Search Results for "smith" - Page 2
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Showing 87 open source projects for "smith"
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adapter trimmer
We implement a very simple approach. Each read is searched for the jun
...If a match to either side of the junction is found then the entire 38bp juncton is clipped. This means the algorithm can tolerate an indel error in one of the sides of the junction, but not both. Optionally Smith-Waterman alignment can be turned on with -w which resolves this issue, although the code is less tested. eg. this will be caught: CTGTCTCT-TA-TACACATCTAGATGTGTATAAGAGACAG but not this: CTGTCTCT-TA-TACACATCTAGATGT-GTATAAGAGACAG -
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SQLExecutor: A Simple JDBC framework
Tiny and easy to use JDBC framework, simplifies usage of JDBC driver
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 (originally published on Developer.com ) here: http://softtechdesign.com/products/SQLExecutor/SQLExecutor.htm -
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Kinannote
Protein Kinase Identification and Classification
...Citing Kinannote: Kinannote, a computer program to identify and classify members of the eukaryotic protein kinase superfamily Jonathan M. Goldberg; Allison Griggs; Janet L. Smith; Brian Haas; Jennifer Wortman; Qiandong Zeng Bioinformatics 2013; doi: 10.1093/bioinformatics/btt419 http: http://bioinformatics.oxfordjournals.org/content/29/19/2387.full pdf: http://bioinformatics.oxfordjournals.org/content/29/19/2387.full.pdf+html -
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SW#
smith waterman, gpu, cuda, alignment
SW# (swsharp) is a library for sequence alignment based on CUDA enabled GPUs. It utilizes Hirschbergs and Ukkonens algorithm for memory efficiency and additional speed up. The library is scalable for use with multiple GPUs. Some parts of the library utilize MPI for CUDA enabled clusters. This work has been supported in part by Croatian Science Foundation under the project UIP-11-2013-7353. Database search now... -
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BABA stands for Basic-Algorithms-of-Bioinformatics Applet. This project aims to create a set of bioinformatic algorithms presented didactically. The algorithms available at the moment are: Needleman&Wunsch, Smith&Waterman, Four Russians and Nussinov.
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Math Objects is a template based math library for C++ that can handle complex mathematical objects. It can compute the Smith form for matrices of polynomials and the Smith-McMillan form of transfer function matrices
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Sword Of The Spirit
Bible Study and Search Desktop Application
Bible Study and Search Desktop Application. Compare to Pure Bible Search. Use when Studying your King James Bible Codes (by Michael Hoggard at Bethel Church). Includes King James with Strongs numbers and the Strongs Concordance. Includes Frequently Asked Questions (FAQ) Former employee of Pentecostal Church Of God (PCG) -
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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. -
Your monitoring isn't a stack. It's a pile. Fix that.Replace Datadog, New Relic, and Sentry without adding three more dashboards.
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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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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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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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Stan The Man 2
2.5D scroller featuring a middle school teacher fighting for a raise!
In Episode 2, Stan's caught in an age old tale of a man with a dream: Stan the Man goes on a journey to get a raise at Elk Valley High School where he's a mediocre teacher! EXPLOSIONS, DRAMA, AND TURMOIL INCLUDED! Walter Ferrell - Programmer Garrett Smith - Music And support from Relapse Studios Remastered in the latest outdated 2D graphics, sound and music as high definition as your mind wants it to be, and physics, we present to you the second installment of that high school teacher you've grown to love- Stan The Man. In Episode 2, Stan's caught in an age old tale of a man with a dream: Stan the Man goes on a journey to get a raise at Elk Valley High School where he's a mediocre teacher! ... -
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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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Guitar Smith
The rocksmith free and open source clone
Isn't it time to have a Rocksmith clone that does not need a usb cable to learn to play? I think it is. This project to open to anyone willing to help. Also we should be able to import tab for custom songs! -
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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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...The given sequences are aligned by Sequence Alignment methodology - arranging sequences of DNA, RNA, protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. The sequence Alignment is done by using The Smith-waterman algorithm - a general local alignment method also based on dynamic programming. In this project user has an option to save sequence in either of these formats. FASTA format or CLUSTAL format.Medical Fields can make use of this application .
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Computer Timer and Reminder
A timer you set so you can do more than sit down all day!
...You state it can use improvement, but please next time contact me, to tell me what can be improved before leaving a negative review and not explaining what! Thank you, Tyro Smith -
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rfMaxima is an RF toolbox for the wxMaxima computer algebra system.
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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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Downloads of open source phpBB modifications, hacks, templates, and add-ons created by Thoul of www.phpbbsmith.com.
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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
