GAMUT: A genomics big data management tool.

Efficient analysis of Single Nucleotide Polymorphisms (SNPs) across genomic samples enable in deciphering the relationship between genotype and phenotype. The core principle behind SNP comparison is to arrive at a probable list of variants that can differentiate two sets of data (populations). Such SNPs have direct applications in array design, genotype imputation and in cataloging of variants in regions of interest. We have developed GAMUT (Genomics bigdAta Management Tool), a big data-based solution for efficient run-time comparison of SNPs across large datasets based on partition of samples belonging to different populations taking into account user-defined splits. The tool is based on client-server architecture with MongoDB at the back-end and JSF with PrimeFaces as the front-end. It is readily deployable on wild-fly server as well as a docker container. Spark-based parallel data uploader enables optimal loading times. GAMUT enables dynamic querying of the large datasets consisting of multiple samples using text-based, chromosome position-based as well as gene-name based options. Various charting options like bar and pie charts along with tabular formats are available to ease the analysis of the queried data. The resultant data pertaining to comparison of genomewide SNPs can also be downloaded in different formats like text, html, json for further stand-alone analysis. GAMUT is available for download at: https://github.com/bioinformatics-cdac/gamut.

Anvaya: a workflows environment for automated genome analysis.

Anvaya is a workflow environment for automated genome analysis that provides an interface for several bioinformatics tools and databases, loosely coupled together in a coordinated system, enabling the execution of a set of analyses tools in series or in parallel. It is a client-server workflow environment that has an advantage over existing software as it enables extensive pre & post processing of biological data in an efficient manner. "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," which automate data-flow between tools that hitherto, required manual intervention. It also provides a set of 11 pre-defined workflows for frequently used pipelines in genome annotation and comparative genomics ranging from EST assembly and annotation to phylogenetic reconstruction and microarray analysis. It provides a platform that serves as a single-stop solution for biologists to carry out hassle-free and comprehensive analysis, without being bothered about the nuances involved in tool installation, command line parameters, format conversions required to connect tools and manage/process multiple data sets at a single instance.

Signals for a transition from surface to bulk emission in thermal multifragmentation.

Excitation-energy-gated two-fragment correlation functions have been studied between E(*)/A = (2-9)A MeV for equilibriumlike sources formed in 8-10 GeV/c pi(-) and p+197Au reactions. Comparison with an N-body Coulomb-trajectory code shows an order of magnitude decrease in the fragment emission time in the interval E(*)/A = (2-5)A MeV, followed by a nearly constant breakup time at higher excitation energy. The decrease in emission time is strongly correlated with the onset of multifragmentation and thermally induced radial expansion, consistent with a transition from surface-dominated to bulk emission expected for spinodal decomposition.