MMPC :: Bioinformatics

Coordinating Unit

The Coordinating Unit is responsible for the creation of the software and informatics infrastructure for the consortium as well as facilitating the efforts of the mouse phenotyping centers. This page provides information about the infrastructure created for the consortium.

Lab Personnel

Mike Aufiero Programmer Architect	Jasmine Jones Data Curator	Co-Nesha Evans Social Media Coordinator

Biostatisticians/Bioinformatics

Ashok Sharma Professor	Hongyan Xu Professor

Infrastructure Information

MMPC IT Infrastructure
Our programming paradigm is to develop software systems based on an n-tier architecture, where we create the presentation layer, business logic and data layer into separate software systems. These systems have been developed to minimize maintenance, but provide a robust scalable model for future growth and interactions at the national level with other organism databases. These systems have been designed using the unified modeling language (UML) with the designs available to the general public. The two UML modeling tools we use are Rational Rose and Powerdesigner.

MMPC WebServices
MMPC has a broad array of WebServices available for implementing methods related to client accounts, the order process and catalog services. The following documentation is provided to assist the MMPCs understand the nomenclature and usage of these services. Please click here to view the pdf document.

MMPC Data Model
The core relational data model for the MMPC was created using SQL Server 2000 and was based on a number of existing schemas containing our key subject areas: animal models, genotypes (including array experiment data), histopathology, and phenotype Assays. The Mouse Models of Human Cancer Consortium (MMHCC) and the Jackson Labs were particularly helpful, and shared several successful models. Currently DiaComp Data Model has been migrated to SQL Server 2005 and has been modified to include MMPC (National Mouse Metabolic Phenotyping Centers) Data Schema. The current version of the database addresses several domains, including DiaComp - MMPC administration, models, strains, publications, external database references, experiments, phenotype assays, microarray data, histology, images and dataset persistence. Current data model has 250 tables, 55 functions, 994 stored procedures, 141 data views and a total of 9344 lines of code.

MMPC Administration Data Model

MMPC Science Data Model

* Note: Above links require Internet Explorer version 5.0 or above to view Data Model with Zoom capability. Also please make sure to accept ActiveX warning to start viewer. Viewer has links to different data schemas on Navigation Dropdown Box, you will need to click go Next to the Links to load different schema.

MMPC Object Model
The MMPC Object Model (MMPC-OM) created for the consortium fully describes the activities of the MMPC and provides an OOP API to access the data generated by the consortium. The MMPC-OM was designed using Powerdesigner and UML, written in C# and compiled as a .NET DLL. The object model contains both administrative and domain specific classes. However, only the data centric classes are available to the public. The Domain classes provide both object specific classes (e.g. Model, Strain, Experiment, Protocol, etc.) as well as DataManager and SearchCriteria classes used to retrieve data from the system. These DataManager classes are specific for each of the data types maintained by MMPC. For example, the StrainMgr class provides methods to retrieve strain specific data. The SearchCriteria classes are also datatype specific and are used by the DataManager classes to query the database using different type specific parameters. For example, the StrainSearchCriteria class provides queryable properties specific for the Strain data in the system.

MMPC Object model base was modified to add MMPC (National Mouse Metabolic Phenotyping Centers) schema. Currently common object model for both consortium contains classes to serve DiaComp and MMPC consortium web portals.

In order to provide the broadest access to the data, we are also creating a WebService that exposes specific portions fo the MMPC-OM to the public. Specifically, the WebService will provide access to all the object specific classes as well as the DataManager and SearchCriteria classes. This provides a mechanisms for programmers to create local MMPC-OM objects in other languages. The current version of the MMPC-OM has 185 object classes.

Lab Personnel

Biostatisticians/Bioinformatics

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