(last update Oct. 11 2011)

Oct 12
Time Ritz 1/2 G2 C1 C2
08:00 Freebit Workshop   Bioinformatics Practical course Ractome Practical Course
14:00 Opening cerimony.       
14:30 David Holmes: Beyond the genome: high dimensional microbial  ecophysiology mapped by comparative genomics and metagenomics.      
15:30 Ana Teresa Freitas:CRAVELA: Navigating through the seascape of pre-miRNA candidates.      
16:05 Robin Haw:Reactome: Forging connections between pathways, networks and cancer.       
16:40 Cristina Marino Buslje: Networks of High Mutual Information Define the Structural Proximity of Catalytic Sites: Implications for Catalytic and Other Functional Residues Identification.       
17:15   Cocktail    


Oct 13
Time Ritz 1/2 G2 C1 C3
08:00 FreeBit Workshop. Developing Free Software   Macromolecular Structure, Protein Function De novo genome assembly
09:00 Tiago Sobreira: A new computational methodology for the rational design of specific protein kinase C inhibitors peptides.   IT Workshop  
09:35 Gustavo Parisi: Protein conformational diversity: using old evidence in new bioinformatic tools. Ana Tereza Vasconcelos      
10:10 Danilo Gonzalez-Nilo: From atoms to biotechnology: integrating structural bioinformatics and molecular simulation for the new challenges of transdisciplinary research.      
10:45 Coffee Break      
11:15   Poster Session   Laptop meetings
12:45 Lunch     Laptop meetings
14:00 Life Technologies Leonardo Varuzza: Ion Torrent: The Open Source Sequencer      
14:30 Ana Tereza Vasconcelos: SABIA: A new version for next generation sequencing platforms.      
15:30 Susan Higashi: Analysis of Composition-Based Metagenomic Classification.      
15:45 Alessandra C Faria-Campos: FluxNGS: A Data Management System for Next-Generation Sequencing Protocols and Data      
16:00 Anderson Santos: The Corynebacterium pseudotuberculosis pan genomics reverse vaccinology      
16:15 Ana Carolina Landim Pacheco: Proteome screening, homology modeling of hypothetical genes and nanoscale imaging of Leishmania flagellum are used to identify radial spoke proteins      
16:30 Christian Probst: Trypanosoma cruzi Orfeome and regulome projects: initial toolset and dataset enabling integrative analyses      
16:45 Francisco Melo: Structure-based prediction of transcription factor affinities and specificities      
17:00 Coffee Break Coffee Break Coffee Break Coffee Break
17:30 Arthur Olson: Interacting with Protein Interactions.      
18:30 Leandro Neumann Ciuffo: Supporting Scientific Collaborations through Research and Education Networks      
20:30   Dinner    
Oct 14
Time Ritz 1/2 G2 C1 C3
08:00 FreeBit Workshop. Developing Free Software   Macromolecular Structure, Protein Function De novo genome assembly
09:00 Julio Collado-Vides: Editing and modeling knowledge on gene regulation of Escherichia coli K-12 within RegulonDB.      
09:35 Fernan Aguero: TDR Targets: a chemogenomics resource for neglected diseases.      
10:10 Aristóteles Góes-Neto: Detecting network communities: an application to phylogenetic analysis.       
10:45 Jan Baumback: Finding expressed key pathways.      
11:20 Coffee Break      
11:45   Poster Session   Laptop meetings
12:45 Lunch     Laptop meetings
14:00 Erik Lindahl: Dynamics and Function of Voltage- and Ligand-gated Ion Channels.      
15:00 Celia Fontanillo: Combined analyses of genome-wide expression and copy number profiles to identify causal genes in cancer.   FreeBit meeting  
15:15 Mina Cintho: Classification of HIV virus mutations      

Fabiano Sviatopolk-Mirsky Pais: Assessing the efficiency of multiple sequence alignment programs

15:45 Fabio Ribeiro Cerqueira: Machine learning approach for evaluating identifications of peptides and proteins in complex mixtures      
16:00 Paula Fernandez: Genomic tools to support functional studies on agronomically relevant plants: The case of INTA Castelar's Biotechnology Institute and its collaborations      
16:15 Jorge Luiz Soares de Pina: Study On The Performance Of Particle Swarm Optimization Variants In
Molecular Docking Using Autodock
16:30 Coffee Break Coffee Break Coffee Break Coffee Break
17:00 Javier De Las Rivas: Human interactome: steps to unravel the complexity and functional meaning of the human protein-protein interaction network.      
18:00 Bioinformatics education: Floriano Paes Silva Jr., Alan Durham, Vasco Azevedo e Jeroniza N. Marchaukoski.  Chair Alan Durham   SOIBIO meeting  
19:30     RSG student activity Prosul Project Meeting
Oct 15
Time Ritz 1/2 G2 C1 C3
08:00 FreeBit Workshop. Developing Free Software   Macromolecular Structure, Protein Function De novo genome assembly
09:00 Cristiano S Botelho: FluxTransgenics: A Comprehensive Management System for Plant Transformation Facilities.      
09:15 Fernanda Almeida: Provenance Description to Extract Knowledge from Hemotherapy Information Systems      
09:30 Newton Shydeo Brandão Miyoshi: Computational Framework to Support Integration of Biomolecular and Clinical Data within a Translational Approach      
09:45 Gabriela Guardia: A UML Profile for the OBO Relation Ontology       
10:00 Deive Oliveira: Historical changes in UniprotKB/Swiss-prot keywords patterns      
10:15 Cláudia Thompson: Molecular evolution of Klebsiella pneumoniae glycosyltransferases      
10:30 Natasha Andressa Nogueira Jorge: Searching for FMN and SAM riboswitches in the human genome      
10:45 Coffee Break Coffee Break Coffee Break Coffee Break
11:15 AB3C meeting      
12:15 Closing Cerimony      
15:00       AB3C Director's meeting


IT Workshop - The X-meeting 2011 will have a special session on IT infrastructure. The main motivation for this workshop is the identification of an imbalance, in many of our institutions, between the needs of the bioinformaticians and the way the IT infrastructure is setup (restrictions, network setup, access, etc.). The objective of this parallel session will be to describe the needs of bioinformaticians to the IT professionals and discuss examples where satisfactory solutions were developed and others where improvements are necessary. In addition, solutions for bioinformatics hardware implementations will be discussed..

Bioinformatic tools and methods to build and study gene coexpression and protein interaction networks (Instructor: Dr. Javier De Las Rivas) - Introduction to the basic concepts, terminology and types of biological networks, with special focus on gene coexpression networks and protein-protein interaction networks. Overview of the most important databases storing biomolecular network information. Definition of protein-protein interaction networks and presentation of tools to build and explore this type of networks. Use of Cytoscape, open-source program for the visualisation and analysis of networks. Exercises guided to the construction of your own gene/protein networks in Cytoscape.

Reactome (Instructor: Robin Haw) - Reactome Pathway and Network Analysis (Instructor: Robin Haw) - Reactome is an expert-authored, manually-curated, peer-reviewed database of reactions, pathways and biological processes. This practical course will introduce the Reactome database, website and our suite of pathway and network analysis tools. Participants will learn to: browse and query pathway knowledge, integrate network and pathway data, ?use pathway and expression analysis tools to analyze experimental datasets, annotate gene lists using Reactome BioMart, and discover network patterns related to cancer and other diseases using the Reactome Functional Interaction Network Cytoscape plug-in.

De novo assembly bacterial genome using next generation sequencing data (Instructors: Vasco Azevedo, Artur Silva, Rommel Ramos, Louise Cerdeira, Anderson Santos, Luis Guimaraes and Vinicius Abreu) - Day 1: Overview NGS Technologies / Improving data quality / Introduction to genome assembly. Day 2: De novo bacterial genome assembly / Finishing genomes / In silico gaps closure. Day 3: Overview structural annotation / Automated pipeline for structural annotation.

FreeBit Workshop. Developing free software (Instructor: Jose R. Valverde) - Developing free software provides many advantages, both to the academic and the commercial developer. This course will provide a summary introduction to the advantages of the Free Software model answering the most relevant practical questions for developers, such as: What kind of Free Software licenses are there and which one should I use? How do I share the workload with other developers all over the world? What tools are best suited to Free Software development? How do I exploit and support Free Software? 

Macromolecular structure, protein function (Instructor: Cesar Avila) - Modern Deep Sequencing and Proteomics are producing a large amount of data about known and novel proteins in a large variety of organisms. Annotating genes and understanding the role of new proteins is a major challenge that has driven major research efforts to mine collected data and provide scientists with suitable, free and easy to use tools addressing this problem. Attendants to this course will learn about the various approaches that can be used, from sequence analysis, to structural analysis and modelling, and will come out with a large arsenal of Free Software tools they can use at their home institution to efficiently analyze protein function.