Problems with LIMS Biocode database

Replies to This Discussion

Permalink Reply by Steven Stones-Havas on July 1, 2012 at 6:35pm

Hi Gunter,

I suspect you're using version 8 of the database (the error message will confirm that for you).  The most recent few versions of the plugin all use version 9 of the database.  I have written a MySQL script which updates the database, and you can find it linked at the bottom of the plugin download page:

http://software.mooreabiocode.org/index.php?title=Download

thanks

Steve

Permalink Reply by Gunter Fischer on July 1, 2012 at 7:30pm

Dear Steve,

many thanks. Now it works.

Regards

Gunter

Permalink Reply by Gunter Fischer on July 13, 2012 at 1:50am

Dear Steve,

we are starting to use Biocode, however we found that the workflows are not compatible with our DNA storage system from Themo Fisher. We use Thermo Fisher 2D barcode tubes in 96 well boxes and the VisionMate SR single rack scanner to read the barcodes. The idea of the system is not to store the location of a particular sample in a 96 box in a database but to store only the barcode. So if a tube is transferred from one box to the other it doesn't matter. You only scan your affected boxes again and the information of the sample storage is updated. Are there any plans to add such functions to Biocode including the support of barcode scanners?

This would help a lot.

Regards

Gunter

Permalink Reply by Steven Stones-Havas on July 13, 2012 at 1:57am

Hi Gunter,

We currently support using 2d-barcoded tubes for extraction reactions.  When you create your extraction plates, you can choose "Import Extraction Barcodes"  from the tools menu in the bulk editor.  If you move these tubes into a new configuration, simply create a new extraction plate, import the barcodes, and then choose "Fetch extractions from barcode"  This will move your extractions from their original locations in the database to this new plate (leaving gaps in the plates they were originally in).

Unfortunately we only have this functionality for extraction plates at this time, but we are looking at adding it to other reactions in the future.  I'm also not sure if the system is compatible with the output of your barcode scanner.  If it isn't, please send me a sample output file and I'll do my best to add support for it.

cheers

Steve

Permalink Reply by Gunter Fischer on July 14, 2012 at 12:48am

Hi Steve,

thanks for your quick answer. Do you know the software VisionTracker from Thermo-Fisher. It is a sort of freezer-rack-box-tube storage management system, actually not very good but it fulfills its purpose. The principle idea is, that every freezer, every rack and every box gets a unique number in the system, when you change the location of a 2D barcode tube from one box to another in a different rack, the database automatically updates the storage locations through a box scan. This makes a lot of sense because for a particular project you collect samples from different storage locations but to safe time you sort them back randomly, through a barcode scan of the affected boxes the system is quickly updated.

Does Biocode support such a function?

Are there any plans to support Barcode scanners directly in Biocode, e.g. adding a barcode scanning module to Biocode?

thanks

Gunter

Permalink Reply by Gunter Fischer on July 16, 2012 at 5:07am

Dear Steve,

many thanks.

Can you email me a template output file from your barcode scanner. That would be very kind, it would allow us to play around with output wizard of our system

thanks

Gunter

Permalink Reply by Huarong Zhang on July 17, 2012 at 5:05am

I found the way to "Import Extraction Barcodes ". The output from barcode scanner cannot be used directly. We have to modify the csv output and save as an txt file. This txt file can be imported into extraction plates.

Huarong

Permalink Reply by Steven Stones-Havas on July 18, 2012 at 3:10am

Hi Gunter, 

I've put the file up on the web at the link below.  It shouldn't be too dificult to map your data to this format, but if you would like to send me an example file, I'll try to improve the plugin to read it.

M030_1Col.txt

We basically look for a tab delimited line containing a well and then the barcode.  It doesn't matter if there are spaces before or after the well, and the semicolons don't have to be included either.  We also skip over any lines that do not contain exactly two tab delimited fields.

Permalink Reply by Gunter Fischer on July 16, 2012 at 5:10am

Dear Steve,

one more question. Is it possible to import Tissue Sample ID's into the Bulk Edit, or can they only be added manually?

Maybe you can email me the barcode scanner output file to gfischer(at)kfbg.org

many thanks

Gunter

Permalink Reply by Steven Stones-Havas on July 18, 2012 at 3:12am

We don't support the automatic loading of tissue sample id's.  Would you lay them out in the same way as your barcode scans?  This could be something we could possibly add support for in the future.  

Currently, the easiest way is to copy and paste them from something like excel - you can swap the direction that the bulk editor displays wells (from A01, A02, A03 etc to A01 B01 C01 etc) to help you paste the values.