Search Results for "reference" - Page 50
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Showing 2124 open source projects for "reference"
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SOAPdenovo2
Large-size genome de-novo assembler
What's next of SOAPdenovo2: MEGAHIT is the formal successor of SOAPdenovo2 MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph http://www.ncbi.nlm.nih.gov/pubmed/25609793 https://github.com/voutcn/megahit Latest Code on GitHub: https://github.com/aquaskyline/SOAPdenovo2 SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for human-sized genomes. The program is specially designed to assemble Illumina short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. SOAPdenovo2 is the successor of SOAPdenovo. Cite the paper published in GigaScience (see website below) if you want to cite SOAPdenovo2. -
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libpop3
a lightweight ANSI C library for handling POP3 mailboxes
libpop3 is a very light POP3 library for C. It allows to list, fetch and remove messages from a POP3 mailbox. This library is using the RFC1939 as reference, and uses most basic POP3 commands to provide maximum compatibility across different servers. libpop3 is written in pure ANSI C89 without any external dependencies, thus it can be compiled and used on anything, anywhere. Since it is very light, it is designed to be used as a static library (but you could just as well incorporate its code right into your project). -
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Spherical Harmonics Manipulator
Software to make fast synthesis of spherical harmonics global models
This software computes synthesis of spherical harmonics models on sparse coordinates or grids (provided in a geodetic or geocentric reference system). It exploits basic parallelism using openmp directives. A solution with MPI has not be taken into account since it cannot be so easily manageble by final users. -
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NGS_AMAS
All-Mapping tool using Adaptive Seeds
AMAS is designed to find all possible mapping locations of NGS reads in a reference genome with up to a given number of errors (mismatches+gaps). AMAS features an efficient and accurate strategy of partition and filtration of adaptive seeds to speed up the read mapping while preserving the sensitivity. -
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vtens_EI_clock1
vtens_EI_clock1. GPGPU
vtens_EI_clock1. Discovering Regulatory Network Topologies Using Ensemble Methods on GPGPUs With Special Reference to the Biological Clock of Neurospora crassa -
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Aspose Maven for Eclipse
Aspose Maven for Eclipse lets you create Aspose Maven based projects.
This is new Eclipse IDE Plugin released by Aspose pty ltd, but for creating the Aspose Maven based projects in Eclipse IDE. Comes with "Aspose Maven Project Wizard" which let you create Aspose Maven based project by selecting Aspose Java APIs through the wizard steps and add the references of Aspose APIs Maven dependencies into the newly created Maven Project's pom.xml. Created Aspose maven based project will always contain the selected Aspose Java APIs latest version Maven... -
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A free Java based reference library for reading and saving Portable Shogi Notation (psn) files. Also, a document explaining the creation of ‘*.psn’ files and their relation to '*.kif' files.
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xxe
Intentionally vulnerable web services exploitable with XXE
An XML External Entity attack is a type of attack against an application that parses XML input. This attack occurs when XML input containing a reference to an external entity is processed by a weakly configured XML parser. This attack may lead to the disclosure of confidential data, denial of service, port scanning from the perspective of the machine where the parser is located. This zipped Ubuntu VM is set up as a Capture the Flag with those that successfully exploit the XXE vulnerability able to place their name on a leaderboard. ... -
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Chunk File Upload Memory limited devices
iphone and android has limited memory.
Uploading file from a browser application to the server from memory limited devices such as iphone The purpose of this project is to give a reference implementation to upload big files which are taken by the screen shot from an iphone on safari or chrome as well as on android os. The device limited memory does not allow the big file; usually images file but can be any file to load into memory. The limitation make the file upload from a browser or even from a native application is not possible. ... -
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HistoryLoc
HistoryLoc is a practical system to track place names over time.
The goal of the HistoryLoc project is to develop a practical means to track place names over time. It will do this by developing a C/C++ library and a reference program. -
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PRADA
PRADA : Pipeline for RNA-Sequencing Data Analysis
Massively parallel sequencing of cDNA reverse transcribed from RNA (RNASeq) provides an accurate estimate of the quantity and composition of mRNAs. To characterize the transcriptome through the analysis of RNA-seq data, we developed PRADA. PRADA focuses on the processing and analysis of gene expression estimates, supervised and unsupervised gene fusion identification, and supervised intragenic deletion identification. PRADA currently supports 7 modules to process and identify... -
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PC Delphi
The PC Delphi System
Reference Implementation for the PC Delphi project, a ranking system utilizing pairwise comparisons and the Delphi method in order to enable collaborative decision making. Binaries available here: http://discomalaria.net/PC_Delphi/ -
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mobiQ Lab
Create your own mobile test lab using popular opensource tools
...A client server approach let you submit tests from anywhere within your network. You can run tests in parallel on multiple devices, access reports and configure devices. The comprehensive reference guide will help you understand MobiQ in depth. Go to Files to download it. -
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CIMS
Crosslinking induced mutation site analysis
This package includes the scripts to detect statistically reproducible crosslinking induced mutation sites (CIMS) and cross linking induced truncation sites (CITS) from HITS-CLIP data. References: Moore, M.*, Zhang, C.*, Gantman, E.C., Mele, A., Darnell, J.C., Darnell, R.B. 2014. Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis. Nat Protocols, 9:263-293. Zhang,C.†, Darnell, R.B.† 2011.... -
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LibppGam
pp->gamma cross sections parametrization
This library contains the parametrization of pp->gamma cross section functions based on Phys.Rev. D90 (2014) 12, 123014 (astro-ph/1406.7369) work. The functions are written in Python, Fortran and Matlab. Please, if you use this library DO NOT reference to this webpage, instead reference to Phys.Rev. D90 (2014) 12, 123014 (astro-ph/1406.7369), "Parametrization of gamma-ray production cross-sections for pp interactions in a broad proton energy range from the kinematic threshold to PeV energies" by Ervin Kafexhiu, Felix Aharonian, Andrew M. Taylor, Gabriela S. Vila -
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UniPyRange
Tool to fetch protein/DNA truncation constructs from Uniprot DB
... - Requires BioPython (3) and Bioservices Package (4) (1) The UniProt Consortium UniProt: a hub for protein information Nucleic Acids Res. 43: D204-D212 (2015). (2) RefSeq: an update on mammalian reference sequences. Nucleic Acids Res. 2014 Jan 1;42(1):D756-63. (3) Cock PJ et al. Bioinformatics (2009) (4) Cokelaer et al, Bioinformatics (2013) -
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igafem
Open source 3D Matlab Isogeometric Analysis Code
...The work is funded under the FP7 Initial Training Network Funding under grant number 289361 'Integrating Numerical Simulation and Geometric Design Technology.' If you use this code or inspired by it please cite the following reference in your work: VP Nguyen, C Anitescu, S Bordas, T Rabczuk. "Isogeometric analysis: an overview and computer implementation aspects". Mathematics and Computers in Simulation, (2015), pp. 89-116, Vol 117. -
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Maggie OpenMax Player
The OpenMax based Media Player for Embedded platform
...The component plugins are implemented to realize the demo playback functionalities. The code could be found under the directory: omx_il/vendors, which could be the reference code to guide your writing the libraries upon the different embedded platforms. 2) Mag Player library, the multimedia player based upon the Mag OpenMax layer. It provides the set of APIs to control the media playback and displays the playing status. -
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libnifty
Nifty pthread modules for C programs
...libnifty modules provide APIs that are safe, simple, and easy to use. Using libnifty will help to make your threaded programs stable, scalable and performant. libnifty modules are based on a common core that implements reference-counted objects that are accessible via handle-based APIs. This core is extensible in object-oriented style via single inheritance, with strong static type checking and runtime type checking. -
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NoiseRed
Protein alignment noise reduction
The project consists of reading alignments and removing noisy columns that fall under three requirements: 1) more than 50% are indels; 2) more than half of the proteins show unique amino acid in the given column; and, 3) if no amino acid appears more than twice in the column analyzed. The efficiency is tested by generating trees and comparing them with reference trees. Furthermore, a statistical analysis is performed to infer the suitability of the method. -
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MSL
http://dx.doi.org/10.1002/jcc.22968
...Philosophy The main goal is to create a set of tools that enable the computational study of macromolecules with relative ease at all levels, from simple operations (for example, load a PDB and measure a distance or edit a dihedral) to complex applications (protein modeling or design). MSL is developed in the Senes Lab at the University of Wisconsin-Madison and by a team of developers/users from other research laboratories. Reference: Kulp DW, Subramaniam S, Donald JE, Hannigan BT, Mueller BK, Grigoryan G, Senes A. Structural informatics, modeling, and design with an open-source Molecular Software Library (MSL). J Comput Chem. 2012 vol. 33 pages 1645-61 Download article at http://dx.doi.org/10.1002/jcc.22968 -
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Aspose Maven for NetBeans
Creates a new NetBeans maven based project for Aspose APIs.
This is another NetBeans IDE Plugin released by Aspose pty ltd, but for creating the Aspose Maven based projects in NetBeans IDE. Comes with "Aspose Maven Project Wizard" which let you create Aspose Maven based project by selecting Aspose Java APIs through the wizard steps and add the references of Aspose APIs Maven dependencies into the newly created Maven Project's pom.xml. Created Aspose maven based project will always contain the selected Aspose Java APIs latest version Maven... -
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Freestyle Learning (FSL) and Open University Support System (OpenUSS) are specifications for Learning Content System (LCS) and Learning Management System (LMS). They provide J2SE, J2ME and J2EE reference implementations on those specifications.
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Homeo Medica
HomeoMedica a free and easy-to-use clinic management system.
Homeo Medica is a free, open source, light-weight and easy-to-use windows based clinic management software just for You.. Save your time to keep track of medicines. [[NEW VERSION IS UPLOADED]] -
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MFImport
Measurement Flight Import
Based on ATSDB, this application allows reading text-based GPS trails from Measurement Flights, adding of Mode S/A attributes and inserted into the database.
