Bioinformatics Products

Bioinformatics team at C-DAC, is envisaged to serve as a provider of high end computing applications thereby enabling the bioinformatics researchers at academic and industrial organizations to accelerate the rate of their research endeavors and hence product development. The team has been developing and designing useful tools, services and solutions for researchers all over the world. The software development team in Bioinformatics efficiently exploits advantages of complete Software Development Life Cycle. The team expertises in applications development using new age technologies like web services, J2EE, Struts, AJAX, Core JAVA, C++ etc. along with software development over high performance computing clusters, grid technology and new age HPC like Cloud Computing. As an effort in this direction, the team is engaged in building application driven problem solving environments for parallel computing clusters, application specific access portals for Grid computing along with standalone applications.

 

MGAViewerMGAViewer: Multiple Genome Alignment Viewer

To address above-mentioned challenges we have developed a visualization tool viz., MGA-viewer. It is a multiple genome alignment viewer which highlights via pictorial depiction of the conserved and variant regions in prokaryotic genomes. Such a tool aids in providing valuable insights to study evolutionary biology and understand the genome dynamics where events such as gene duplications, insertions, deletions and inversions can be effectively captured. More »

 

Anvaya : A Workflow Environment for High Throughput Comparative Genomics

Anvaya Comprehensive analysis of heterogeneous genomic data requires a flexible platform for running complex queries that is capable of integrating and analyzing large amount of genomic data in pipeline. Anvaya is a software application consisting of interface to Bioinformatics tools and databases in a workflow environment, to execute the set of analyses tools in series or in parallel. One of the unique features of Anvaya is the rules engine that defines rules for logical connection between the existing tools. Anvaya offers the user, novel functionalities to carry out exhaustive comparative analysis via custom tools which are tools with new functionality not available in standard tools and built-in PERL parsers. Anvaya also provides a set of 11 pre-defined workflows for frequently used analysis.

 

GenoPIPE : An Automated Genome Annotation Pipeline on High Performance Cluster

Genopipe The phenomenal growth rate of nucleotide sequencing technologies has enabled rapid generation of volumes of genomic data resulting in a challenge for development of high-throughput pipelines for the downstream analysis of the genomic data. Comparative genomics plays a vital role in the annotation and analysis of closely related organisms. Simultaneous annotation of multiple closely related genomes using a uniform protocol for gene prediction as well as functional annotation can result in improved assignment of annotation. GENOPIPE is an automated pipeline for high-throughout comparative genomics, based on the detection of orthologous groups, which serve as the seed for subsequent annotation and analysis. It also provides data on SNP, paralogs and probable protein coding regions missed by the gene prediction algorithms, hence serving as a reliable supplementary pipeline for prokaryotic genome annotation. The data generated using GENOPIPE helps to understand two important aspects of the bacterial infection i.e., host-specificity and pathogenicity.

CloudConnect: is an easy to use web interface for connecting Cloud.

CloudConnectIt simplifies use of Infrastusture As Service(IAAS) feature of Cloud. CloudConnect abstracts creation of security group, management of network topology, creation of Virtual machine ,elastic block storage & snapshot, automatic mounting of elastic block storage to virtual machine.CloudConnect also provides web based terminal for connecting to virtual machine. CloudConnect simplifies access to IaaS by abstracting creation of security group, management of network topology, creation of Virtual machine, elastic block storage & snapshot, automatic mounting of elastic block storage to virtual machine. CloudConnect is J2EE application developed using JSF, Primefaces, Jcloud api. CloudConnect hides complexities associated with use of LAAS cloud. CloudConnect is portable across clouds while giving user full control to use cloud-specific features.

Past Products

TaxoGrid : Phylogeny on Grid

Taxogrid The phenomenal growth rate of nucleotide sequencing technologies has enabled rapid generation of volumes of genomic data resulting in a challenge for development of high-throughput pipelines for the downstream analysis of the genomic data. Comparative genomics plays a vital role in the annotation and analysis of closely related organisms. Simultaneous annotation of multiple closely related genomes using a uniform protocol for gene prediction as well as functional annotation can result in improved assignment of annotation. GENOPIPE is an automated pipeline for high-throughout comparative genomics, based on the detection of orthologous groups, which serve as the seed for subsequent annotation and analysis. It also provides data on SNP, paralogs and probable protein coding regions missed by the gene prediction algorithms, hence serving as a reliable supplementary pipeline for prokaryotic genome annotation. The data generated using GENOPIPE helps to understand two important aspects of the bacterial infection i.e., host-specificity and pathogenicity.

BioUtils : An interface to Bioinformatics Utilities

Bioutils The phenomenal growth rate of nucleotide sequencing technologies has enabled rapid generation of volumes of genomic data resulting in a challenge for development of high-throughput pipelines for the downstream analysis of the genomic data. Comparative genomics plays a vital role in the annotation and analysis of closely related organisms. Simultaneous annotation of multiple closely related genomes using a uniform protocol for gene prediction as well as functional annotation can result in improved assignment of annotation. GENOPIPE is an automated pipeline for high-throughout comparative genomics, based on the detection of orthologous groups, which serve as the seed for subsequent annotation and analysis. It also provides data on SNP, paralogs and probable protein coding regions missed by the gene prediction algorithms, hence serving as a reliable supplementary pipeline for prokaryotic genome annotation. The data generated using GENOPIPE helps to understand two important aspects of the bacterial infection i.e., host-specificity and pathogenicity.

iMolDock : An interface for Molecular Docking on High Performance Cluster/Grid

iMolDock Pharmaceutical companies are always searching for new leads to develop into drug compounds. One search method is virtual high-throughput screening (vHTS). In vHTS, protein targets are screened against databases of small-molecule compounds to see which molecules bind strongly to the target. Grid enabling docking modules could build effective High Throughput molecular docking pipeline. iMolDock is a cluster-based/ grid-based portal, which provides an interface to Molecular Docking. Molecular Docking techniques are crucial for rational drug discovery process. iMolDock provides two flows: Cluster-based which is a serial flow of filter-omega-fred modules of dock6 and Grid-based, where the input file is split into multiple sub-inputs. Each input file is processed by the filter-omega-fred pipeline in parallel on various grid nodes, hence providing a speed-up in providing output.

 

iMolDockGenomeGRID : Bioinformatics Problem Solving Environment on Grid

GenomeGrid, a grid portal, provides unique solution to highly complicated supercomputing grid with its user-friendly web interface for sequence analysis codes like Smith-Waterman (S-W), FASTA, BLAST, ClustalW and molecular modeling codes like AMBER enabling bioinformatics expertise to utilize maximum amount of available resources. In addition to the development of Grid portal, an application-specific scheduler was built on the Grid environment. It takes input from the user through web interface and depending on the input parameters and the availability of the grid resources, spawns job on to the available grid resource. GenomeGrid implementation design was done on basis of Model- View-Controller (MVC) architectural design recommended for interactive applications using the J2EE technologies.

Contact Us

Dr. Rajendra Joshi
Associate Director & HOD Bioinformatics Group
Centre for Development of Advanced Computing
Pune University Campus,
Ganesh Khind,
Pune - 411 007 India.
Fax: +91-20-2569-4084 Email: rajendra[at]cdac[dot]in