Wednesday - September 1st

• BSB IS1: 16:15 - 17:30 (chair: Carlos E. Ferreira)
  - Satoru Miyano (Univ. Tokyo)
  Title: Supercomputing for Systems Biology. [+]
  
  Abstract: We present our research activities in Systems Biology that use the supercomputer system at Human Genome Center of University of Tokyo (75 TFLOPS currently, and 225 TFLOPS from January 2011). We developed a series of computational methods based on Bayesian network with nonparametric regression and state space model combined with dimension reduction techniques for computing large gene networks from transcriptome data. These computational methods for computing gene networks were applied to drug target pathway search and analysis. For a given drug, we took time-course gene expression data for the drug responses. We also made a set of gene expression data obtained by knock-downs of several hundreds of carefully selected genes (one knock-down for each microarray measurement). From these data, we computed Bayesian networks of 1000 genes by intensively using the supercomputer system. We show how we could explore these computed networks for analyzing dynamic features of the networks and for searching drug target genes and hubs in the networks. The dynamic model based on state space model is also used for investigating the systems behaviors responding an anti-cancer drug and we predicted differentially regulated genes that were proven very powerful to prediction of survival in lung cancer. In parallel, we developed a software tool Cell Illustrator (CI) which aims at analyzing and simulating complex dynamic causal interactions and processes such as metabolic pathways, signal transduction cascades, gene regulations. We have been developing an XML format Cell System Markup Language CSML (http://www.csml.org/) for describing biological systems with dynamics and ontology (Cell System Ontology). In 2008, we released a Java web start software Cell Illustrator Online 4.0 (CIO) (http://cionline.hgc.jp/) combined with CSML databases including TRANSPATH that has more sophisticated GUI functions such as automatic pathway layout algorithms using ontology information. Furthermore, we developed a supercomputer based computational method for automatic parameter estimation of dynamic models by using a technology called “data assimilation” which "blends" simulation models and observational data "rationally". This technology will be a strong computational strategy with which we can estimate personalized models from general biological models by using individual measurement data.


• IWGD IS1: 18:00 - 19:15
  - Maria Emilia Walter (UnB)
  Title: BioAgents: a multiagent system to support annotation in genome projects. [+]
  
  Abstract: Enormous volume of DNA and RNA sequences of organisms are continuously being discovered by genome sequencing projects around the world, by automatic sequencers nowadays based on massively parallel sequencing technologies. The annotation phase in these genome projects has the objective of identifying biological function for each sequence. In this talk we first discuss generic characteristis of computational pipelines to support high-throuput genome projects, and after present BioAgents, an annotation system based on the multiagent (MAS) approach. The system simulates biologists knowledge and experience for annotating DNA or RNA sequences in genome sequencing projects. BioAgents was defined with a cooperative approach, where different specialized intelligent agents work together to suggest proper manual annotation. The three-layer system architecture was implemented using JADE - Java Agent DEvelopment Framework, and Drools - a Java production rule system. We have done experiments with real data from three different Sanger genome projects already concluded, and paln to use it in three new high-throughput genome projects that are beginning to be developed in the MidWest Region of Brazil.
  
  

Thursday - September 2nd

• BSB IS2: 09:15 - 10:30 (chair: Maria Emilia Walter)
  - Marta Mattoso (UFRJ)
  Title: Where did this data come from? The role of provenance in managing scientific workflows.


• IWGD IS2: 10:45 - 12:00
  - Steve Bryant (NCBI)
  Title: The PubChem project.


• IWGD IS3: 18:00 - 19:15
  - Katia S. Guimarães (UFPE)
  Title: Dealing with biological datasets – Size, meaning, coverage, specificities, and bias. [+]
  
  Abstract: For three decades, computational methods have been used to help solve biological problems. In the last decade, biological datasets of different kinds have been growing at escalating rates, as well as the number of computational approaches to manage, analyze, predict and model the data. Bioinformatics is a cross-disciplinary field that grew with the genomics revolution, and depends on the particularities of the biological datasets to face new challenges.
  
   
• BSB IS3: 19:15 - 20:30 (chair: Duncan Ruiz)
  - Peter F. Stadler (Univ. Leipzig)
  Title: Discovery of structured RNAs from short-read high throughput sequencing data.

Friday - September 3rd

• BSB IS4: 09:15 - 10:30 (chair: Katia Guimarães)
  - Paulo Cavalcanti Gomes Ferreira (UFRJ)
  Title: Next-genetation sequencing: challenges and opportunities for bioinformatics. [+]
  
  Abstract: The amount of data produced by next-generation sequencing increases exponentially as the cost of sequencing a genome continues to fall. The aplications include a new sequencing, variation discovery, transcriptome analysis, small RNA sequencing and DNA–protein interaction analysis. Given the variety of applications, this new environment requires great flexibility and it places inumerous challenges and opportunites for bioinformatics such as the increasing need for disk space, memory and processing capacity, development and adaptation of software, and the flexibility . Another important question is how much of the work should be done in house, in the molecular biology labs, by scientists, posdocs and graduate students, and how much is carried out in collaboration with computational biologists or bioinformatics facility.
  
  


• IWGD IS4: 10:45 - 12:00
  - Duncan Dubugras Ruiz (PUCRS)
  Title: How may I help you? [+]
  
  Abstract: Computer Science and Biology seems to be quite different sciences. Each of them owns its proper vocabulary, diverse ways to run research, and specific academic forms on publishing their results. Apparently, Bioinformatics is the bridge between both sciences. In fact, Bioinformatics is a SET of bridges, connecting several subjects in both sides. In this talk we briefly report 5 years of collaboration between LABIO (Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas) and GPIN (Grupo de Pesquisa em Inteligência de Negócios) at PUCRS, present our research lines and summarize our main achievements. In special, we cover our efforts on improving the rational drug design by using scientific workflows and employing KDD (knowledge discovery on databases) techniques, considering the receptor flexibility. Oriented to undergraduate and graduate students, young researchers and newcomers, we intend to draw a picture of this type of partnership, showing how long the road to effective get promising results is, how difficult it is (mainly for students), and how gratifying it can be.