Search Results for "database software"
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Showing 74 open source projects for "database software"
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nmrshiftdb2 is a NMR database (web database) for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties. The nmrshiftdb2 software is open source, the data is published under an open content license. The core of nmrshitdb2 are fully assigned spectra with raw data and peak lists (we have pure peak lists as well).
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MetRFinder
Detection of Heavy Metal Resistance Genes from Bacterial Proteomes
...The modular architecture supports efficient batch processing, organized output management, and reproducible analyses. Note: A detailed User Tutorial PDF is included with the software package to guide installation, database selection, analysis execution, and result interpretation. -
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SPINA
Structure parameter inference approach for endocrine feedback control
SPINA is software for the rapid, reliable and accurate determination of constant structure parameters of endocrine feedback control systems. It is a class of static function tests that require nothing more than steady-state concentrations of hormones or metabolites obtained in vivo. The first version of this cybernetic approach had been developed for the evaluation of the functional status of the thyroid gland, i.e. thyroid's secretory capacity (gain of thyroid, GT or SPINA-GT) and sum... -
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FungiRegEx
FungiRegEx
This tool is a web-based search engine for regular expressions in the proteomes, all the information is obtained from the JGI (Joint Genome Institute) database through a scraper for all the available species; therefore this tool only considers fungi organisms. In this version, we use React JS in front-end and NodeJS + Express for back-end. Full Documentation Available on: https://victormiguelterronmacias.slite.page/p/J7BJU3hXhd72EJ/FungiRegEx-Software-documentation If you want to buy me a coffee: https://www.paypal.com/donate/?... -
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bioweb
polyglot language framework to analyze genetic data
polyglot framework using Python/C++/JavaScript to fast develop applications to analyze biological sequences -
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miRDiana
MATLAB package to find the miRNAs targeting a list of genes
To select miRNA target genes we developed software in MATLAB® (MathWorks®) called miRDiana that collects the union of mouse validated targets from the TargetScan, MicroCosm, mirTarBase and miRWalk 2.0 databases. Firstly, the software downloads each database and preprocesses by standardizing the miRNA and gene names. It strips the miRNA names from the species ids and converts the gene names to the official symbols of the National Center for Biotechnology Information (NCBI) database. -
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Specify Software
Biodiversity Database Platform
Specify is a biological collections and species occurrence database management platform for zoological museums, herbaria and other biodiversity specimen repositories. Specify is supported by grants from the Division of Biological Infrastructure, U.S. National Science Foundation and the State of Kansas. A web browser application, Specify 7, is available on GitHub. In 2015, 450 biological collections worldwide use Specify Software for collections data management. -
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Open-source Python software library and GUI desktop environment for direct bioinformatic analysis of mass-spectrometry data through powerful scripting tools and interfaces to many machine data formats, database search engines, and peptide data formats. For a copy of the source code, check out our Github repositories: mzDesktop: https://github.com/MaxAlex/mzDesktop multiplierz: https://github.com/MaxAlex/multiplierz
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JBioFramework
Growing suite of proteomics simulations for educational purposes
JBioFramework (JBF) is a set of two different chemical separations simulations (2D Electrophoresis and Mass Spectrometry) that are frequently used in chemistry, biochemistry and proteomics research. It is written in the Java programming language and will run on any and all systems that have the JVM installed. As we continue to develop the software over the coming months/years and attempt to quantify the success of our efforts with testing and reviews, user input is very important. Please... -
Build Agents and Models on One PlatformGemini Enterprise Agent Platform is Google Cloud's comprehensive platform for developers to build, scale, govern, and optimize agents and models. Choose from Google's most advanced models and third-party models like Anthropic's Claude Model Family.
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SwisTrack 4 is a powerful software for tracking robots, humans, animals and objects using a camera or a recorded video as input source. It contains interfaces for USB, FireWire and GigE cameras, as well as AVI files.
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An open source workbench for chemo- and bioinformatics built on the Eclipse Rich Client Platform (RCP).
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Visualization of Protein-Ligand Graphs
Compute protein graphs. Moved to https://github.com/MolBIFFM/PTGLtools
NOTE: Project moved to https://github.com/MolBIFFM/PTGLtools. The Visualization of Protein-Ligand Graphs (VPLG) software package computes and visualizes protein graphs. It works on the super-secondary structure level and uses the atom coordinates from PDB files and the SSE assignments of the DSSP algorithm. VPLG is command line software. If you do not like typing commands, try our PTGL web server: http://ptgl.uni-frankfurt.de/ -
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ChelomEx
Isotope assisted discovery of metal chelating agents from LC-MS data
...A built-in graphical user interface and compound library aid in the efficient evaluation of the results. If you use ChelomEx for your research, please cite our Analytical Chemistry paper that describes the software (http://dx.doi.org/10.1021/ac503000e). To comment, send bug reports or suggestions for additional features to be implemented in future versions please send me a message. The current version ChelomEx 1.2 from 06 January 2016 includes the following changes to the original version (ChelomEx 1.0): - function to filter discovered isotope patterns after the first analysis step (isotope pattern search), accessible in the Isotope Pattern toolbar (v1.2) - updates for compatibility with MatLab versions after 2014b (v1.2) - siderophore database update (v1.1) - can now also analyze negative mode data (v1.1) - bug fixes (v1.1) -
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GMOD is a set of interoperable open source software components for visualizing, annotating, and managing biological data. See http://gmod.org for more.
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MassWiz
Proteomics MS/MS database search engine
Open Source MS/MS algorithm with integrated target-decoy based FDR. Reference- http://pubs.acs.org/doi/abs/10.1021/pr200031z , Check out the wiki site for help and support - https://sourceforge.net/apps/mediawiki/masswiz/index.php?title=Main_Page -
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SBSI (Systems Biology Software Infrastructure) is a suite of tools for systems biology, such as parallelized numerical algorithms, and a Java, Eclipse RCP based client for visualizing results, running simulations, and integrating SBML based plugins.
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TUIT
Taxonomic Unit Identification Tool
For the installation instructions please see Wiki page: https://sourceforge.net/p/tuit/wiki/ IMPORTANT: since version 1.0.4.0 TUIT allows to select RDP-like formatted output to improve out of the box compatability with tools, that assume RDP-formatted input. A new field has been added to the properties.xml, please make sure to update it to contain <OutputFormat format="tuit"/> or <OutputFormat format="rdp"/> in the <BLASTNParameters> section. Read our paper in Biotechniques:... -
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Online Signature Verification
Real time signature verification using MATLAB and C#
Online Signature Verification technology requires primarily a digitizing tablet and a special pen connected to the USB port of a computer. An individual can sign on the digitizing tablet using the special pen regardless of his signature size and position. The signature is characterized as pen-strokes consisting x-y coordinates and pressure with the data being stored in a signature database. Dynamic time warping (DTW) and quadratic discriminant analysis (QDA) is used to get results where the... -
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GenoCAD is a CAD software for synthetic biology. This application provides a web-based tool to design plasmids, artificial gene networks, and other synthetic genetic systems composed of standard genetic parts. It includes a parts management system, a rule-based design tool, and a simulation engine. This project has morphed into a SaaS model. The open source code is no longer maintained.
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TopiaryExplorer has moved to GitHub. Find the new project info page here: https://github.com/qiime/Topiary-Explorer. If you need help or would like to add a bug/feature request, please do so there.
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Genomic Binding Sites Analyser (BiSA)
Genomic Region Archiving and Binding Sites Analysis (BiSA)
...The results of overlap analysis can be imported into the Knowledge Base, allowing them to go into downstream analysis and independent annotation. A Venn diagram tool is also integrated into the software to allow users to visualize overlap results. -
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GenomeRunner
Annotation and enrichment of Next-Gen sequencing data
Note: This version requires additional SQLite database files. Contact the developers to obtain them. Use http://www.integrativegenomics.org/ for the latest data and analyses. GenomeRunner is a tool for automating genome exploration. It performs annotation and enrichment analyses of user-provided genomic regions (SNPs, ChIP-seq binding sites etc.) against >6,000 (human genome) epigenomic features available from the UCSC genome browser. Input - any genome-wide data data in .bed... -
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The Blue Obelisk Data Repository lists many important chemoinformatics data such as element and isotope properties, atomic radii, etc. including references to original literature. Developers can use this repository to make their software interoperable.
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Webapp
A web interface to the SnowyOwl gene prediction pipeline
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GUI for DEDA
GUI for DEmography Data Analysis
<This project has been completely rewrote and transformed into a new one: https://sourceforge.net/projects/deday/. 2013/06/26> The graphic user interface for DEDA (DEmography Data Analysis), a scientific software package fitting survivalship data to a number of distributions using maximum likelihood (ML) method. Currently, Weibull (2p), Gompertz and Gompertz-Makeham are supported. IMPORTANT NOTICE: Only the GUI is provided here. In order to perform the analysis, one also need the DEDA...
