Furthermore, data published by different authors for the same species may differ in their results, which may be due to use of different chromosome nomenclatures. The data from various sources need to be analyzed, reconciled, grouped, processed and made readily accessible. Data resources for Chromhome.
The blue coloured families represent at least one species from the family on Chromhome. External data resources 2 are through NCBI Pubmed searches for cross species painting data, Ensembl for karyotype information for sequenced species and specific species genome databases such as Mouse Genome Database or Rat Genome Database. The data comes in different levels of detail ranging from karyotype to homology maps. G-banding a technique of staining partially denatured chromosomes with Giemsa stains forms a pattern of dark and light bands, which enables unequivocal recognition of specific chromosomes.
An idiogram is a graphical representation of a G-banded karyotype. Species like human or mouse have G-banded idiograms and related sequence information that can be obtained from Ensembl. But most other species have only G-banded karyotypes. The Atlas of Mammalian Chromosomes [ 16 ] holds karyotype data for species of which 43 have idiograms that are used in Chromhome. Retrieval of information from the database is through a series of SQL scripts and the result-set can be exported easily in text formats.
This database forms the central repository for overall Chromhome data organization giving the added benefits of concurrency, scalability and transaction supports.
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To convert the pictorial data to numerical genome based data for Chromhome, the total genome size in basepairs is used to calculate the approximate size of each chromosome in a species. The C-value is expressed in picograms and can be converted to the number of nucleotides in the genome by an established formula [ 19 ]. For species with no genome size information, the genome size of a closely related species or species from the same family is considered. Based on the measurements of the lengths of chromosomes and size of chromosome homologous regions, an idiogram and homology maps are created for each species.
The data are presented as G-banded karyotypes or idiograms for the species. In the homology maps, probe chromosomes are depicted as blocks on chromosomes of the target species to show homologies between them. Software system architecting consists of deciding what tiers are needed for the application and what services are required at each tier. The Chromhome application is designed and architected in accordance with separation of concerns and design-by-contract DBC principles of software best practices [ 20 ].
Accordingly, the application architecture forms the n-tier enterprise model Figure 2 with an interactive client layer, presentation layer, business logic layer and the data layer.
A number of industry-standard open source solutions are employed to build Chromhome. Chromhome n-tier architecture. The Web Client layer is the web browser layer through which the user selects the target, probe and method species combination and sends a http request. The request goes through the middle tier that connects to the database layer through JDBC Java Database Connectivity and retrieves the information from the database. The data is processed in the middle tier through a series of programs and is sent back to the web browser, where the client can view the homology maps.
These are saved on the server side and invoked by clients in the runtime. The server component is deployed as a J2EE web application a servlet that intercepts the script requests from the client, interprets them, and serves them as Flash runtime binaries. Apache Jakarta Tomcat [ 22 ] is used as the web server for Chromhome application. Tomcat along with OpenLaszlo provide the presentation tier.
The instance variables in the class are mapped with the columns in the table. Combining Spring Framework [ 24 ] with Hibernate greatly reduces the amount of plumbing code.
Spring and Hibernate frameworks support the business logic tier of Chromhome application. The whole project is tailored to follow Rational Unified Process RUP with use case driven, architectural-centric and iterative ingredients. During the initiation phase of the project, the important use cases were identified and the event flows were documented.
Use case realizations were achieved through sequence diagrams. The Database Model describes the data which must be stored and retrieved as part of the overall Chromhome design. This describes the tables and data in detail and enables generation of DDL Data Definition Language scripts to create and setup databases. Chromhome Data Model diagram Figure 3 represents the schema with entity-relationship multiplicity.
The main sequence diagram of Chromhome is shown in Figure 4.
The initial user request is handled by the java class, ChManager. It communicates with the business object class ChBO, to fetch the requested data. Business object class wraps all the application logic and through the data utility class, PersistenceUtil, it organizes the data retrieval. Species, FeatureType, Homology and FeatureAnalysis are some of the domain classes that are mapped to database tables.
Chromosome Atlas: Fish, Amphibians, Reptiles, and Birds - Volume 2 | Kurt Benirschke | Springer
MapManager component handles the idiogram and homology map generation. The initial selection view is shown in Figure 5. The screen represents two views. The view on the left provides easy to use UI User Interface elements to facilitate effective user interaction with the application. The user can select target and probe species and the method to get the chromosome maps.
Atlas of Mammalian Chromosomes
The view on the right presents the resulting homology maps and species information Figure 6. The selection view on the left presents two sets of species on two separate tabbed views. The target is the species on whose chromosomes the probe species chromosomes are hybridized to obtain the chromosome homology maps.
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Selecting the target species through a mouse click brings up another tab view presenting a set of probe species that has homology data with the selected target species. Further selection of probe species presents another tab view of methods available for the given target-probe combination.
When the user selects a method, the homology map is displayed on the right, for that unique target-probe-method combination. In the homology map, the probe species chromosomes are marked along the sides of the target species chromosomes. Help Centre. My Wishlist Sign In Join.
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Free Preview. Buy eBook. Buy Softcover. FAQ Policy. About this book Since the publication of the first Atlas of Mammalian Chromosomes in the continuous compilation of mammalian karyotypes has become a useful instrument in cytologic and taxonomic studies. Show all. Show next xx.