GenoMEDIA,

a Middleware Platform

for Distributed Genomic Information

P.E. Gros, J. Hérisson, N.Ferey, R.Gherbi

LIMSI-CNRS

Université Paris-Sud,

Orsay, France

Huge, Distributed and HeterogeneousInformation (example of E. coli K12)

gcgtataacgtattattctggtcgcacccgccagagcagaaaatattggggcagcggcgcgggcaa

MRITIILVAPARAENIGAAARAMKTMGFSDLRIVDSQAHLEPATRWVAHGSGDIIDNIKVFPTLAESLHDVDFTVATTARSRAKYHYYATPVELVPLLEEKSSWMSHAALVFGREDSGLTNEELALADVLTGVPMVADYPSLNLGQAVVATTA

Integration

• Need of data/tool integration and visualization– Goals

• To allow users (biologists) to link tools and databases

• To offer some kind of integration transparency

• To propose a visualization paradigm suitable for huge data exploration by users (biologists)

– « distributed » approach• Communication ??

• Location ??

GenoMEDIA Approach

DBDB

Tool

Tool(pubmedlink)

Tool(entropy)

Unified DBSQL

Select entropyentropy(sequence) from S_cerevisiae where PubMedLinkPubMedLink(‘lastT’, name)>.5

Agent1 ??

ANS : Application Naming Service service location, group notion, no centralization,

loadbalancing

Agent 1(0)

Agent 1(1)

Agent 2cache

cache

cache

Clientcache

??????

??????

Agent 1(0):(loc 1,charge 1)

Agent 1(0):(loc 1,charge 1)

Agent 1(0):(loc 1,charge 1)

Location

Lydia : Communication

• We want :

– An efficient communication scheme• Futur model

– A transparent communication model• Encapsulation

– A multi-platform interface through LDL• (C/C++, Java, SQL...)

Lydia Example (entropy, curvature)

TypeAbstract Math_ADN{calcul_entropy(String s):floatcalcul_Curvature(String s) :float}

class Math_ADN: public Servant{private value calcul(value v)public ://to implemente float calcul_entropy(char * s) float calcul_Curvature(char *s)}

Interface in C++ for the Servant

class Math_ADN : public Call{ public :static Future * calcul_entropy(char * s)staticFuture * calcul_Curvature(char *s)

}

Interface in C++ for the Client

Compilation of the script for the Servant

Compilation of the script for the Client

Lydia, ANS, GenoMEDIA

Through the LDL, Lydia et ANS links components to a Database

Select generate_coord3Dgenerate_coord3D(sequence) from S_cerevisiae where PubMedLinkPubMedLink(‘lastT’, name)>.5

Sequence S. cerevisiae SGBD

generate_coord3Dgenerate_coord3D et PubMedLink LydiaC_x | C_y | C_z | W_x | W_y| W_z-4.71 | 3.31 | 2.97 | 4.75 | 3.45 | -2.82 2.16 | 6.25 | 5.22 | 2.23 | 7.28 | -4.58

GenoMEDIA Stack

SQL SGBD

SQL Translator

JVM

ANS

Lydia

Agent Stub

RMI Direct

Native

DNS Naming

JDBC, ODBC, PHP,QT……

An Application View of GenoMEDIA

Conclusions & prospects

• A good tools integration

• A good Database integration through “view notion”

• We look for a good representation and exploration of generated data (Virtual Reality ?)

• We look for a good integration GUI

GenoMEDIA data flow

User function(skeletton)

Lydia ANSIP mTCP/IP

User function(stub)

Lydia ANSIP mTCP/IP

Genomic Database(Genbank)

SGDB

HTTPDWeb Browser http

Applications Xml

First results : factual data