1. A web portal for management of biological data and applications
Matteo Gnocchi, Alessandro Orro, Davide Di Pasquale, Luciano Milanesi Institute for Biomedical Technologies – CNR, Segrate, Italy

2. Outline introduction motivation architecture ported tools
genotype management system
phenotype management system
web portal
xml-rpc interface
liferay web interface
genetic analysis
linkage analysis

3. Introduction Motivations
management of huge amount of data coming from a molecular biology laboratory
availability of many tools for data analysis
home made
heterogeneous (formats and interfaces)
not integrated in any framework

4. Introduction
implementation of a web-based application for resources integration
technologies
ad-hoc solution based on xml-rpc
liferay
main field
data management of data coming from genetics laboratory
medical genetics studies (association studies, linkage analysis)

5. Architecture

6. Ported tools genotypes data management
local database for gene annotation
UCSC,
phenotype data management
statistical aplpications
in development . . .
linkage analysis

7. Genotypes data management
management of data coming from ht genotyping platforms (Illumina, Affymetrix)
postgresql + python (scripts)

8. Genotypes data management
data representation

9. Genotypes data management
main features (bmc bioinformatics, 26 march 2008)
some LIMS features
users/projects
samples (by projects)
metadata (chips)
genotypes manipulation
data import/exports
most important input formats (ped, map, ...)
standard data from Affymetrix and Illumima
interface
only command line

10. Genotypes data management
python API
metadata
getAvailChips()
getChipInfo(chipname: string)
dataset management 
getDatasets(project: string)
newDatasset(name: string, project: string)
user/permissions/groups/ projects
addUser, addGroup, addProject
delUser, ...
etc.

11. Web portal
middleware
porting of the API interface to RPC-XML interface
porting the command line application to XML-RPC

12. Web portal portal implementation of a liferay based portal
user management mapping portal user <-> appl user
applications as portlets a resizable and independent windows into the portal that implement a single application
each portlet uses one or more web services in order to accomplish its task

13. Web portal

14. Web portal

15. Phenotype management
phenotype: every info of a sample (patient) related to his clinical/demographics/medical status
heterogeneous data
treatment
temporal reference
management software
metadata : defining new phenotypes
insert/delete/edit of phenotype value
import/export
based on mysql + python
cmdline interface -> xml-rpc

16. Phenotype management

17. Phenotype management

18. Data analysis
Genotype/Phenotype can be combined together and analyzed with many tools
case/control (association)
Linkage analysis
Quality control
Stratification analysis
computation
No computational intensive -> xml-rpc
Linkage analysis -> glite

19. Linkage analysis
Linkage Analysis is a genetic analysis that permits the discovery of genetic correlations in complex diseases following their transmission through family generations.

20. Linkage analysis

21. conclusions
The application developed represents an easy way to interact with the various biological data and informationcase/control (association)
Liferay and Xml-rpc
Future works
Interaction with HP computing infrastructures
XML-RPC –> WSDL (compatibility with WF systems)

22. thank you for your attention