Search Results for "reference" - Page 45
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Showing 2126 open source projects for "reference"
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CT collimation measurements using CR plates. Please reference Bjarnason TA, Yang CY. CT radiation profile width measurement using CR raw data. Journal of Applied Clinical Medical Physics. 2015;16:501-507. Available from: http://www.jacmp.org/index.php/jacmp/article/view/5512
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OpenVPN for Docker
OpenVPN server in a Docker container complete with an EasyRSA PKI CA
...Extensively tested on Digital Ocean $5/mo node and has a corresponding Digital Ocean Community Tutorial. Pick a name for the $OVPN_DATA data volume container. It's recommended to use the ovpn-data- prefix to operate seamlessly with the reference systemd service. Users are encourage to replace example with a descriptive name of their choosing. Initialize the $OVPN_DATA container that will hold the configuration files and certificates. The container will prompt for a passphrase to protect the private key used by the newly generated certificate authority. Miscellaneous write-ups for advanced configurations are available in the docs folder. ... -
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XParallax viu
Software for automated astrometry
XParallax viu is a free software tool for automated astrometric data reduction of astronomic CCD images. It helps astronomers to perform an accurate astrometric reduction of dozens ore even hundreds of images which can be used in subsequent data analysis process. Fit headers generated by this software are fully compatible with other commonly used image utilities like SAO DS9 or Aladin Sky Atlas. -
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ardublockEdu
ArduBlock is a Block Programming Language for Arduino.
ArduBlock is a Block Programming Language for Arduino. The language and functions model closely to Arduino Language Reference. This version of ArduBlock is tweaked to more closely resemble the Arduino language, and is meant to teach kids programming basics before transitioning to C or C++. -
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RGAAT
Reference based genome assembly and annotation for new genome
This program can assemble and/or annotate genome for new genome and known genome upgrade using sequence alignment file (SAM or BAM format), sequence variant file (VCF format or five coloum table (tab-delimited, including chromosome, position, id, reference allele and alternative allele)) or new genome sequence file (FASTA format) based on reference genome sequence file (FASTA format) and annotation file (TBL, GTF, GFF, GFF3 or BED format). -
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Pathoscope
Predicts strains of genomes in Nextgen seq alignment file (sam/bl8)
...Please visit github for the latest version of the software: https://github.com/pathoscope PathoScope takes next-generation sequencing reads from a mixture sample and predicts which genomes are present. We use a Bayesian framework combined with an initial reference-based alignment to assign reads to the correct genome of origin. Pathoscope 2.0: Wiki: http://sourceforge.net/p/pathoscope/wiki/Home/ Tutorial: http://sourceforge.net/projects/pathoscope/files/pathoscope2.0_v0.02_tutorial.pdf Clinical Pathoscope version: http://sourceforge.net/p/pathoscope/wiki/clinical_pathoscope/ PathoQC download: http://sourceforge.net/projects/pathoscope/files/pathoqc_v0.1.4.tar.gz/download Publications: http://www.microbiomejournal.com/content/2/1/33 http://www.biomedcentral.com/1471-2105/15/262 http://genome.cshlp.org/content/23/10/1721 Support: PS: Please send an email to mani2012 at bu dot edu if you have any questions. -
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...PLEASE NOTE: The Biskit source code as well as any later releases are now hosted on https://github.com/graik/biskit The sourceforge repo is only kept here for reference.
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...Yet for applications like metagenomics, where a large amount of data is involved, DIAMOND still takes too much time. We introduce AC-DIAMOND, which attempts to speed up DIAMOND via better SIMD parallelization and reference indexing. Experimental results show that AC-DIAMOND is about 4 times faster than DIAMOND on aligning DNA reads or contigs while retaining the essentially the same sensitivity.
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CATO Clone Alignment Tool
Identifies clone sequences corresponding to set of reference sequences
Specialized sequence alignment software that helps associate the most likely matches of clone sequences to a set of reference sequences. Both sets of sequences are assumed to be nucleotides. -
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Starling Extension Particle System
A particle system for the Starling framework
The Starling Extension Particle System is an ActionScript extension for the Starling framework that enables developers to integrate particle effects created with the "Particle Designer" tool by 71squared into Starling-based applications. The demo-directory contains a sample project. To compile it, add a reference to the Starling library and add the source directory that contains the particle system classes. The project contains 4 sample configurations. Switch between configurations in Demo.as by hitting the space bar. -
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PEM
A Matlab® Tool for Geodetic Reference Frame Definition
PEM allows calculating both the expected velocity value for any point located on the Earth providing a Euler pole (direct problem) and inferring the Euler pole parameters by inverting the observed velocities at a set of sites located on a rigid block (inverse problem). PEM is developed in Matlab® framework and is designed for easy-to-use file exchange with the GAMIT/GLOBK software package, and has a user-friendly graphical user interface (GUI). -
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riboshape
Predicting ribosome footprint profile shapes from transcript sequences
...It applies kernel smoothing to codon sequences to build predictive features, and uses these features to builds a sparse regression model to predict the ribosome footprint profile shapes. Reference: Liu, T.-Y. and Song, Y.S. Prediction of ribosome footprint profile shapes from transcript sequences. Proceedings of ISMB 2016, Bioinformatics, Vol. 32 No. 12 (2016) i183-i191. -
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Adventure: Revisited
Reenactment of the classic Atari 2600 game
...This may be the first instance of some sort of bizarre hybrid. As mentioned above, I used a dissassembled and annotated version of the original game's source code as a reference in creating this software. Certain pieces of the code could be considered "emulation" - for example, the player/missile collision detection is, in a way, emulating that particular part of the original hardware. I also kept all the game data in the same format as the original source where practical to ensure the most accuracy possible. -
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tabipb
A treecode-accelerated boundary integral Poisson-Boltzmann solver
...The linear system is solved by GMRES iteration and the matrix-vector product is carried out by a Cartesian terraced which reduces the cost from O(N^2) to O(N*logN), where N is the number elements. REFERENCE: W.H. Geng and R. Krasny, A treecode-accelerated boundary integral Poisson-Boltzmann solver for continuum electrostatics of solvated biomolecules, J. Comput. Phys. 247, 62-87 (2013) This material is based upon work supported under NSF Grant DMS-0915057, DMS-1418966, DMS-1418957. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the NSF. -
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kakagei
It is a reference implementation of kakagei
It is a reference implementation of kakagei. -
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Techne (R) CAD/CAM
2.5D CAD CAM emphasis on CAM and toolpaths
...So you can create a square that will be machined at a specific depth but the depth will be constant accross the square. It is not/does not: A general purpose CAD (AutoCAD) type program. Support reference dimension on the drawing. Export or import major CAD file formats. -
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GeoNet is a software to perform rigorous least squares adjustment of topographic (Total station, GNSS and levels) observations directly in a global reference frame.
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SVUnit
Systemverilog Unit Test Framework
SVUnit is a unit test framework for developers writing code in systemverilog. Verify systemverilog modules, classes and interfaces in isolation with SVUnit to eliminate bugs before they infest your design! -
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de novo assembly validation
de novo clustering of assembled contigs into two groups
This project deals with de novo assembled contigs to cluster them into two groups forming the lengthwise clusters. These two groups are correctly assembled contigs and wrongly assembled contigs. For non-model organisms, without reference genome, it is very hard to state that which contig is correct and which is not. With this project, the proposed unsupervised clustering method (K-means) based clustering is done utilizing the depth of reads mapping based coverage information. The coverage based features are used for clustering. The same can also be found at SCBB software page (http://scbb.ihbt.res.in/SCBB_dept/Software.php). -
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TermEvaluator
A tool for evaluating automatic terminology extraction.
*For citation please kindly reference the following work: -Inkpen D., Paribakht, T. S., Faez F., and Amjadian, E. 2016. International Journal of Computational Linguistics and Applications. This is a tool to evaluate terminology extraction performed on corpora. Human judges can choose if an extracted term is correct, or incorrect. Already known terms (say from a dictionary) can be imported to the tool and marked automatically as correct by the tool so that the annotators won't have to judge them. ... -
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Import from github_com
Python module finder/loader from github, like in golang
...The idea is to remove the friction of “clone → install → import” when you just want to try out a single file or small repo. It hooks into Python’s import machinery so that when you reference a GitHub path, it fetches the code, stores it locally (often with caching), and makes it importable in the current environment. This is helpful for prototyping, teaching, or quickly exploring other people’s utilities without polluting your global site-packages. It also demonstrates how flexible Python’s import system is and can be used as a reference for custom importers. ... -
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GPX to UTM reference converter
Convert your GPX coordinates to UTM reference coordinates
Just select Garmin GPX file, and software automatically converts waypoints to UTM reference coordinates and saves to the file specified. Requirements: JAVA 8 and Visual Studio Redistributable 2010 x86 -
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allim
Allelic imbalance meter (Allim), a new tool for measuring allele speci
...Since mapping bias is the largest problem for reliable estimates of allele specific gene expression using RNA-seq, Allim combines two different measures to account for mapping biases. First, Allim generates a polymorphism aware reference genome that accounts for the sequence variation between the alleles of both parents (or parental lines). Second, Allim includes a sequence specific simulation tool to estimate the remaining mapping bias. This estimated mapping bias is then incorporated in the statistical tests for allelic imbalance -
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Brainstorm Network
Software to organize a brainstorm as a complex network.
...With this organization the users are able to visualize the main points of the brainstorm (the hubs in the network). Moreover, they can access the information through the rede, interactively, clicking on the edges or nodes! All information is associated with a reference list (imported from a bibtex file). This project uses Python, Web2py, MariaDB and VIS.js (D3.js). -
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TAG
A tool for metatranscriptome assembly using metagenome graph
TAG is a tool for metatranscriptome assembly using de Bruijn graph of matched metagenome as the reference. TAG is an application of a reads mapping algorithm that we developed for mapping of short reads onto a de Bruijn graph of assemblies. A hash table of junction k-mers (k-mers spanning branching structures in the de Bruijn graph) is used to facilitate fast mapping of reads to the graph. We have shown that TAG helps to assemble substantially more transcripts from metatranscriptomic datasets that otherwise would have been missed or truncated because of the fragmented nature of the reference metagenome. ...
