2011-02-25

Graphics update, again ...

So IE8 (and probably older ones, too) did not scale the PNGs correctly, probably resulting in lots of scrolling through the large ideogram images. Now the original ideograms are scaled down to 780px width, fitting into the layout.

But, please, use Safari, Chrome, Firefox or at least IE 9 (preview available through Microsoft).

2011-02-25

Graphics update

There has been a rewrite of the graphics plotting for the static part of the website. Now, ideograms, histograms and case specific matrix plots are available as SVG + PNG + PDF. preferentially, embedded SVGs are served to the browser; however, for Internet Explorer (older than version 9) and very old versions of Mozilla/Firefox/Safari, PNGs are used (which lack the links and scaling option ...). For convenience, all image types are linked for download.

Feedback would be appreciated ...

2010-12-09

Some support for Internet Explorer

Although nobody should use Internet Explorer at all, many users first reach the site using some IE version. Since most pages did not work at all with most versions of IE, I have adapted the code to allow at least rudimentary use of the site:

  • IE does not parse XML, which on the other hand is needed for inline SVG graphics. Since most pages were therefore invisible starting with the recent site overhaul, the pages are now served to IE as HTML. This makes most of the content (apart from SVG images) now visible. Safari, Firefox, Chrome and Opera etc. get XML/XHTML pages with the full content.
  • IE doesn't understand the section tag, which led to broken appearance of all pages. The annotation has been reverted to div with associated CSS formats ...

Although this fixes some problems, still no connection plots (HTML5 canvas) and especially no imbalance matrix plots (inline SVG) will be visible. Please, use a standards compatible browser!

2010-11-12

New site structure

As of today, all pages of the site are generated dynamically (however relying sometimes on pre-computed datasets). With that comes some changes in the navigation layout and help infoe (e.g. the "?" sign opens some icon info and site specific help link, if available).

arrayMap pre-alpha

We are working on a genomic array data information site, which will provide additional per-array data and visualization options not yet available. Although links may lead to the new site, it is considered pre-alpha (What letter would that be? Beats even Google!) and shouldn't be used for serious (?!) science. However, enjoy and comment.

New matrix plot visualization

After being pointed to the utility of some case/imbalance matrix plot options by Ivo Kwee, I implemented a case-by-case imbalance matrix plot graphic format as one of the Progenetix visualization standards. You will encounter it all over the site; for some static images, pls. visit our image blog.

2010-09-21

Deep linking

Some deep linking options were broken (thanks, Paul Kleihues). Although deep linking is discouraged, some options are considered safe; those are described under Link to Progenetix Pages, and should be fine now and in the foreseeable future.

2010-04-29

Server outage

Due to some connection issues after server relocation, the web site was intermittently non-accessible this morning (European time). Fixed.

2010-04-20

Data Update

  • 24010 cases from 821 publications
  • 19152 CGH
  • 4817 array CGH

Re-intoduction of Single Case Ideograms

The case lists and array plotting interface allow now the direct plotting of chromosomal ideograms. The output is in SVG format; so users of Internet Explorer are out of luck, I guess. Never versions of Safari and Firefox work fine.

2010-04-02

Better Linking for Array Plot Options

  • clicking the GEO and EBI icons on top of the publication list will now search for all publications for which the EBI/GEO accession is known
  • the publication list will now better link to aCGH series available for plotting (sometimes those are linked through their PMID; those where not shown previously)

2010-03-31

New & Re-introduced Features

Some data analysis features have been made available (again), which had existed in some form in previous versions of the site. These are:

  • survival plots: data can now be filtered for cases with available clinical followup & survival information
  • KM-plots: for the cases with survival information, KM-plots can be generated displaying the difference in survival for changes involving genomic regions vs. the cases without those changes
  • circos plots, with optional limitation tho changes involving a specific region

2010-01-25

Code Updates

The code updates seem finished (pending bug reports). Among the new/improved implementations are:

  • the re-introduction of the ISCN ish cgh annotation converter (thanks to Nikolas Stoecklein for pushing me ...)
  • a multi-locus search as part of the "Locus Scores" engine as well as for the visualization & clustering part
  • improved performance (e.g. clustering 2000 cases @ 86 bands is now no problem, though still there is a soft limit somewhere near 5000, due to browser time-outs)
  • ...

Integration of this News blog into the site

Again a move of the "News & History" pages: With the introduction of this Wiki system, news will now be hosted here, abandoning progenetix.blogspot.com.

2009 and older