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2020-acm-tos_ares

ARES

ares

buranji

cdhit_for_ribocensus

CDHIT for RiboCensus

colas

COLAS This is the source repository for the algorithm source code of the COLAS project. This code base is used for implementing atomicity algorithms developed in the following papers. The tool is desgined to be deployed as a docker container, whihc can be deployed on AWS, OpenStack Cloud and a single stand-along machine. The code is written in C/C++ and GO. References: Kishori M Konwar, N. Prakash, Erez Kantor, Muriel Medard, Nancy Lynch, and Alexander A. Schwarzmann. Storage-Optimized Data-Atomic Algorithms for Handling Erasures and Errors in Distributed Storage Systems, In Proceedings of the 30th IEEE International Parallel & Distributed Processing Symposium (IPDPS 2016), pp. 720-729 (2016). Kishori M Konwar, N. Prakash, Muriel Medard, Nancy Lynch. RADON: Reparable Atomic Data Objects in Networks, In Proceedings of the 20th International Conference on Principles of Distributed Systems (OPODIS 2016). pp. 28:1-28:17 (2016). Kishori M. Konwar, N. Prakash, Nancy Lynch and Muriel Medard. A Layered Architecture for Erasure-Coded Consistent Distributed Storage, In Proceedings of the Principles of Distributed Computing (PODC’17) (2017).

concensus

A set of consensus algorithms in Go where we started from epaxos as the initial code base and modified

correlation_network

With the advent of vast biological data sets biological and medical studies are increasingly relying on computational methods to extract knowledge from the data. Creating correlation-network is one of the methods of reducing the complex data into potential co-occurence of species or microorganisms. This repositor has the codes used in the following paper. Jody J. Wright, Kishori M. Konwar and Steven J. Hallam. Microbial ecology of expanding oxygen minimum zones, Nature Reviews Microbiology 10, 381-394 (June 2012).

disc2020-snow-revisited

distributedmetabolism

ec2pgdb

ecgroupcache

fastpro_single-cell-rna

Fast processing 3' Single-cell RNA pipeine

fuzzyclassifier

This code implements the fuzzy knowledge-based network based on the linguistic rules extracted from a fuzzy decision tree. A scheme for automatic linguistic discretization of continuous attributes, based on quantiles, is formulated. A novel concept for measuring the goodness of a decision tree, in terms of its compactness (size) and efficient performance, is introduced. Linguistic rules are quantitatively evaluated using new indices. The rules are mapped to a fuzzy knowledge-based network, incorporating the frequency of samples and depth of the attributes in the decision tree. New fuzziness measures, in terms of class memberships, are used at the node level of the tree to take care of overlapping classes.The effectiveness of the system, in terms of recognition scores, structure of decision tree, performance of rules, and network size, is extensively demonstrated on three sets of real-life data.

highperformancelowclust

The MPILowClust

hmmer-2.3.1_for_ribocensus

HMMER 2.3.1 for RiboCensus

jgi-download

katomicity

This code implements katomicity and erasure code

key-value-erasure-code

kishori82.github.io

koonkie_mp_trnascan

Slight modificaton of tRNAScan-1.4, the changes are confined to output formatting. Not that this is not the original website by the developers of tRNAScan-1.4.

lacit

lowclust

luitpad

LuitPad is a stand-alone, fully Unicode compliant software designed for rapid typing of Assamese words and characters based on approximate phonetic. There are two main typing options; one which is based on approximate sound of words and the other based on the sound of characters, both of which are efficient and user-friendly, even for a first-time user.

metacount

metapathways_python.3.0

MetaPathways is a meta'omic analysis pipeline for the annotation and analysis for environmental sequence information. MetaPathways is a modular annotation and analysis pipeline that uses a user-friendly graphical user interface and knowledge engine data structure to predict metabolic interaction networks from environmental sequence information. Currently, MetaPathways supports genomic read quality control, open reading frame (ORF) prediction, ORF annotation, and environmental pathway-genomes database (ePGDB) construction compatible with the Pathway Tools browser by SRI.

metapathways_python_koonkie.3.0

This is a cloud based meta'omic analysis pipeline for the annotation and analysis for environmental sequence information. MetaPathways is a modular annotation and analysis pipeline that uses a user-friendly graphical user interface and knowledge engine data structure to predict metabolic interaction networks from environmental sequence information. Currently, MetaPathways supports genomic read quality control, open reading frame (ORF) prediction, ORF annotation, and environmental pathway-genomes database (ePGDB) construction compatible with the Pathway Tools browser by SRI.

metapathways_rpkm

C++ implementation of reads per kilobase mapped statistic. Functional analysis of de novo assembled environmental sequence information is impeded by the lack of quantitative ORF annotations. ORF counts are affected by both sequencing depth and ORF length, longer ORFs naturally encompass more reads, making quantitative comparisons between samples difficult. To resolve this, we have implemented a bwa-based version of the RPKM. Intuitively RPKM is a simple proportion of the number of reads mapped to a sequence section, normalized for sequencing depth and ORF length. This tools is now a part of the MetaPathways pipeline.

metataxa

multi-seq

This project is under development

nca2020-oreas-cassandreas