Now showing items 1-9 of 9

  • Exploiting different levels of parallelism in the biological sequence comparison problem 

    Sánchez Castaño, Friman; Ramírez Bellido, Alejandro; Valero Cortés, Mateo (2009-04-23)
    Conference report
    Open Access
    In the last years the fast growth of bioinformatics field has atracted the attention of computer scientists. At the same time, de exponential growth of databases that contains biological information (such as protein and ...
  • Long DNA sequence comparison on multicore architectures 

    Sánchez Castaño, Friman; Cabarcas, Felipe; Ramírez Bellido, Alejandro; Valero Cortés, Mateo (Springer Verlag, 2010)
    Conference report
    Restricted access - publisher's policy
    Biological sequence comparison is one of the most important tasks in Bioinformatics. Due to the growth of biological databases, sequence comparison is becoming an important challenge for high performance computing, especially ...
  • On the scalability of 1- and 2-dimensional SIMD extensions for multimedia applications 

    Sánchez Castaño, Friman; Álvarez Mesa, Mauricio; Salamí San Juan, Esther; Ramírez Bellido, Alejandro; Valero Cortés, Mateo (Institute of Electrical and Electronics Engineers (IEEE), 2005)
    Conference report
    Open Access
    SIMD extensions are the most common technique used in current processors for multimedia computing. In order to obtain more performance for emerging applications SIMD extensions need to be scaled. In this paper we perform ...
  • Parallel processing in biological sequence comparison using general purpose processors 

    Sánchez Castaño, Friman; Salamí San Juan, Esther; Ramírez Bellido, Alejandro; Valero Cortés, Mateo (Institute of Electrical and Electronics Engineers (IEEE), 2005)
    Conference report
    Open Access
    The comparison and alignment of DNA and protein sequences are important tasks in molecular biology and bioinformatics. One of the most well known algorithms to perform the string-matching operation present in these tasks ...
  • Performance analysis of sequence alignment applications 

    Sánchez Castaño, Friman; Salamí San Juan, Esther; Ramírez Bellido, Alejandro; Valero Cortés, Mateo (Institute of Electrical and Electronics Engineers (IEEE), 2006)
    Conference report
    Open Access
    Advances in molecular biology have led to a continued growth in the biological information generated by the scientific community. Additionally, this area has become a multi-disciplinary field, including components of ...
  • Preliminary analysis of the cell BE processor limitations for sequence alignment applications 

    Isaza, Sebastian; Sánchez Castaño, Friman; Gaydadjiev, Georgi; Ramírez Bellido, Alejandro; Valero Cortés, Mateo (Springer, 2008-07-21)
    Conference report
    Restricted access - publisher's policy
    The fast growth of bioinformatics field has attracted the attention of computer scientists in the last few years. At the same time the increasing database sizes require greater efforts to improve the computational performance. ...
  • Quantitative analysis of sequence alignment applications on multiprocessor architectures 

    Sánchez Castaño, Friman; Ramírez Bellido, Alejandro; Valero Cortés, Mateo (ACM Press. Association for Computing Machinery, 2009)
    Conference report
    Restricted access - publisher's policy
    The exponential growth of databases that contains biological information (such as protein and DNA data) demands great efforts to improve the performance of computational platforms. In this work we investigate how bioinformatics ...
  • Scalability analysis of progressive alignment in a multicore 

    Isaza, Sebastian; Sánchez Castaño, Friman; Gaydadjiev, Georgi; Ramírez Bellido, Alejandro; Valero Cortés, Mateo (IEEE Press. Institute of Electrical and Electronics Engineers, 2010)
    Conference report
    Open Access
    Sequence alignment is a fundamental instrument in Bioinformatics. In recent years, numerous proposals have been addressing the problem of accelerating this class of applications. This, due to the rapid growth of sequence ...
  • The SARC architecture 

    Gaydadjiev, Georgi; Isaza, Sebastian; Ramírez Bellido, Alejandro; Cabarcas, Felipe; Juurlink, Ben; Álvarez Mesa, Mauricio; Sánchez Castaño, Friman; Azevedo, Arnaldo; Meenderinck, Cor; Ciobanu, Catalin (2010-10)
    Article
    Open Access
    The SARC architecture is composed of multiple processor types and a set of user-managed direct memory access (DMA) engines that let the runtime scheduler overlap data transfer and computation. The runtime system automatically ...