1. EMBOSS over a Grid 1

2. 1st EELA Grid School December 4th of 2006 Eduardo MURRIETA LEON Romualdo ZAYAS-LAGUNAS Pierre-Alain BRANGER Jérôme VERLEYEN Roberto RODRIGUEZ César BONAVIDES Alfredo HERNANDEZ EMBOSS over a Grid

3. 3 Introduction

4. 4 Index Bioinformatics Bioinformatics EMBOSS EMBOSS Objectives Objectives

5. EMBOSS over a Grid 5 What is Bioinformatics? Bioinformatics Bioinformatics  What is it? ToolsDatabase EMBOSS EMBOSS Objectives Objectives State of art - Analysis of genes expression - Need for prediction of protein structure - Analysis of sequence - A huge amount of knowledge to store

6. EMBOSS over a Grid 6 What is Bioinformatics? Bioinformatics Bioinformatics  What is it? ToolsDatabase EMBOSS EMBOSS Objectives Objectives Bioinformatics as a solution - To help life science data analysis - Use in a lot of domain (human genome project)

7. EMBOSS over a Grid 7 Type of Tools Bioinformatics Bioinformatics What is it?  Tools Database EMBOSS EMBOSS Objectives Objectives Searching (knowledge extraction) - Blast (nucleotides, proteins) Alignment - Clustal Phylogeny - Phylip

8. EMBOSS over a Grid 8 Database Bioinformatics Bioinformatics What is it? Tools  Database EMBOSS EMBOSS Objectives Objectives Various organization - NCBI : United States - EMBL : Europe - DDBJ : Japan

9. EMBOSS over a Grid 9 Overview Bioinformatics Bioinformatics EMBOSS EMBOSS  Overview Tech. Char. ArchitectureGUIsUse Objectives Objectives The European Molecular Biology Open Software Suite - From EMBnet Package of software: - a set of sequence analysis program - a toolkit for creating robust bioinformatics applications or workflows - Database searching - Identification of motif - Presentation tools for publication

10. EMBOSS over a Grid 10 Technical Characteristics Bioinformatics Bioinformatics EMBOSS EMBOSSOverview  Tech. Char. ArchitectureGUIsUse Objectives Objectives Software requirements - Linux Distribution - gcc compiler and graphic libraries Hardware requirements - 100 to 400 Mb free disk space - 512 Mb of RAM Execution requirements - Input data size : From 20 Kb to 100 Mb - Output : From 20 Kb to 1 Mb

11. EMBOSS over a Grid 11 EMBOSS Architecture Bioinformatics Bioinformatics EMBOSS EMBOSSOverview Tech. Char.  Architecture GUIsUse Objectives Objectives Main parts - ACD Files - Programs (API) - Inputs / Outputs (sequences, databases)

12. EMBOSS over a Grid 12 ACD Files Bioinformatics Bioinformatics EMBOSS EMBOSSOverview Tech. Char.  Architecture GUIsUse Objectives Objectives ACD Files - Ajax Command Definition Files - stored in $EMBOSS_DIR/acd application: intconv [ documentation: "Convert ints to ajints" groups: "Test" ] section: input [ information: "Input section" type: "page" ] infile: infile [ parameter: "Y" knowntype: "integer long data" information: "Standard format information" ] endsection: input

13. EMBOSS over a Grid 13 Programs Bioinformatics Bioinformatics EMBOSS EMBOSSOverview Tech. Char.  Architecture GUIsUse Objectives Objectives Programs - Binary files written in C and stored in $EMBOSS_DIR/bin - Use of libraries AJAX (Asynchronous Javascript and XML) NUCLEUS (specific of molecular sequence analysis)

14. EMBOSS over a Grid 14 Input/Output Bioinformatics Bioinformatics EMBOSS EMBOSSOverview Tech. Char.  Architecture GUIsUse Objectives Objectives Sequences - succession of letters representing the structure of a real or hypothetical DNA molecule or protein - ASCII TEXT extracted from huge Databases EMBOSS can access to various format of database - Embl, Fasta, Genbank, Swissprot … - access by Id of genes, by description keywords …

15. EMBOSS over a Grid 15 GUI for EMBOSS Bioinformatics Bioinformatics EMBOSS EMBOSSOverview Tech. Char. Architecture  GUIs Use Objectives Objectives wEMBOSS, Jemboss …

16. EMBOSS over a Grid 16 Use of EMBOSS Bioinformatics Bioinformatics EMBOSS EMBOSSOverview Tech. Char. ArchitectureGUIs  Use Objectives Objectives Study of Haptoglobin protein in different species - Extraction from Swissprot DB. (“seqret”) - 10 Mamalians species (human, rat, mouse,rabbit) - Alignment (“emma”) - Calculate the phylogenetic tree

17. EMBOSS over a Grid 17 Use of EMBOSS Bioinformatics Bioinformatics EMBOSS EMBOSSOverview Tech. Char. ArchitectureGUIs  Use Objectives Objectives Example of a generated tree

18. EMBOSS over a Grid 18 Objectives Bioinformatics Bioinformatics EMBOSS EMBOSS Objectives Objectives « Get EMBOSS running over a Grid » - EMBOSS jobs execution on a grid through command lined - Retrieving jobs results - Be able to execute a complete workflow / pipeline sequence analysis (i.e Use of EMBOSS) Complementary functions EMBOSSed Databases research Wrapping applications for EMBOSS over a Grid Web interface and Project manager for EMBOSS Have a BioGrid portal

19. EMBOSS over a Grid 19 Muito obrigado! Questions