Open Source Linux Data Management Systems - Page 24
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Data Management Systems for Linux
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MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
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Gimias
Graphical Interface for Medical Image Analysis and Simulation
GIMIAS is a workflow-oriented environment for solving advanced biomedical image computing and individualized simulation problems, which is extensible through the development of problem-specific plug-ins. In addition, GIMIAS provides an open source framework for efficient development of research and clinical software prototypes integrating contributions from the Physiome community while allowing business-friendly technology transfer and commercial product development. -
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The Python Computer Graphics Kit is a collection of Python modules that contain the basic types and functions to be able to create 3D computer graphics images (focusing on Pixar's RenderMan interface).
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TRAK Architecture Framework
Simple, pragmatic architecture description - for system-thinkers
TRAK is a general systems-thinkers'/system-centric architecture framework. It is simple, user-friendly, pragmatic and not limited to IT. TRAK has won an INCOSE award and is also a finalist in the 2011 IET innovation awards. TRAK allows you to describe a system, its parts (which can include people, software, other systems and physical things) and how it relates to the residual world. It covers everything from the enterprise, concept, procurement of the solution, the introduction or withdrawal of the system from service to its assurance. It allows threats,risks and mitigation to be linked to the design. TRAK is a derivative of MODAF but is based on ISO/IEC 42010 - the international standard for architecture description. There is a minimal process in which the architect selects the viewpoints (specifications for views) that address the task sponsor's concerns. It has rules that ensure that the description is consistent and also readable by the non technical audience. You -
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The TRANSIMS Studio application is an integrated development environment for the TRansportation ANalysis and SIMulation System (TRANSIMS). Components include a run time environment to execute TRANSIMS in parallel, as well as a full featured GUI.
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WxGeometrie
Le couteau-suisse du prof de maths
Calculatrice graphique en français, destinée aux professeurs ou aux étudiants du collège et du lycée. Elle permet de faire du calcul formel, de tracer des courbes et des figures géométriques exportables en png, eps ou svg. Linux, Windows... Cette version n'est plus maintenue. Nous vous recommandons d'utiliser désormais la nouvelle version, nommée Géophar : http://sourceforge.net/projects/geophar -
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Aplicatiu per fer comandes on-line i gestionar les comandes i les factures dels socis d'una cooperativa de consum ecològic on els membres participen en la gestió de l'entitat.
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123VCF
An Intuitive and Efficient Tool for VCF file filtration
123VCF has been developed to make the filtration step of VCF files efficient and more importantly easy to understand. It can be used in the most important step of whole exome/genome sequencing data analysis in the research and also clinical settings. User manual: https://dl.adbioinformatics.net/123VCF/123VCF_Manual.ver2.pdf If you use 123VCF, please cite its paper: Eidi, M., Abdolalizadeh, S., Moeini, S. et al. 123VCF: an intuitive and efficient tool for filtering VCF files. BMC Bioinformatics 25, 68 (2024). https://doi.org/10.1186/s12859-024-05661-5 _____________________________________ Authors: Milad Eidi, Samaneh Abdolalizadeh, Soheila Moeini Supervisors: Javad Zahiri, PhD - Masoud Garshasbi, PhD Department of Neuroscience, University of California San Diego, California, USA Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran -
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As of 2018-06-28, this project has moved to https://github.com/AdamaJava. This copy of the code will remain but all new code updates and releases will be from the new site. Java code developed by the Australian ICGC team for operating on next-generation sequencing data. This code is currently being maintained and expanded by the QIMR Berghofer Genome Informatics team (http://www.qimrberghofer.edu.au/lab/genome-informatics/) More details and documentation can be found on the wiki: http://sourceforge.net/p/adamajava/wiki/Home/
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Alevin2
Tool for the evaluation of ALgorithms for Embedding VIrtual Networks
ALgorithms for Embedding VIrtual Networks Software to evaluate Virtual Network Embedding Algorithms. -
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Arexx Data Logger UI
A web UI to Arexx temperature loggers
This project aims at displaying and analysing data recorded by Arexx temperature loggers on Unix operating systems. Although the code is currently implemented for etching data from Arexx loggers, the UI itself is completely independent and can be reused with other temperature databases. -
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AtomProbeLab
Matlab-based analysis of Atom Probe Data
A collection of scripts and functions for the analysis of atom probe tomography data. Currently, this includes: standard file operations, plotting mass spectra, mass spectra analysis and mass peak overlap solving. For more information see the Wiki: https://sourceforge.net/p/atomprobelab/wiki/Home/ Quick overview video: https://youtu.be/8rJHce7M5UU More in-depth video using the APT school demos live script: https://www.youtube.com/watch?v=cyrLHCzZwuw For details of the maximum likelihood method used to solve peak overlaps see the following papers: https://doi.org/10.1017/S1431927616012782 and https://doi.org/10.1017/S1431927618016276 for the quantification of the uncertainty. If you are looking for Dan Haley's "weights" program, go here https://sourceforge.net/projects/apttools/files/extras/ -
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BMDExpress Data Viewer
A Visualization Tool to Analyze BMDExpress Datasets
Regulatory agencies increasingly apply benchmark dose (BMD) modeling to determine points of departure for risk assessment. BMDExpress applies BMD modeling to transcriptomic datasets to identify transcriptional BMDs. However, graphing and analytical capabilities within BMDExpress are limited, and the analysis of output files is challenging. We developed a web-based application, BMDExpress Data Viewer for visualizing and graphing BMDExpress output files. BMDExpress Data Viewer is a useful tool to visualize, explore and analyze BMDExpress output files. Visualizing the data in this manner enables rapid assessment of data quality, model fit, doses of peak activity, most sensitive pathway perturbations and other metrics that will be useful in applying toxicogenomics in risk assessment. Tool Link: http://apps.sciome.com:8082/BMDX_Viewer/ Publication Link: http://onlinelibrary.wiley.com/doi/10.1002/jat.3265/abstract -
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Calculation of camshafts - allows to define a camshaft profile on the set trajectory which should provide the given mechanism. The trajectory can be set graphically, co-ordinates or function.
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DSPatch
The Refreshingly Simple C++ Dataflow Framework
Webite: http://flowbasedprogramming.com DSPatch, pronounced "dispatch", is a powerful C++ dataflow framework. DSPatch is not limited to any particular domain or data type, from reactive programming to stream processing, DSPatch's generic, object-oriented API allows you to create virtually any dataflow system imaginable. *See also:* DSPatcher ( https://github.com/MarcusTomlinson/DSPatcher ): A cross-platform graphical tool for building DSPatch circuits. DSPatchables ( https://github.com/MarcusTomlinson/DSPatchables ): A DSPatch component repository. -
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The DUNS (Diagonalized Upwind Navier-Stokes)code is a 2D/3D, structured, multi-block, multi-species,reacting, steady/unsteady, Navier Stokes fluid dynamics code with q-omega turbulence model. It currently uses a diagonalized ADI procedure with upwind diff
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Diagram (JGraph) driven simulator. Bondgraphs > nonlinear differantial system > plot: implemented for economics and ecology. Network analysis: emergy propagation implemented. Would also fit for electronics, mechanics, cost, GWP, footprint analysis.
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EZ-Access is an audit tool verifying website conformance to the WCAG 1.0 guidelines and acting as a visual deficiency simulator (color blindness, blurred vision,...), enabling web developers to find accessibility issues.
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Eviewbox is a java imaging suite, its purpose is to view and spread native DICOM medical images and allowing for 2D reconstructions. EViewbox applet will allow to see the DICOM images on every platform.
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Firefly UML
A free, easy-to-use and user-friendly Java-based UML editor.
Firefly UML is a 100% pure Java application designed to create and edit UML conform diagrams. With class diagrams, sequence and instance diagrams, Firefly UML provides a solid selection from the vast range of existing UML diagram types. Firefly UML is really easy to learn as it provides you multiple ways of access to the same function - be it mouse action, hotkey, context menu or toolbar icon. And the best thing is: once you have learned how to handle one type of diagram, you also have learned how to deal with the other diagram types, because they all follow the exactly same user interaction patterns. Besides being user-friendly, Firefly also offers powerful features which other free editors usually do not. For example, you can import your existing Java project into Firefly and generate nice-looking class diagrams within a matter of minutes. You can also go the other way around and export your model as skeleton Java code. -
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G2C (Geospatial to Civil) The LandGML Interoperability Experiment initiated by Autodesk, U.S. Army Corps of Engineers Engineering Research and Development Center, and Galdos Systems. this open source tool transforms LandGML into LandXML documents.
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GCDPlot is a Microsoft Excel VBA program for geochemistry and geology data analysis. GCDPlot can use the Microsoft Excel data to plot scatter, ternary chart and discrimination diagrams that can be add, delete and modify by user.
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GMOL
A tool for 3D genome structure visualization
GMOL is an application designed to visualize genome structure in 3D. It allows users to view the genome structure at multiple scales, including: global, chromosome, loci, fiber, nucleosome, and nucleotide. This software was built upon the pre-existing Jmol package by Prof. Cheng's group. The software is developed in Prof. Jianlin Cheng's Bioinformatics, Data Mining and Machine Learning Laboratory in the Computer Science Department at the University of Missouri - Columbia, USA. The project is supported by the National Science Foundation (grant no. DBI1149224). If you use GMOL in your research, please cite: Nowotny, Jackson, Avery Wells, Oluwatosin Oluwadare, Lingfei Xu, Renzhi Cao, Tuan Trieu, Chenfeng He, and Jianlin Cheng. "GMOL: an interactive tool for 3D genome structure visualization." Scientific reports 6 (2016): 20802. -
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GWT Highcharts is a freely available open source library that provides an elegant and feature complete approach for including Highcharts and Highstock visualizations within a GWT application using pure Java code. Note: the source code for this project is now being maintained on GitHub here: https://github.com/squinn/gwt-highcharts
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GeoJAGS
JAGS module with covariance functions and the CAR model.
A module for JAGS containing several covariance functions for point-referenced data analysis and a function that creates the precision matrix for the proper CAR model for areal data analysis. -
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HBS-tools
a set of tools for hairpin bisulfite-seq data analysis
The emerging genome-wide hairpin bisulfite sequencing technique facilitates the determination of DNA methylation fidelity and accurate methylation calling. Here we present HBS analyzer, the first command line based open-source tool to process genome-wide hairpin bisulfite sequencing data. It accepts Illumina paired-end sequencing reads as input, performs alignment to recover the original (pre-bisulfite-converted) DNA sequences and calls methylation status for cytosines on both DNA strands.