TaxoGrid: Molecular Phylogeny on Garuda Grid
Molecular phylogeny is a fundamental aspect of understanding the evolution and is one of the downstream genome analysis pipelines. This pipeline has been incorporated in TaxoGrid portal and deployed on the Indian grid computing initiative GARUDA. TaxoGrid is a grid-based portal which implements the phylogenetic analysis, viz. ortholog detection using database similarity searching, multiple sequence alignment and phylogenetic reconstruction. The analysis is executed in an automated manner as a bioinformatics workflow and is capable of efficiently handling voluminous data owing to the availability of parallel implementation of tools over the vast compute resources of grid.
Keywords: Embarrassingly parallel, scientific computing, molecular phylogeny, bioinformatics workflow, grid.
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ABOUT THE AUTHORS
Amit Saxena
Amit Saxena received MCA degree from Mohan Lal Sukhadia University, Udaipur, India, in 2003. His research interests include grid computing and Java related technologies.
Rajendra Joshi
Rajendra Joshi received his PhD in Biochemistry from National Chemical Laboratory, Pune in 1994. His research interests include use of high performance parallel computers for biological research. He has ~25 papers published in international peer reviewed journals.
Sonal Dahale
Sonal Dahale received M. Sc. (Biochemistry) degree from DAVV University, Indore India, in 2006. Her research interests include molecular phylogeny and metabolic pathway reconstruction. She has published in PlosOne journal.
Sankalp Jain
Sankalp Jain received M.Tech (Computer Science) degree from DAVV University, Indore India, in 2008. His research interests grid computing and perl programming.
E. Ramakrishnan
E. P. Ramakrishnan received ME (Computer Science) degree from Anna University, Chennai, India, in 2008. His research interests include user interface design and implementation in Java.
Vivek Gavane
Vivek Gavane received M.Tech (AI) degree from RJPV University, Bhopal India, in 2005. His research interests artificial intelligence and parallel programming.
Renu Gadhari
Renu Gadhari received BE (Computer Science) degree from BAMU University, Aurangabad India, in 2006. Her research interests development in J2EE.
Pankaj Vats
Pankaj Vats received M.Tech (Bioinformatics) degree from SASTRA University, Tamil Nadu, India, in 2007. His research interests include Genome Analysis and Machine learning.
Sunitha Manjari K
Sunitha Manjari Kasibhatla received Advanced Diploma in Bioinformatics from University of Pune in 2000. Her research interests include comparative genomics. She has published 6 research articles in journals like PlosOne, Nucleic Acids Research, BMC Bioinformatics, Proteins Peptide Letters, Journal of Virology and Journal of Bacteriology.
Rashmi Mahajan
Rashmi Mahajan received M. S. (Computer Science) degree from UNCC University, North Carolina USA, in 1998. Her research interests software design and development using OOPS and Java technology.
Amit Saxena
Amit Saxena received MCA degree from Mohan Lal Sukhadia University, Udaipur, India, in 2003. His research interests include grid computing and Java related technologies.
Rajendra Joshi
Rajendra Joshi received his PhD in Biochemistry from National Chemical Laboratory, Pune in 1994. His research interests include use of high performance parallel computers for biological research. He has ~25 papers published in international peer reviewed journals.
Sonal Dahale
Sonal Dahale received M. Sc. (Biochemistry) degree from DAVV University, Indore India, in 2006. Her research interests include molecular phylogeny and metabolic pathway reconstruction. She has published in PlosOne journal.
Sankalp Jain
Sankalp Jain received M.Tech (Computer Science) degree from DAVV University, Indore India, in 2008. His research interests grid computing and perl programming.
E. Ramakrishnan
E. P. Ramakrishnan received ME (Computer Science) degree from Anna University, Chennai, India, in 2008. His research interests include user interface design and implementation in Java.
Vivek Gavane
Vivek Gavane received M.Tech (AI) degree from RJPV University, Bhopal India, in 2005. His research interests artificial intelligence and parallel programming.
Renu Gadhari
Renu Gadhari received BE (Computer Science) degree from BAMU University, Aurangabad India, in 2006. Her research interests development in J2EE.
Pankaj Vats
Pankaj Vats received M.Tech (Bioinformatics) degree from SASTRA University, Tamil Nadu, India, in 2007. His research interests include Genome Analysis and Machine learning.
Sunitha Manjari K
Sunitha Manjari Kasibhatla received Advanced Diploma in Bioinformatics from University of Pune in 2000. Her research interests include comparative genomics. She has published 6 research articles in journals like PlosOne, Nucleic Acids Research, BMC Bioinformatics, Proteins Peptide Letters, Journal of Virology and Journal of Bacteriology.
Rashmi Mahajan
Rashmi Mahajan received M. S. (Computer Science) degree from UNCC University, North Carolina USA, in 1998. Her research interests software design and development using OOPS and Java technology.
