated. Will definitely give it a try, thanks Nick & Franck.
Matthew
Franck,
If you are listening, can you help?
I’d really like to run your program on linux (ubuntu), but I am getting many errors:
OK, so I tried it on Ubuntu Jaunty 64-bit,
Jaunty 32-bit, Hardy 32-bit, and on my netbook Karmic 32-bit. All of
them a no-go. This program spits no errors other than the dialog “An exception of class FunctionNotFoundException was not handled. The application must be shut down. Exception Message: Could not load SCDynamicStoreCopyProxies from SystemConfiguration.framework” and
when I try to debug it (using strace), all the program outputs is that
it segfaults — which I think to myself, “no sh*t, sherlock”. From the cryptic text in the dialog,
it appears that it is not properly handling the error thrown when a
function *in its own binary* is not found. I arrive at this conclusion
just based on the fact the function name starts with “SC”.
Wine failed
on all of them, too. I ran it in XP on a virtual machine, and I’m
willing to bet wine is failing because they use what appears to be a
very non-standard window system.
Is it possible that you have a solution or should I, too, stick with PlasmaDNA?
Thanks for any help,
Matthew
Franck
Hi Matthew,
Well the truth is that I could never really debug the Linux version. I did not have the development framework running on Linux. I now have it so I will give a try. My scare is that each implementation of Linux is different. My test using Ubuntu were actually not that bad so I decided to let the Linux version of Serial Cloner be public (with some warning though on my web site) but it seems worst than I thought. What I know is that, so far, the web functions of Serial Cloner should be avoided at the moment – it may behave better in the next version.
In conclusion, I can only promise that I will try to debug better the Linux version for the next release although my main focus, sorry, will still be Windows and MacOS versions. But if you are interested to beta test the next version whenever I will have progressed, please, drop me an email (serialcloner at serialbasics.com).
best,
Franck
Oana
Good news, then, I’ll try the new version. I have used serial cloner on my mac for my gateway cloning and it was a great help: easy to figure out, quick, basic tools i need readily available. And it’s free. Even if I have a licenses for other programs, this is the first one I open. I am curious if they implemented recombination possibilities for the later generation gateway vectors.
Liam
Hi Franck
I to would appreciate a stable linux version. I know this is freeware, but perhaps you could consider opening up the code, some that a linux coder could implement a linux build.
Thanks
MadGenius
Hi Franck,
I agree with Liam – open up the code so that someone can make it work on Linux.
@Matthew & Liam – I’m trying out CLC sequence viewer right now – runs on Java, and works quite well on Linux.
(http://www.clcbio.com/index.php?id=28)
matt
agree – as linux + open-source fan i would also love to see this under an open-source license – hoping some linux developers would jump in. Right now i am using chromas and pdraw for creating plasmid cards and sequence analysis. But as my main os of choice is kubuntu i would love to have a stable version on this system – tried it out but didn´t get it to work yet.
Sebastian
Hi Franck,
thanks in advance for this nice piece of software.
I am running Serial Cloner2.0 on WinXP and was about to create a customized DNA Ladder with the “virtual cutter” tool,(which worked fine so far) when it suddenly crashed(for the first time). The program is stil useable since, but each time i try to start the virtualcutter the same bug occurs.
**error message**
“An exception of class OutOfBoundsException was not handled. The application must shut down.”
Which is a pity since i really did appreciate this feature.
Re-installing SC2.0 didnt helped as well.
Franck
Hi Sebastian,
do not hesitate to contact me at using the email address indicated on my web site.
Anyway, sorry to learn that you had a pb using Serial Cloner. Sometimes, the pref file gets corrupted. Please try to start the soft while pressing [CTRL] and [SHIFT]. Serial Cloner should ask you whether it may reset the prefs. Say ‘yes’.
I hope it will solve your problem.
Best,
Franck.
Cristian
Hi Franck,
I just wanted to let you know that the Serial Cloner is a great Software, way better than the one which everyone used in the past and now is not freeware nowadays..I don’t even want to pronounce its name anymore…because some guys let you first use it and exactly when you need it mostly, they decide to trade it for lots of money. And then you are in such a bad position, that even if the lab doesn’t have enough money, you are forced to buy it because you think there is nothing out there, which can keep up with their bloody software…well, they should know that there is something out there and that is Serial Cloner. I hope only one thing: that this software will be freeware forever…One question: when are you going to launch the next version? The one with customized scanning? Thanks and keep up the great work,Cris
Franck
Hi Cristian,
yes, sorry. It is taking more time than expected because of so many other stuff to get going in the lab. The version is ready. I just need time to write a small documentation and to update my web site… Hopefully, soon !
Gardo
I must agree. I downloaded this program a while ago and it’s been really helpful. I like the virtual restriction digest. I can visually compare my gel band sizes to the virtual band sizes and create my own customized ladder. You can do almost anything you can do in a commercial software. All of this for free. Thanks for sharing Serial Cloner!
Franck
Dear all,
Just a quick message to announce you that I released version 2.1 of Serial Cloner.
It is a much improved version so I strongly advice users to update. A non-users to give a try !
It is still, and will always be, a freeware (although donations are welcome).
Main improvements (among tens of changes) :
- [NEW] Define user’s Feature Collection (DNA, Peptide)
- [NEW] Import/Export Features collections
- [NEW] Export Sequences in GenBank format (with Features)
- [NEW] Directly send BLAST request to NCBI.
- [NEW] Two Companion Software to import MacVector files and to Reset Serial Cloner
- [ADDED] Search for a peptide sequence using the Find window.
- [ADDED] Scan and Display Features in the Sequence Map window.
- [ADDED] New “Copy Formatted (Full Seq + Features)”
- [ADDED] An pop-up drawing to illustrate cloning using the Build a Construct window
- [ADDED] Warns the user when using the Anti-Parallel, Reverse or Complement commands on only a portion of the sequence
- [UPDATED] Resizing the Sequence Window is now possible
- [UPDATED] A pdf file describing Features definition and detection in version 2.1
- [CORRECTED] Various bugs and interface glitches
- [CORRECTED] Much improved Linux version (although still not officially supported)