Search Results for "a note" - Page 2
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Showing 76 open source projects for "a note"
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...For a longer high-level description of Hadoop-BAM, refer to the article "Hadoop-BAM: directly manipulating next generation sequencing data in the cloud" in Bioinformatics Volume 28 Issue 6 pp. 876-877, available online at: http://dx.doi.org/10.1093/bioinformatics/bts054 Note that the library part of Hadoop-BAM is mainly for developers with experience in using Hadoop. The command line tools of Hadoop-BAM should be understandable to all users, but they are limited in scope. See the SeqPig project for a higher-level interface to the file formats supported by Hadoop-BAM: http://seqpig.sourceforge.net See Seal for Hadoop-based read alignment tools, Seal: http://biodoop-seal.sourceforge.net
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Auto Primer3
Automatically design primers to genes/coordinates using primer3.
PLEASE NOTE: THIS PROJECT PAGE WILL NO LONGER BE UPDATED - PLEASE USE THE GITHUB PAGE (https://github.com/gantzgraf/autoprimer3) TO FIND THE LATEST RELEASE (https://github.com/gantzgraf/autoprimer3/releases/latest). AutoPrimer3 retrieves gene information, DNA sequences and SNP information from the UCSC genome browser and uses primer3 to automatically design primers to genes or genomic coordinate targets. -
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GESPA
Accurately predicts disease association of single nucleotide mutations
...A host of annotations are provided: orthologous and paralogous multiple sequence alignments, UCSC annotations, reports detailing conservation of a nsSNP in alignments, and links to external nsSNP and gene information such as relevant publications. GESPA is connected to a constantly updating SQL server allowing for fast data retrieval. NOTE: REQUIRES Java 1.7.0+. Port 1433 cannot be blocked by firewall, network, or antivirus program. Please cite: http://tinyurl.com/oj7p84a -
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LiDSiM
LImits of Detection SImulation for Microbes
...For more details about LiDSiM and its functioning, please see "Estimating the Computational Limits of Detection of Microbial Non-Model Organisms" Mathias Kuhring and Bernhard Y. Renard (http://onlinelibrary.wiley.com/doi/10.1002/pmic.201400598/abstract) PLEASE NOTE, it is recommended to read the paper and the readme.txt file before using LiDSiM. -
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glSatellite Demo
Technological demo of OpenGL ES 2 Android NDK
...It reads public NORAD satellite database and shows the satellite positions and altitude related to Earth in the form of beams (the height of the beam represents the relative altitude). NOTE: The project has been moved to GitHub: https://github.com/nuald/glSatellite-Demo The old one stays here just for the historical reasons. The 3D features present: - OpenGL ES 2; - rotating, multi-touch zooming and moving the globe; - stars on a fixed background; - each satellite is represented by a beam with a unique color; - identifying the corresponding satellite if a beam has been tapped (based on color picking method). ... -
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...It contains an executable file named LGRID_Client_XX.jar. This is a "double-clickable" jar file, or you can run it from the command line using: java -jar LGRID_Client_XX.jar NOTE: To Install JCE Unlimited Strength Jurisdiction Policy Files If needed, you should install the Java Cryptography Extension (JCE) Unlimited Strength Jurisdiction Policy Files.
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Wrapper for vendors to simplify usage of the Java Speech API (JSR 113). Note that the spec is an untested early access and that there may be changes in the API.
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Network Analyzer
Analyze the network carateristics like Delay, Jitter, Packet loss etc.
...(The receiving host is then required to echo all the packets back to the sender, which can be easily done via iptables rule under linux). Once the eched packets arrives back to the sender, the analyzer will calculate all the related statistics like, packet loss, jitter throughput etc... NOTE: in order to receive the echo packets you must configure the receiving host to echo the incoming packets. In the next release i will provide another java application that just echo on an UDP port. -
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picard
A set of tools for working with high-throughput sequencing data
A set of tools (in Java) for working with next generation sequencing data in the SAM/BAM format. Note that development has moved to GitHub at https://github.com/broadinstitute/picard and support is available on the GATK forum at http://gatkforums.broadinstitute.org/categories/ask-the-team -
Go from Code to Production URL in SecondsSkip the Kubernetes configs. Cloud Run handles HTTPS, scaling, and infrastructure automatically. Two million requests free per month.
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GeoGit
Geospatial Distributed Version Control System
NOTE: this project has been renamed as GeoGig. Use this URL to get to the GeoGig downloads: https://sourceforge.net/p/geogig Welcome to the GeoGit project, exploring the use of distributed management of spatial data. GeoGit draws inspiration from Git, but adapts its core concepts to handle versioning of geospatial data. Users are able to import raw geospatial data (currently from Shapefiles, PostGIS or SpatiaLite) in to a repository where every change to the data is tracked. ... -
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javaGeom
A geometry library for Java
...Provides a general framework for manipulating and creating geometric primitives, computing intersection points between shapes, composing them to create new shapes, and performing some measurements. Important note: the repository has now moved to GitHub: https://github.com/dlegland/javaGeom Please update bookmarks! -
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Docear
An Academic Literature Suite
...It integrates everything you need to search, organize and create academic literature in a single application: a digital library, reference manager, PDF and file manager, note taking and mind mapping. And the best: Docear works seemlessly with many existing tools like Mendeley, Microsoft Word, and Foxit Reader. Docear is free and open source, based on Freeplane, funded by the German Federal Ministry of Technology and developed by scientists from around the world, among others from OvGU, and the University of California, Berkeley. -
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NanocalcFX
Open Source Data Evaluation Software
NanocalcFX is a free and open source evaluation software for a simple yet comfortable solution to deal with thousands of transport kinetics measured with a fluorescence microscope or similar kinetics. Data can be imported from CSV or Excel files or using the dedicated image stack analyser (NISA). You can get sample data at the nanocalcFX homepage. Note that nanocalcFX is currently in a beta state. -
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Cylindrical BLAST Viewer
Alignments in Rotating Cylinder / 3D
3D viewer which arranges BLAST hits and other bioinformatics-related alignments in a rotating, cylindrical display. Feedback appreciated. NOTE: requires Java3d installation. Superceded by Cylindrical Alignment App -
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OOBD supports a self-programable Tool for Vehicle Onboard Diagnostics (OBD) for various platforms like the Windows-Desktop, mobile Phones and Smartphones Please note that we are actual moving this project over to oobd.googlecode.com. The software source code repository is already moved, other areas will follow.
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Specview is a Java GUI_based application for 1-D spectral visualization and analysis of astronomical spectrograms generated by a variety of observatories and instruments. Note that we no longer provide file distributions of this software. You are encouraged to visit the specview web site download page: http://www.stsci.edu/institute/software_hardware/specview/download to retrieve an installer appropriate for your platform.
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NN Image Recognition (with source-code)
This is ANN trained application to predict digits from 0 - 9.
...I trained ANN with 100 samples of each digit. It takes input of 20x20 pixel image and predicts it with Neural Network. It may predict wrong digit due to very low sample data but it work 90% correctly. Note: JRE 1.6 is required to run this application. -
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Open-source weather database system for storage of weather/water observations, forecasts, analysis fields, and hindcasts. includes loading program for GRIB files. Visit project website (http://wdb.met.no) for further information. Please note: this project has now moved to http://wdb.met.no
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The Research Geographic Information Kernel developed by Charles Ehlschlaeger and team. NOTE: Project code has moved to https://github.com/chuckre/DigitalPopulations Documentation is at http://digitalpopulations.pbworks.com/w/page/26034597/FrontPage
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Convert GPS-Tracks to KML
Convert GPS-Tracks user-saved tracks to KML files for Google Earth.
...Under Linux, it uses the virtual file system provided by libgpod (which provides an iPhone-gvfs-bridge) and gvfs-fuse (which offers gvfs virtual filesystems as Linux FUSE filesystems). Please note that this app is rather rudimentary. If you run into problems, please open a ticket to describe the issue; time permitting, I'll try to fix it. -
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...This is a real-time simulator with speed adjustment. Software requires the old MS Java Machine to run. Interested in an updated desktop version? Please drop me a note in the forum or my blog: http://right-handed-monkey.blogspot.com/
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Le projet Gramlab vise à mettre à disposition des entreprises des outils logiciels OpenSource et gratuits, qui peuvent être mis en oeuvre par des développeurs qui ne sont pas spécialistes du traitement des langues. Note : L'outil GLabCorpus Manager nécessite l'installation d'un serveur SolR. Pour le télécharger et plus d'information, veuillez vous rendre dans la section Files.
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Evoker is a graphical tool for plotting genotype intensity data in order to assess quality of genotype calls. It implements a compact, binary format which allows rapid access to data, even with hundreds of thousands of observations. PLEASE NOTE: This source repository is no longer active. See the github link above for the latest version.
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Screensaver is a Lab Information Management System (LIMS) for high-throughput screening of small molecule and RNAi biological assays. It is a Java/JSF/Hibernate/Spring web application that is actively being developed and used at Harvard Medical School. Note: The Screensaver project has moved to GitHub at https://github.com/hmsiccbl/screensaver.
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...The GUI plots the GPX track (latitude vs longitude) and lets the user remove GPS points from the beginning and end of the track respectively. There is also a built-in Command Line Interface. Note: No development anymore since I found out that GpsPrune does all the things I was looking for.
