What is STIC-AmSud ?
The Regional Program STIC-AmSud is an initiative of the French cooperation and their
counterparts from Argentina, Brazil, Chile, Paraguay, Peru and Uruguay, aimed to promote
and strengthen the collaboration and to create networks of research and development in the
field of Information and Communication Science and Technology (ICT), through joint
projects.
Its specific objectives are:
- to develop the cooperation in the field of ICT, through the exchange of researchers
and students among South American countries involved, as well as between them
and France.
- to support basic and applied research projects containing a dimension of potential
transfer and technological innovation, with a regional component, between France
and at least two South American partners.
- to favor, in South America, synergies with other multilateral and regional programs in
this area, particularly with the European Union.
- to favor young researcher participation in order to ensure long-lasting cooperation
networks.
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What is BioCloud-EEAmSud ? (put your mouse over purple items to display the associated information)
BioCloud-EEAmSud is a cooperation project integrated by Brazil, Chile and France following the 2012 STIC-AmSud call. Partners in Brazil are Universidade de Brasilia, Universidade Federal Fluminense, and EMBRAPA-Genetic Resources and Biotechnology (CENARGEN), through the support of the
Coordination of Improvement of Senior Staff of the Ministry of Education in Brazil
(CAPES). In Chile, the main partner is Universidad de Santiago de Chile, through the support of the National Commission for Scientific and Technological Research of
Chile (CONICYT). In France, the institutions involved are Mines ParisTech (CRI) and INRIA-Saclay, through the support of the Ministry of Foreign and European
Affairs (MAEE). The international project coordinator is Pr. Maria Emília Machado Telles Walter (UnB). See all cordinators.
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Project goals
This International Cooperation Project involves three research areas: High Performance Computing, Data Storage/Retrieval and Bioinformatics applications. It will integrate the efforts of the INRIA-Saclay, Mines ParisTech, Universidade de Brasília, Universidade Federal Fluminense, Embrapa-Cenargen and Universidad de Santiago de Chile in order to achieve the following goals:
- Investigate which characteristics of Bioinformatics Applications have to be considered when choosing/proposing a Cloud infrastructure. Characteristics such as large-scale data management, workflow orchestration/integration and resource federation will be investigated.
- Investigate and propose new Bioinformatics tools that are adapted to the Cloud environment.
- Investigate and propose new Bioinformatics algorithms that deal with huge data sets, aiming to reduce execution time and/or the amount of memory needed, making them suitable for Cloud Computing environments.
- Investigate which performance metrics must be taken into consideration when running applications on a Cloud environment.
- Joint publications in Journals and Conferences in the areas of Computer Science and Bioinformatics.
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Retrospective snapshots of the collaboration
Taina Raiol giving a talk at Mines ParisTech during her postdoctoral stay (september 2013) Title: Genome and transcriptome projects in Midwest Brazil: challenges and perspectives. see here | Claude Tadonki (french coordinator - CRI) explaining the main computing details after Taina's talk. |
Christine Eisenbeis, Taina Raiol, and Claude Tadonki in Taina's office at INRIA (Taina's postdoctoral stay was between INRIA and Mines ParisTech (CRI)).
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Rafaelli Coutinho, Ubiratam de Paula, Lucia Drummond (UFF coordinator), and Claude Tadonki, during a visit of Claude at UFF in september 2013. | | Lucia and Claude with the computer science colleagues of UFF |
Alba de Melo, Claude Tadonki, and Maria Emilia Walter at Mines ParisTech (CRI) during their visit in France (april 2013) | Claude, Alba, Christine, and Maria Emilia at Orsay (INRIA-Saclay) | Claude, Ubiratam, rafaelli, and Lucia at INRIA-Saclay. |
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University of Brasilia (UnB): The researchers at UnB have been working on High Performance Computing and Bioinformatics for more than a decade. We have proposed efficient tools and algorithms for Biological Sequence Comparison Applications that run on clusters, grids, reconfigurable hardware, GPUs and, more recently, clouds.
Federal Fluminense University (UFF): The researcher at UFF has been working on parallel and distributed computing for more than two decades. In that period, it has been proposed novel cluster and grid enabled algorithms to solve load balance, fault tolerance and scheduling problems in several combinatorial optimization applications.
Embrapa-CENARGEN: The researchers at the Bioinformatics Laboratory from Embrapa Genetic Resources and Biotechnology are involved in next generation sequencing analysis for several projects (SNP discovery, Metagenomics,
Transcriptomics, genome sequencing and re-sequencing). Due to the large number of data to be analyzed, we are using a distributed computational environment based on a grid computing infrastructure SGE and Galaxy as the framework to control the processing.
University de Santiago de Chile (USACH): The researchers at USACH have expertise in all aspects of parallel and distributed computing applied to Web search engines. This has lead to the formulation of complex discrete-event simulation models of data centers to experiment with new techniques developed for large-scale Web search engines. These researchers are also involved in Yahoo! Labs Santiago, which provides facilities to test solutions in an actual environment consisting of traces from millions of users and terabytes of data deployed in very large clusters running Hadoop. In particular, they have been involved in a project related to the development of simulations models oriented to support capacity planning methods for Yahoo! vertical Web search engines.
Mines ParisTech (CRI): The researchers at USACH have expertise in all aspects of parallel and distributed computing applied to Web search engines. This has lead to the formulation of complex discrete-event simulation models of data centers to experiment with new techniques developed for large-scale Web search engines. These researchers are also involved in Yahoo! Labs Santiago, which provides facilities to test solutions in an actual environment consisting of traces from millions of users and terabytes of data deployed in very large clusters running Hadoop. In particular, they have been involved in a project related to the development of simulations models oriented to support capacity planning methods for Yahoo! vertical Web search engines.
INRIA-Saclay (Grand Large): At INRIA-Saclay, the researchers have expertise in performance evaluation models and power-aware systems. They have been working on performance evaluation for more than a decade, with important scientific contributions.
BioCloud coordinators
Université Paris-Sud/INRIA-Saclay | France
| Christine Eisenbeis |
Mines ParisTech | France
| Claude Tadonki |
Universidade de Brasilia | Brazil
| Maria Emília Machado Telles Walter |
Universidade Federal Fluminense | Brazil
| Lúcia Drummond |
EMBRAPA-Genetic Resources and Biotechnology (CENARGEN) | Brazil
| Roberto Coiti Togawa |
Universidad de Santiago de Chile | Chile
| Mario Inostrosa-Ponta |
International Project Coordinator | | Maria Emília Machado Telles Walter |