Search Results for "data model"
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Showing 19 open source projects for "data model"
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Biber is a sophisticated bibliography processing backend for the LaTeX biblatex package. It supports a unsurpassed feature set for automated conformance to complex bibliography style requirements such as labelling, sorting and name handling. It has comprehensive Unicode support.
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Pretty Damn Quick (PDQ) analytically solves queueing network models of computer and manufacturing systems, data networks, etc., written in conventional programming languages. Generic or customized reports of predicted performance measures are output.
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MetaErg
Metagenome Annotation Pipeline
MetaErg is a stand-alone and fully automated metagenome and metaproteome annotation pipeline published at: https://www.frontiersin.org/articles/10.3389/fgene.2019.00999/full. If you are using this pipeline for your work, please cite: Dong X and Strous M (2019) An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs. Front. Genet. 10:999. doi: 10.3389/fgene.2019.00999 The instructions on configuring and running the MetaErg pipeline is available at GitHub... -
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datasw
datasw, a tool for rapid processing of HPLC-SAXS data.
Small-angle X-ray scattering (SAXS) in solution is a common low-resolution method which can efficiently complement high-resolution information obtained by crystallography or NMR. Sample monodispersity is key to reliable SAXS data interpretation and model building. Beamline setups with inline high-performance liquid chromatography (HPLC) are particularly useful for accurate profiling of heterogeneous samples. The program DATASW performs averaging of individual data frames from HPLC-SAXS... -
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Hamstr
A tool for directed ortholog search in ESTs and proteins
HaMStR has moved to https://github.com/bionf/hamstr where it is now part of the HaMStR-OneSeq package. HaMStR is a profile hidden Markov model based tool for a directed ortholog search in EST or protein sequence data. The program takes a pre-defined core group of orthologous sequences (core orthologs) and a set of sequences from a search taxon as input. HaMStR then combines in a two-step strategy a pHMM based search and a reverse search via BLAST to extend the core ortholog group with novel... -
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ViralFusionSeq [VFS]
Accurately discover viral integration events and fusion transcripts
.... VFS combines soft-clipping information, read-pair analysis, and targeted de novo assembly to discover and annotate viral-human fusion events. A simple yet effective empirical statistical model is used to evaluate the quality of fusion breakpoints. Minimal user defined parameters are required. Source code with user manual and installation guide of VFS is available at sourceforge's "Files" section. Citation: http://www.ncbi.nlm.nih.gov/pubmed/ -
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GMOD is a set of interoperable open source software components for visualizing, annotating, and managing biological data. See http://gmod.org for more.
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miRNA Temporal Analyzer (mirnaTA)
Differential expression analysis tool for miRNAs in temporal studies
..., and the normalized data is analyzed using linear regression model to locate any miRNAs which are differentially expressed in a linear manner. Any miRNAs with P-value<0.05 are considered statistically significant. Remaining miRNAs which did not fit in linear model are further analyzed in two different methods: (1) if the number of time points <3, CDF of the normal distribution, and (2) if the number of time points is >= 3, ANOVA is utilized. http://www.gigasciencejournal.com/content/3/1/20 -
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ADM to GPX
Convert a Garmin ADM database file to a GPX file
User data exported from later model Garmin GPSmap marine GPS sets consists of ADM files written to a VFAT-formatted SD card. This data includes user-generated waypoints and routes, and recorded GPS tracks. adm2gpx converts this data to industry-standard GPX records that may be imported into third-party mapping and GPS software. -
SKUDONET Open Source Load BalancerSKUDONET is designed to enhance service quality with advanced load balancing capabilities. Allowing scale your infrastructure effortlessly while maintaining unwavering data security, ensuring the continuity of your operations.
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hrefinder
Detection of homologous recombination events from SNP data
This software detects homologous recombination events (HREs) from SNP data. Based on SNP alleles calls and locations, it breaks the genomes into locally colinear blocks, and looks for cases where SNPs do not agree with the vertical pattern of inheritance in a phylogeny. It applies a dynamic programming algorithm to model whether changes within a block are likely a result of mutations, sequencing errors, or HRE. We use information from the nearby SNPs, so that if 1-2 alleles in a series of SNPs... -
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HPeak
A HMM-based algorithm for defining enriched regions from ChIP-seq data
HPeak is a hidden Markov model-based approach that can accurately pinpoint regions to where significantly more sequence reads map. Testing on real data shows that these regions are indeed highly enriched by the right protein binding sites. Command (single-end): perl /compbio/software/HPeak3/HPeak.pl -sp HUMAN/MOUSE -format BED -t TREATMENT.inp -c CONTROL.inp -n OUTPUTPREFIX -fmin 100 -fmax 300 -r 36 -ann -wig -seq -interfiles Command (pair-end): perl /compbio/software/HPeak3/HPeak.pl -sp... -
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segment
Solve the Viterbi algorithm in a data stream
It is often necessary to assign a series of discrete values to continuosly variable data sequenced by time, position, etc., thereby parsing the data into fewer and larger segments of variable width. The 'segment' utility takes an input data stream as a Hidden Markov Model and applies the Viterbi algorithm to find the most likely segmentation path through the data. -
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SOAPstreaming
Hadoop-based Framework for Analyzing Large Scale NGS Data
SOAPstreaming, a flexible hadoop-based framework for systematically analyzing large scale NGS data. SOAPstreaming uses an enhanced Hadoop streaming strategy of MapReduce model to parallelize tools, which offers great scalability and efficiently reduces running time of large NGS datasets. Moreover, it has nice expansion capability to integrate new tools for different analysis needs, which more and more tools will be added in this framework. -
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This project aims the requirement of managed informations / documents in the treatment of patients, i.e. integrated care. The underlaying data model implements standards of electronic health recording, the project is based on a SQL db and Java EE framework. This is currently a student driven project for educational purposes.
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Config::Model enables a project developer to provide a graphical configuration editor for his users. For this, the developer must describe the structure and constraints of his project's config (i.e. the config model). Files are available on CPAN
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The Genomic Diversity and Phenotype Data Model (GDPDM) captures molecular and phenotypic diversity data. MySQL databases are used to implement the schema. This project develops software tools (written in Java, Perl, etc.) associated with this model.
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KML is a knowledge base with support of logical modeling. Advanced model is used to represent knowledge as a set of statements similar to natural language sentences. This project hosts a set of model storage library and server (vrb-ols) and clients.
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A pure-Perl web application environment running under Apache and mod_perl, including an object-oriented data access layer, dynamic content generation, a flexible authorization and security model, application distribution and browser-based administration.
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The Inverse Ocean Model (IOM) is a software system for developing customized data-assimilation systems for numerical ocean models. It has also been used with general purpose hydrodynamic and geodynamic models.
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