During the last weeks, the last seeds of newly confirmed lines have left the lab for 2012. Since the coming holidays may interfere with international delivery, the next seed will be put into the mail not before the second week of 2013.
We wish all our users a Merry Christmas and a Happy New Year, and GREAT phenotypes for the experiments in 2013!

We have updated the tool in SimpleSearch that visualises the insertion positions of (predicted) T-DNA insertions in the A. thaliana genome. The new tool has been newly written from scratch, with contributions from Nils Kleinboelting and a number of students from the BSc and MSc curricula "Bioinformatics and Genome Research" of Bielefeld University, including Benedikt Brink and Andreas Kloetgen. The new tool has the following main features:
- Confirmation sequences are displaid graphically as "mapped" bars. This tells the location of the insertion as deduced from the confirmation data.
- For an increasing number (but not yet all) of confirmed insertions, the predicted AND the updated insertion position is shown.
- It is now possible to switch between a "Insertion view" and a "Line view". The line view shows the data for a single line including (if available) the confirmation sequences and primers, while the insertion view shows all insertion predictions mapped to a given genome region.
- In the insertion view, higher numbers of insertion predictions that are placed to a single locus are collected in a "multi triangle". Multi triangles (see the larger triangles here) may resolve into individual triangles when you zoom in, and vice versa.
An example is available here for insertion view, and here for line view. 

The SimpleSearch interface has been updated to allow better access to genotyping and primer information. There is now a page that displays the data for each insertion allele for that we had success in the confirmation process. This additional function is mainly relevant for DUPLO, but it is also helpful for "normal" GABI-Kat alleles. An example for a "normal" GK allele is this one: 220B01/At2g40950; and an example for a GK allele that contributed to DUPLO is 144H10/At5g42000. Also, quite some small bugs and glitches have been fixed.
In addition, a bug in the "Search for genome range" search code was fixed that prevented the display of intergenic insertion predictions. Now, the insertions listed for a genome range should be all available insertion predictions, sorted according to the prediction insertion position. Example for a region on chromosome 4

Several batches of newly confirmed GABI-Kat lines have recently been donated to NASC. Today, we donated 100 additional lines. Now, we have crossed the border of 11,000 lines donated to NASC! In total, we have now donated 147,767 seed bags representing individual stocks to NASC. See here for the exact number.

Since an unknown time, but at least for about 3 weeks, new data were not forwarded from our internal LIMS to SimpleSearch. In addition to confirmation sequences of newly confirmed lines, also the data that allow request tracking were affected. The problem has been fixed.  

Our most recent paper has been published recently in the 2012 database issue of NAR, and meanwhile the print version is available online with open access. Please note that we ask you to cite this NEW publication if you use our lines in your experiments. Also our "Disclaimer" (or MTA) has been adopted to include the new reference.  

Due to Easter vacations, and because of the start of the summer lecture term at Bielefeld University, answers to questions sent by Email to info[at]gabi-kat.de had been delayed recently. We will clean up the backlog by the end of this week.

The "engine" of the GABI-Kat website has been updated to Joomla version 2.5.4. Joomla! is the content management system (cms) we use to maintain this site. The separator shown in the "breadcrumbs" has been fixed to display the small graphic that is expected, and several inconsistencies in the display of links (should be in green like the link to Joomla!) or headings (should be displayed in black) have been corrected.