Search Results for "user mode linux" - Page 3
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Showing 172 open source projects for "user mode linux"
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PlaTypUS
Plasmodium Typing Utility Software
The goal of PlaTypUS is to establish a unified Plasmodium whole genome analysis tool, that aligns short read sequences in an agreed upon manner, with many quality control steps, and calls both SNVs and CNVs in a community agreed standard way. We also seek to provide this analysis in a stand-alone graphic user interface so that labs around the world can analyze their own whole genome sequencing data, rather than relying on outside institutes. -
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Elastic network models (ENMs) have been shown to generate the dominant functional equilibrium motions of biomolecules quickly and efficiently. MAVEN simplifies ENM generation, allows for diverse models to be used, and facilitates useful analyses.
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[DEPRECATED] Gene Ontology
The DEPRECATED legacy location of the GO, see http://geneontology.org
The DEPRECATED legacy of the Gene Ontology project on SourceForge. Please see http://geneontology.org for current software and downloads. -
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q pipeline manager
q: integrated platform for pipeline configuration and management
The q utility is a platform for creating and managing data analysis pipelines. It expands the value of your existing job scheduler - either Grid Engine or TORQUE PBS - through numerous functions that help you organize, submit, monitor, manage and share your informatics work. Data processing pipelines require high-level organization and parallelization of work to optimize resource utilization and decrease the time to results. q (from queue) allows complex job sequences to be efficiently... -
Our CPQ covers your entire sales-to-production process. Configure products, calculate pricing, send quotes to customers, secure and order, and generate engineering documents. All with Configure One Cloud.
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The DeconSeq tool can be used to automatically detect and efficiently remove sequence contamination from genomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface. More at http://deconseq.sourceforge.net
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A bioinformatics tool to PRe-process and show INformation of SEQuence data. The tool is written in Perl and can be helpful if you want to filter, reformat, or trim your sequence data. It also generates basic statistics for your sequences.
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AutoMap
AutoMap is a tool for structural biology and drug design.
AutoMap takes a series of poses obtained from molecular docking and applies the site, epitope and conformational mapping techniques to the poses to select likely ligand binding modes. -
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Bioinformatic tools for analyzing an orfeome using translated ORFs and compares each ORF to the provided Orfeome/Proteome. Our script uses NCBI BLAST run locally and MySQL as the main engines in a new and interisting way. It is designed specifically for Poxvirus genomes, and provides the VACV-COP nomenclature and Cowpox Ortholog groups per each ORF. The BLAST stats are generated when compared to the Proteome you provide. It can be easily adapted for other genomes.
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Streamline your customer flow with our SMS-powered waitlist, reservations, and queue management app for restaurants, health care providers, and many other businesses.
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Ergatis is a web-based utility used to create, run, and monitor reusable computational analysis pipelines, utilizing the Workflow engine. It contains pre-built components for common bioinformatics analysis tasks.
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The Blue Obelisk Data Repository lists many important chemoinformatics data such as element and isotope properties, atomic radii, etc. including references to original literature. Developers can use this repository to make their software interoperable.
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ClinStudyWeb is designed to provide a flexible infrastructure for managing patient and assay data from clinical studies. It uses a plugin system for study-specific web forms and arbitrarily complex test classifiers, and supports XML import/export.
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DAWGPAWS is a suite of command line programs written in Perl that accelerates annotation of genes and transposable elements in plant genomes by automating the process of running annotation programs and facilitating combined evidence annotation curation.
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CoVEC
Consensus Variant Effect Classification
The package provides SVM models to be used with SVMlight (http://svmlight.joachims.org/) for drawing a consensus out of individual 3rd-party predictions about the effect of mutations. The 3rd party tools are SIFT, Polyphen2, SNPs&GO and Mutation Assessor. The package also provides a series of Perl modules and scripts to assist in the preparation of data. The modules can be used to build custom tools and pipelines, whereas the scripts provide basic executable implementations based on the... -
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WHATCH'EM
WHATCH’EM simulates mosquito container water temperature
WHATCH’EM simulates the highly non-linear manner in which atmospheric conditions and container characteristics determine water temperature and height, leading to results that are not always intuitive and likely not simulated by simpler empirical models. WHATCH’EM has the capacity to be utilized for other mosquitoes and other container-inhabiting arthropods. -
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easyPAC
easy Primer prediction from Alignments and Consensus sequences
Primer prediction from alignments and consensus sequences. easyPAC applies all standard quality tests to degenerate primer and primer pairs and optionally maps all primer candidates to an arbitrary number of reference files like repeat databases or genomes to ensure target specifity. -
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Pop-seq
Population simulator to solve next generation sequencing questions
Pop-seq is a perl based simulation tool, for generating any kind of mapping population using an user defined recombination landscapes. Combined with the Seq-sim tool you can generate pooled or bar-coded next generation sequencing biased outcomes. This tool were used to solve reappearing question in a experimental design (e. g. of how many plants or sequencing depth is advisable in a back crossed or out crossed scenario ) -
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GenOO-HTS
A Modern Perl Framework for High Throughput Sequencing analysis
GenOO-HTS [jee-noo] is an open-source; object-oriented Perl framework specifically developed for the design of High Throughput Sequencing (HTS) analysis tools. The primary aim of GenOO-HTS is to make simple HTS analyses easy and complicated analyses possible. GenOO-HTS models biological entities into Perl objects and provides relevant attributes and methods that allow for the manipulation of high throughput sequencing data. Using GenOO-HTS as a core development module reduces the overhead... -
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mobcalPARSER
A cross-platform interface for the *.mfj file format.
mobcalPARSER is a command line based PERL frontend/interface for MOBCAL with limited wrapper functionality. "MOBCAL - A Program to Calculate Mobilities" is available from Professor Martin F. Jarrold's webpage http://www.indiana.edu/~nano/software.html. -
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A tool to identify genomic structural variations from paired-end and mate-pair sequencing data
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slurp
IO buffering in parallel environments with large files
'slurp' and 'glurp' are related utilites that help with buffering of file input and output (IO) in parallel environments with large files. They read and write files using a much larger buffer than typical system and program defaults. -
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SunlightCBM is a suite of perl scripts for constraint-based modelling and flux-balance analysis in metabolic networks.
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RICmerge
Improved Isobaric Label Reporter Ion Assignment
This script and underlying data are in support of the manuscript entitled "Improved reporter ion assignment of raw isobaric stable isotope labeled LC-MALDI-TOF/TOF MS/MS spectral data for quantitative proteomics". Authors: Thomas Jakoby, Andreas Tholey and Bart H.J. van den Berg* * = corresponding author bvdberg@live.com -
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Gdraw
An app and a Perl library for genome feature drawing
Gdraw is an genome visualization tool, including a GUI application and a Perl library. The GUI application creates the drawing interactively. It can also create the drawing by import annotated sequence files (such as Genbank, EMBL). Its backend library can be used in user-written perl scripts to create highly customized drawings. -
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Genome-tools provides flexible tools and a simple API for genomic sequence processing on genomes published in the standard Genbank format. A CGI-based web interface is also available. Please cite: Lee, W., Chen S.L. BioTechniques 33:1334-1341 (Dec 20