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Madeline 2.0 Pedigree Drawing Engine
2009.09.23 New Web Feature! - Our experimental web-based Madeline service now works in all modern browsers, now including Internet Explorer versions 6, 7 and 8 thanks to Google's new Chrome Frame plugin. This Google plugin adds advanced features required by the Madeline web application that are missing from Microsoft's Internet Explorer series of browsers. Using Madeline's web service in other browsers such as Firefox, Safari, Google Chrome, and Opera does not require a plugin.
2009.05.23 New Feature! - Madeline 2.0 PDE now draws curved connectors in the background showing the placement of children adopted by relatives in a pedigree. Madeline 2.0 uses the Pedigree Standardization Task Force (PSTF) recommended graphics for children who are "adopted in". For showing "adopted out", Madeline uses square brackets that face outward. In addition, Madeline identifies "adopted in" children with individual ids prefixed with a plus sign, "+" while "adopted out" individual ids are prefixed with a negative sign, "-".
2009.05.22 - OpenHelix, LLC, has published a web tutorial on Madeline 2.0 PDE. OpenHelix provides on-demand multimedia narrated tutorials on a large number of popular free web-based bioinformatics tools. We are honored that OpenHelix decided to include Madeline 2.0 PDE as part of their suite of online tutorials.
2009.05.22 - New Feature! - Madeline 2.0 PDE now draws curved connectors in the background between individuals who are drawn more than once on a graph.
In the past, such individuals were only marked with unique indentifying letters, "A", "B", "C", etc. Tracking down matching individuals on large or complex graphs could be time-consuming. The new background connectors make large and complex graphs easier to read and understand with much less effort.
2009.05.20 - New Feature! -
Madeline 2.0 PDE now supports the display sterile and infertile individuals using PSTF-recommended
graphics. To display sterile individuals, include a column called Sterility in
the data file. To display infertile individuals, include a column called Infertility
in the data file. Then simply include labels such as "azoospermia" or "tubal ligation"
in the appropriate column for the relevant individuals. Labels will appear in small
type below the symbols as shown in the pedigree above. Leave these columns blank (or containing
the standard dot "." as a missing symbol) for fertile individuals.
2009.05.12 - New Feature! -
Madeline 2.0 PDE now supports the display of divorced (double-slash), separated (single slash),
and other relationship-ended (squiggle slash) couples. To use this
feature, simply include a column called RelationshipEnded in the data
file.
Since individuals can have multiple partners, be sure to mark both
individuals of a pair. For example, mark divorced couples using
D or divorced. Mark separated couples using
S or separated. If the reason why a relationship ended
is unknown, or if the relationship represents a casual relationship which has ended,
you can use any non-missing label of your choosing. A general label such as Y
or yes is sufficient.
In order to indicate multiple relationship breakups such as is shown in the example above,
we mark individual m103 with a generic label Y as shown, and then mark his partners
respectively with one of the more specific labels (i.e., D for m106 or S
for m105). When more specific information is not available, or the relationship represents
a casual relationship which has ended, then we just use a generic label such as Y (m113).
The Madeline 2.0 Pedigree Drawing Engine is a pedigree drawing program designed to handle large and complex pedigrees with an emphasis on readability and aesthetics. Although the program takes inspiration from Madeline v. 0.935, the Madeline 2.0 Pedigree Drawing Engine, or just Madeline 2.0 for short, is in fact a completely new and different program written from scratch by Ed Trager, Ritu Khanna, and Adrian Marrs.
For complex pedigrees we use a hybrid algorithm in which consanguinous loops are drawn as cyclic graphs whenever possible, but we resort to acyclic graphs when matings can no longer be connected without line crossings. A similar hybrid approach is used to avoid line crossings for matings between far-flung descendants of different founding groups. Written in object-oriented C++ and released under the GNU General Public License (GPL), Madeline 2.0 reads input files specified on the command line and generates pedigree drawings without user interaction. Pedigree output in scalable vector graphics (SVG) format can be viewed in browsers with native SVG rendering support such as Firefox 1.5+ and Opera 9.0+, or in vector graphics editors such as Inkscape.
A Brief History
Sometime around 1996 Ed Trager began to writing a program for preparing, visualizing, and exploring human pedigree data used in genetic linkage studies. This became the program known as Madeline which remains in use by researchers worldwide. In addition to converting pedigree and marker data into various formats required by linkage analysis software, including Crimap, Genehunter, Allegro, Mendel, Merlin, PedCheck, and Simwalk2, Madeline also provides functionality for querying pedigree data sets and for drawing pedigrees. The current development version is 0.936 and the stable version is 0.935.
Madeline 0.935 remains a capable program, but it's pedigree drawing routines have many limitations because the program was originally only designed to handle single descent trees of simple nuclear families. Consanguinous loops, multiple mated individuals, and multiple founding groups often occur in the extended family pedigrees used in modern genetic studies, and much work has been invested in finding better ways to visualize these kinds of pedigrees.
In the Madeline 2.0 pedigree drawing engine, we have tried to create a much more robust pedigree drawing engine to address the limitations of the older program and to provide the worldwide research community with a better tool for pedgiree visualization.
Find Out More
Click on the following resources to find out more about Madeline 2.0:
Fun Facts About Madeline 2.0 from Ohloh
Using Madeline 2.0 on the Web
If you are using a web browser with the ability to render SVG graphics natively (currently this means Firefox 1.5+ or Opera 9.0+), then you can use our interactive public web service:
Please note that this is currently an experimental service. By using this service, you agree to use at your own risk as there is no warranty of performance or protection against data loss.
Getting Madeline 2.0
Checking out code from the Subversion Repository
We recommend that you check out Madeline 2.0 from our Sourceforge project Subversion repository using a command such as the following:
svn co https://madeline2.svn.sourceforge.net/svnroot/madeline2 madeline2
Checking out the code from the Subversion repository guarantees that you will be getting the latest code and access to the most recent features and bug fixes.
Downloading Stable Releases
At the current time Madeline 2.0 is under rapid development. We therefore recommend you check out the latest code from our Subversion repository.
Contact
For more information, contact the developers: