Bayesian Networks
Bayesian networks are very well suited to model the statistical relations of genetic material
of relatives in a pedigree. They can directly be applied in kinship analysis with any type of pedigree of relatives
of the missing persons. An additional advantage of a Bayesian network approach is that it makes the analysis tool
more transparent and flexible, allowing to incorporate other factors that play a role such as measurement error
probability, missing data, statistics of more advanced genetic markers etc.
The computational engine of Bonaparte uses automatically generated Bayesian networks and Bayesian inference methods,
enabling to correctly do kinship analysis on the basis of DNA profiles combined with pedigree information. It is
specifically designed to handle large scale incidents with thousands of victims and missing persons.
In addition, it has a graphical user interface, including a "drag and drop" pedigree editor. Data-interfaces to
other laboratory systems (e.g. for the DNA-data input) are also available.
Technical Aspects
Bonaparte is based on client-server architecture. This means that the computational
core—the part of Bonaparte that actually computes the probabilities—and
the Bonaparte database run on a dedicated server (or servers). Clients communicate with
this server over a network. Since all computations are performed on the server,
you don′t need expensive client hardware.
Features
- Failed allele support
- Arbitrary large pedigrees
- Can handle inbred pedigrees
- Concurrent user system with UNIX style access rights.
- Database with "roll back" capability
- Automated import from existing data sources (for example: CODIS) through XML
- Automated (scheduled) matching procedures
- Matches against elimination profiles to find contaminated samples
- Custom population statistics and mutation models
- Manual matching procedures
- Drag and drop pedigree editor
- Supports import of Microsoft Excel files with profile data (STR, Y-STR and Mitochondrial DNA)
More information about Bonaparte can be found in the brochure.
Safe Storage: the Database
The Bonaparte database is designed with three things in mind
- The database should have the capability to be "rolled back" to any previous state.
- The database must be support a concurrent user system.
- Easy crash recovery
The "roll back" capability means that a user is able to select a historic version of the database—a view
of the database at time t that filters out data created after time t—and work with that database.
The purpose of this is that (for legal reasons) it might be required to re-confirm old matches or investigate what data was
exactly available at what time.
This versioning is accomplished by keeping a full edit history of all data, e.g. users can inspect who modified what, when and how.
Concurrency is implemented through the use of private branches. A user can start editing
an object and work with this new object, while the rest of the users still see the object
as it was before that editing took place. Only when the user chooses to publish his modifications they become visible to the other users as well.
Since Bonaparte is a client-server based system; it is sensitive to network service interruptions or browser crashes. In order to
minimize the loss of work in such events, a crash recovery mechanism has been implemented. The system automatically saves
users′ work data to a private branch. In case of a crash, all users have to do is restart their browser and they can resume
editing where they left off.
The XML Data Interface
There are two ways of getting data into Bonaparte: via the Excel import functionality provided
in the graphical user interface (STR, Y-STR and Mitochondrial profile data) or via the XML import (any data; for example
profiles, individuals, pedigrees and sample information).
The latter option is used to connect the system to existing infrastructure.
The use of XML as import format ensures that data from any source can be imported,
whether it is coming from CODIS, Postgresql, Excel files or even text files (from robots). All imported data is validated against
rules in XML Schema (XSD) files.
The XML format documentation is available upon request.
The Graphical User Interface
For the GUI we choose an AJAX based approach.
The use of asynchronous communication ensures that users suffer a lot less GUI
lag than is the case with conventional web sites.
An alternative Java based interface will soon available (Q2/Q3 2012).
Try our fully operational demo
A free demonstration version of the Bonaparte system is available, but since the system is client-server based you cannot simply download it. Instead we have Bonaparte running on one of our servers. All you have to do is register (if you have not already done so) and use the credentials we provide you to log on.
