Search Results for "smith" - Page 2
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Showing 68 open source projects for "smith"
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MatODE
Matlab interface to the Open Dynamics Engine (ODE)
MatODE is a simple Matlab toolbox for interfacing to the Open Dynamics Engine rigid body physics simulator (ODE, by Russell Smith), created by the Delft Biorobotics Lab (Delft University of Technology, Delft, The Netherlands). The system to be simulated is defined in an XML file, while the joint positions and motor signals can be sensed and actuated from a Matlab script. Examples are provided. Starting at version 0.30, MatODE is only available for Windows and Linux 64-bit. ... -
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SWAPHI-LS: Alignment on Xeon Phi Cluster
Smith-Waterman long DNA sequence alignment on Xeon Phi clusters
The first parallel Smith-Waterman algorithm exploiting Intel Xeon Phi clusters to accelerate the alignment of long DNA sequences. This algorithm is written in C++ (with a set of SIMD intrinsic extensions), OpenMP and MPI. The performance evaluation revealed that our algorithm achieves very stable performance, and yields a performance of up to 30.1 GCUPS on a single Xeon Phi and up to 111.4 GCUPS on four Xeon Phis sharing a host. -
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la2vcd2
Convert Logic Analyzer and Oscilloscope data to VCD
This is a fork of la2vcd, http://www.brouhaha.com/~eric/software/la2vcd/ by Eric Smith. It adds a library build, analog data, and several other features. It is used as a library by OpenGpib (http://opengpib.sourceforge.net) for displaying analog and digital waveforms in GTKWave (http://gtkwave.sourceforge.net another excellent project). Much appreciation to Eric for his preliminary work! I've forked it since there has been no development besides mine since 2005. -
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SWAPHI: Smith-Waterman on Intel Xeon Phi
The first protein sequence database search on shared-host Xeon Phis
The first parallel algorithm to accelerate the Smith-Waterman protein database search on shared-host multiple Intel Xeon Phi coprocessors. By searching against the UniProtKB/TrEMBL database, SWAPHI achieves a performance of up to 58.8 billion cell updates per second (GCUPS) on a single Xeon Phi and up to 228.4 GCUPS on four Xeon Phis. -
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CUDAlign
CUDAlign is a tool that aligns huge DNA sequences in CUDA capable GPUs
CUDAlign is a tool able to align pairwise DNA sequences of unrestricted size in CUDA GPUs, using the Smith-Waterman algorithm combined with Myers-Miller. It produces the optimal alignment of 1 million base sequences in 45 seconds using a GTX 560 Ti. Many optimizations are being developed for this software. Look at the following papers for detailed information: [1] Edans Sandes, Alba Melo. Retrieving Smith-Waterman Alignments with Optimizations for Megabase Biological Sequences using GPU. ... -
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This is a code for the sentence parsing that does its job properly and FAST. The main problem is that you really need a database of abbreviations so that phrases such as "Dr. Smith" are not calculated as 2 sentences, which means that the good parser must be language dependent. I am also providing a list of all English abbreviations with the code. USAGE: parser p = new parser(); p.parseDoc("in.txt", "out.txt"); in.txt is the String for the filename that you wish to parse out.txt is the String for the filename that you want to have as an output
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Phonebook directory for Cisco VoIP
Phone directory for Cisco with LDAP or MySQL integration
...Additionally there is an LDAP and/or MySQL Server needed to fetch the data from. The original php script for phone directory with MySQL integration was started 2003 by Brandon Tatton and Jared Smith. The php script for LDAP servers was provided by Gael Marronnier. I modified both versions and changed the way how it is presented on the phone. -
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GraFIX is a software and a method to detect fixations in low and high quality data, consisting of a two-step process in which eye-tracking data is initially parsed by using adaptive velocity-based algorithms, before it is hand-coded using the graphical interface, allowing accurate and rapid adjustments of the algorithms' outcome. GraFIX is released under the GPLv3 public license (http://www.gnu.org/licenses/). Please cite as: Saez de Urabain, I.R., Johnson, M.H., Smith, T.J., (2014) GraFIX: A semiautomatic approach for parsing low- and high-quality eye-tracking data. Behavior Research Methods. doi:10.3758/s13428-014-0456-0 Download the paper at: http://link.springer.com/article/10.3758/s13428-014-0456-0
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Our Free Plans just got better! | Auth0You asked, we delivered! Auth0 is excited to expand our Free and Paid plans to include more options so you can focus on building, deploying, and scaling applications without having to worry about your security. Auth0 now, thank yourself later.
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rfMaxima is an RF toolbox for the wxMaxima computer algebra system.
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Downloads of open source phpBB modifications, hacks, templates, and add-ons created by Thoul of www.phpbbsmith.com.
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This is a code for the sentence parsing that does its job properly and FAST. The main problem is that you really need a database of abbreviations so that phrases such as "Dr. Smith" are not calculated as 2 sentences, which means that the good parser must be language dependent. I am also providing a list of all English abbreviations with the code. You can always tweak the code to get a nicer output, but the main idea is still there, and completed with this little program.
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NeedlemanWunsch
Fast global sequence alignment for the masses!
MOVED TO GITHUB: https://github.com/noporpoise/seq-align Global optimal sequence alignment using the Needleman-Wunsch algorithm. Aligns DNA, RNA, protein sequence and more! See our sister project local alignment using Smith-Waterman: http://sourceforge.net/projects/smithwaterman/ -
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A simple JDBC framework (JAR) by Jeff Smith. Employs database independent, unchecked exception code. Supports Oracle, mySQL, HSQL, and PostgreSQL--can be easily extended to new databases. See article (origninally published on Developer.com) here: http://softtechdesign.com/products/SQLExecutor/SQLExecutor.htm
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Swift Sequence Alignment Program
GPU-based DNA sequence alignment program using Smith-Waterman
Swift is a DNA sequence alignment program that produces gapped alignment using the Smith-Waterman algorithm. It takes in a query file (FASTA format) and a reference file (FASTA format) as input. It outputs the reference name, read name, gapped alignment, alignment score, alignment start and end positions, and alignment length. I gave a talk on Swift in the GPU Technology Conference 2012. The talk can be accessed at http://www.gputechconf.com/gtcnew/on-demand-GTC.php? -
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SCRplus
Image converter for producing ZX Spectrum screens
...Besides the normal 16-colour Spectrum screen, it can also produce 64-colour ULAplus images. The ULAplus is a plug-in replacement for the ZX Spectrum ULA, and is developed by Chris Smith (see http://www.zxdesign.info/ ). Since version 0.18 it has a user-friendly GUI based on GTK+. -
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mubiomics
Scripts for processing next-gen sequencing data
...Included are quality control, read demultiplexing and microbiome characterisation scripts for use with usearch, pplacer and RDP classifier. The package was used to produce the data presented in Smith et al. (2012) "The Cervical Microbiome over 7 Years and a Comparison of Methods for its Characterization". -
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SmithWaterman
Fast local sequence alignment for the masses!
MOVED TO GITHUB: https://github.com/noporpoise/seq-align An implementation of the Smith-Waterman local sequence alignment algorithm. See our sister project global alignment using Needleman-Wunsch: http://sourceforge.net/projects/needlemanwunsch/ -
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JFinisher
JFinisher is software for alignment, editing and manipulation DNA seqs
JFinisher is software for alignment, editing and manipulation of biological sequences. It aims to assist in the finishing of genome assembly. Starting from a reference sequence, the program align contigs using Smith-Waterman local alignment algoritm with auxiliary methods, allowing management of the alignments generated. It has graphical interface for manipulation and visualization of the actions, uniting features that help in editing the sequences. It has internal projects manageable and ability to export results in the standard formats of the area. -
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Free-EOS est une solution "clés en mains" de serveur francophone Intranet/Internet ouvert, destiné aux entreprises ou espaces multimédia (EOF, EPN, Cybercommune, etc.). Basée sur Linux et e-smith, elle gère des postes Windows, Linux ou MacOS.
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A javascript calendar control for web client development. The interaction is inspired by windows system calendar selector. It is tiny, pure javascript, easy to use, and control style by css.
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Smith is an powerful scriptlanguare witch is still in development. Smith has an own IDE and is at the moment only available for Linux It will be full Integrated into Lazarus for more power. For more Information see the Wiki: http://smith.akaikee.de
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A simple javascript version of Smith Html Editor for web client. It is very tiny and have most functions done. And currently it works fine in Chrome and IE7+.
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A log anomaly detector tool which uses a modified Smith Waterman algorithm to identify matching (or non-matching) messages, against archived syslog messages in real time.
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