Softwares As Service
These applications are available as service on CLOUD:
Mobile Apps for Android OS: I make Applications in Java for Android OS devices such as for mobile phones and tablets. Some sample registration and screensaver apps are provided for download to the following links: Registration Database App , ScreenSaver App .
WasDocs : Android App for keeping information and notes classified. Can be downloaded from Play Store https://play.google.com/store/apps/details?id=com.abiotek.wasdocs .
BWT+: UltraFast Accurate Read Aligner based on popular Burrows-Wheeler Transform algorithm. Tested on a local machine.
MSECT : Massive String/Sequence Exhaustive Comparison Tool is primarily a bioinformatics application for comparing several strings of the order of several gigabytes to terabytes for exhaustive extraction of the component of interest. However, it can be applied to any string of interest such as financial data. MSECT operated on BLAST for Celera and NCBI human genomes and returned the set of results which comprised of about 15 terabytes of space from operation of only 6 gigabytes of data! The results could then be parsed to applications such as InSilicoCGH or can be used to find copy number variations (CNVs), SNPs, InDels and other structural variations. This application was tested on Sharcnet cluster in Ontario, Canada. Below is a sample output from Celera vs NCBI genome at a loci of interest.
GenomeBreak: A versatile tool for rapid and exhaustive detection of SNPs and InDels in a genome. This software has multiple versions to adapt to the clients resources and needs and was tested on requin supercomputer at Groningen, The Netherlands, for 'Genome of The Netherlands' GoNL project. This software is an evolved version of MSECT application and I developed it while working for my startup in Delhi. This is the only application to date in bioinformatics world which can find InDels in the wide range of as low as 1 base-pair to as long as 1,000,000 base-pair to be able to visualize on FISH microscope.
Below is a sample bioinformatics confirmation discovery of paternal mitochondrial leakage inheritance via SNPs found by GenomeBreak ( A105A - father, A105B - mother, A105C - daughter & A105D - daughter ) that was published in UPCP 2012, Florence.
ProteomeBreak : This application is a Java based standalone script that is useful for noise removal and thereby prediction of signal strength of a Maldi CE-MS data.
InSilicoCGH : This mimics the Comparative Genomics Hybridization microarray bench work on a computer. Feeds in input from MSECT result. Tested on Sharcnet cluster in Ontario, Canada.
CNVdetector : This feeds in the input from InSilicoCGH result. Based on user criteria can extract copy number variations at regions of interest. Tested on Sharcnet cluster in Ontario, Canada.
InDelSNIPER : This application is useful for finding out small insertions and deletions and SNPs from an aligned BAM format file. Can be operated locally on laptop as well.
Parallel Gene Hunters: mpiGlimmer, mpiTigrScan, smpGlimmer, smpTigrScan . These applications were tested at LosLobos cluster at University of New Mexico.
Improved Collective MPI calls codes: In case you want improved performance with collective call function in Message Passing Interface such as collective point-to-point communication, all-to-all personalized communication, etc. I built some C++ based functions for these operations. Perhaps they will be merged with OpenMPI or MPICH2 eventually. These codes were tested on Titan cluster at Mississippi State University.
HokieCrossBow : A private cloud adapted version of SNP detector from NGS data Crossbow which uses bowtie as aligner and modified SOAPsnp as SNP finder. This is essentially a bug fix version of CrossBow 1.2.0 with added automated wrapper script on top of it for ease of scalable performance on local cluster while retaining cloud functionality. It was tested on HokieSpeed supercomputer at Virginia Tech.
DrGenie : Doctor Genie looks for expression levels and differentiation of a gene and determines SNPs and InDels in the gene of interest and does genotyping. It is suitable for evaluating RNA-Seq data analysis on cloud for transcription analysis.