(last update Oct. 11 2011)
Oct 12 | ||||
Time | Ritz 1/2 | G2 | C1 | C2 |
08:00 | Freebit Workshop | Bioinformatics Practical course | Ractome Practical Course | |
12:00 | ||||
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 | |||
19:00 |
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 | |||
19:30 | ||||
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 | |||
15:30 |
Fabiano Sviatopolk-Mirsky Pais: Assessing the efficiency of multiple sequence alignment programs |
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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 |
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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 | ||
19:00 | ||||
19:30 | RSG student activity | Prosul Project Meeting | ||
22:00 |
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 | |||
14:00 | ||||
15:00 | AB3C Director's meeting | |||
17:00 | ||||
19:00 |
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.