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!
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!
Progenetix/arrayMap JSON format update, and a bug fix
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, $infile;
open OUTFILE, “>”.$outfile;
print OUTFILE JSON::XS->new->pretty( 1 )->encode( $json->decode( <INFILE> ) );
close INFILE;
close OUTFILE;
Also, due to a comment by Felix Kokocinski, we removed a bug where wrongly formatted links (“http:/www. …”) lead to missing image files in the locus score function. The incomplete address is interpolated by Safari, but breaks in Firefox. Thanks!
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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.
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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 using Pages (if not LaTex). And that is just some of the professional interfacing with Apple products.
Thanks.
Michael Baudis
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 visible for anyone (including flaws/errors/problems). Also, we have had feedback about the use of arrayMap as the method of choice for data visualization for the available series.
Though we haven’t published the data, and neither has it been linked yet. So, here we go with what to cite:
- arrayMap - Oncogenomic copy number data in cancer (http://www.arraymap.org)
- arrayMap: A Reference Resource for Genomic Copy Number Imbalances in Human Malignancies. (2011) Cai H, Kumar N and Baudis, M. manuscript in preparation
Anyway, enjoy & share!
Progenetix server outage
Progenetix/arrayMap had a Sunday night server outage. Fixed; sorry for the inconvenience.
