Database Storage System For Clones

Question

[Zach Powers]

I am trying to gather together all of the various clones and DNA-constructs lying around the lab and put them into one database. Since there is no pre-existing database (most info is is scattered on various computers as either excel spreadsheets or plain-text files) I can put it together however I like. I'd like to keep track of simple things like - who made them, whether there are glycerol stocks, where in the fridge they are... etc as well as to keep information about the underlying sequences that we can use for bioinformatics.

Does anyone have suggestions about systems they have put together that have worked or important things to avoid?

thanks zach cp

[Pierre Lindenbaum]

Related: "Lab Management" posts

[Neilfws]

related and very relevant: http://biostar.stackexchange.com/questions/4184/is-there-a-lims-that-doesnt-suck

Answer 1

[Alex Paciorkowski]

Zach, for something like this a simple SQLite database might be the way to go (SQLite3 should be standard on most Linux distros). You could merge all your disparate spreadsheets and files into CSV format, and upload it. If you want to make a nice front-end user interface you can use something like Perl's Catalyst -- the CPAN tutorial has a very functional database model you could modify.

Or, if you don't feel like doing any coding, you could always use OpenOffice's Base.

Answer 2

[Malachi Griffith]

The post related to LIMS options posted by Neilfws has some good options for you. If you are looking for an interface that is specifically designed to deal with the curation, tracking and visualization of plasmids and other DNA-constructs you might consider Vector NTI. From their website:

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Vector NTI software is a completely integrated suite of sequence analysis and design tools that help you manage, view, analyze, transform, share, and publicize diverse types of molecular biology data, all within one graphically rich analysis environment. Vector NTI Software allows you to:

Curate—store and manage collections, visualize maps, and search sequences

Discover—analyze, compare, and contrast sequences

Design—cloning strategy; primers for PCR, cloning, and resequencing; and gel simulations of sequences

Confirm—contig assembly, sequence validation, and literature validation