January 2012
1 post
The arrayMap cancer genome resource manuscript http://arxiv.org/abs/1201.2677 is now available through arxiv.org. The manuscript has been submitted to PLoS ONE where it is currently being processed. Don’t forget the supplementary files. Enjoy!
December 2011
2 posts
Progenetix & arrayMap server hiccups ...
With our servers on the move between facilities at the University of Zürich, there have been some DNS entry hiccups. If you didn’t memorize the previous IP addresses, you may have been out of luck for some hours … Hopefully settled, and I will try to accommodate for DNS server propagation delays in the future.
Improving array search with #MongoDB
After solely relying on structured flat file storage, we have made a first step towards a database back end implemented with #MongoDB. Currently, this is live only for the arrayMap array selection, which is now considerably faster. Feedback, please!
November 2011
3 posts
Progenetix/arrayMap JSON format update, and a bug...
Master and temporary data files for arrayMap and Progenetix are saved in a JSON format, using Perl’s JSON::XS module. To speed up file I/O, we have deactivated the “pretty” option. This improves file I/O and size by approximately a factor of 2, but makes it rather unreadable. A simple way for reformatting the files (in Perl) would be:
my $json = JSON->new;
open INFILE,...
Selection counters
A small interface change in the Progenetix/arrayMap pipeline now shows all case numbers in the feature selector. Enjoy!
For downloads: JSON file format change
We have changed the internal JSON file format, used for data storage and offered as download option. While before the CNA data was concatenated in “GPCCGH” and “GPACGH” fields (e.g. “chr2:41600000-47599999:1::chr6:60500000-170899992:-1”), we now list each segment as a separate entry with nested data. Please adapt your scripts accordingly.
October 2011
2 posts
Clustering visualization
Since there were requests for re-introduction of the dendrograms in the case specific CNA clustering plots, the analysis functions in Progenetix now present the clustered dendrogram-less as well as a version with dendrogram and case IDs. Enjoy!
Steve Jobs, 1955-2011
This site runs on a Mac.
This site is mirrored on Macs. The software is developed mostly on my MacBook Air. The students develop software and manage the data collection on MacBooks and Mac Pros. While talking to people at conferences or in meetings, I use my iPad to present the Progenetix and arrayMap sites. My iPhone acts as AP while on the road. I do presentations in Keynote, and work on papers...
September 2011
1 post
arrayMap: dropping the "coming soon"
Though the manuscript about the resource hasn’t been submitted yet, we’re dropping the “coming soon” from the arrayMap intro page. One reason is that were on even footing with GEO, when googling GEO IDs for oncogenomic arrays/series; sometimes www.arraymap.org ist on top … Alas, we present the data in a way GEO doesn’t offer; making genomic cancer array data...
July 2011
2 posts
Progenetix server outage
Progenetix/arrayMap had a Sunday night server outage. Fixed; sorry for the inconvenience.
arrayMap: plot display optimizations
We are re-plotting ca. 30000 genomic arrays, using the new plot styles. Also, overview plots are now displayed in the list mode when following the “Plot Array Data” link or symbol; this should greatly enhance a speedy array data evaluation. Enjoy www.arraymap.org!
June 2011
3 posts
Plot default changes
We have removed the sex chromosomes (X and Y) from the default histograms. Many genomic array series either do not report changes in those, or even use them for value normalization (i.e., gender specific hybridization results are used for signal intensity normalization). The data, where available, is still part of the dataset and can be visualized in the custom analysis steps.
Database update: 1100 B-NHL added
Progenetix now contains 28882 cases from 940 publications (20270 chromosomal CGH and 8728 genomic array experiments). The recent increase is mostly due to a large set of approximately 1100 B-NHL cases from array experiments, collected as part of our arrayMap project.
May 2011
3 posts
Improved CGH publication listing
Publications for which the cases are counted with another article (e.g. re-publication of the data as part of a larger dataset) will now be listed, with the case numbers set in square brackets (e.g. http://www.progenetix.org/cgi-bin/pgPublicationindexLoader.cgi?PMIDsearch=16314645). Those numbers won’t be counted for the statistics, though.
27751 genomic cancer profiles
The Progenetix database has been updated to now 27751 cases from 927 publications.
Search speed
Progenetix search (publications, arrays etc.) has become much faster; check it out!
April 2011
1 post
arrayMap - genomic array data in cancer →
Testing the arrayMap extension of the Progenetix project. The site is aimed at providing direct access to genomic array data plots and associated information.
December 2010
1 post
November 2010
2 posts
April 2010
1 post
March 2010
1 post
February 2010
1 post
Progenetix - Genomic Copy Number Screening Images...
Genomics is beautiful. And genomic data can produce strikingly beautiful images.
Our research centers around A) large scale oncogenomic data mining & visualisation using Comparative Genomic Hybridization (CGH) data; and B) search for genomic copy number abnormalities in the DNA of children with “genomic syndromes” (that is, developmental peculiarities with a suspected genetic...