Search Results for "mchange-commons-java"
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Showing 20 open source projects for "mchange-commons-java"
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ReViMS
ReViMS, a 3D volume rendering tool for light-sheet/confocal microscopy
Reconstruction and Visualization from Multiple Sections (ReViMS), an open-source, user-friendly software for automatically estimating volume and several other features of 3D multicellular aggregates (i.e., cancer spheroid, zebrafish, fruit fly). ReViMS requires a z-stack of 2D binary masks, obtained by segmenting a sequence of fluorescent images acquired by scanning the aggregate along the z axis, using a confocal or a light-sheet fluorescent microscope. It provides a number of tools... -
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Systems Biology Markup Language (SBML)
A file format for exchanging computational models in systems biology
The Systems Biology Markup Language (SBML) is an XML-based description language for representing computational models in systems biology. Visit the project web site to learn more. -
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An alignment-free standalone tool with interactive graphical user interface for DNA sequence comparison and analysis
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detectMITE
Detection of Miniature Inverted Repeat Transposable Elements
detectMITE - a MATLAB-based tool for detecting miniature inverted repeat transposable elements (MITEs) in genomes. [1] Who are we? Please visit website: http://bioinfolab.miamioh.edu [2] How to cite detectMITE? Ye C, Ji G, Liang C (2016) detectMITE: A novel approach to detect miniature inverted repeat transposable elements in genomes. Sci. Rep. 6, 19688. http://www.nature.com/articles/srep19688 Ye C, Ji G, Li L, Liang C (2014) detectIR: A Novel Program for Detecting Perfect... -
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SILA
Automated bacterial and archaeal genome annotation system
SILA is a system for automated annotation of bacterial and archaeal genomes. It provides accurate gene prediction using a combination of tools (Prodigal and HGF) and a web site for task management and visualization of annotation. This project is in alpha stage. Please use the online service available at: http://www.bioinfo.ufpr.br/SILA/login.jsp Documentation (portuguese only): http://hdl.handle.net/1884/34801 -
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detectIR
Detection of Perfect and Imperfect Inverted Repeats
detectIR - a MATLAB-based tool for detecting perfect and imperfect inverted repeats in genomes. [1] Who are we? Please visit website: http://bioinfolab.miamioh.edu [2] How to cite detectIR? Ye C, Ji G, Li L, Liang C (2014) detectIR: A Novel Program for Detecting Perfect and Imperfect Inverted Repeats Using Complex Numbers and Vector Calculation. PLoS ONE 9(11): e113349. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0113349 [3] detectIR user manual... -
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OpenFlux2 is an extended version of OpenFLUX (https://sourceforge.net/projects/openflux/) - the modern MATLAB-based modelling software for 13C flux analysis (MFA). The following features were implemented in OpenFLUX2, which were not present in original software: integrated support for calculation and analysis of parallel labeling experiments (PLE), extended statistical analysis of parameter estimation results, calculation of fluxes and measurements correlation, structural identifiability...
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PlaTypUS
Plasmodium Typing Utility Software
The goal of PlaTypUS is to establish a unified Plasmodium whole genome analysis tool, that aligns short read sequences in an agreed upon manner, with many quality control steps, and calls both SNVs and CNVs in a community agreed standard way. We also seek to provide this analysis in a stand-alone graphic user interface so that labs around the world can analyze their own whole genome sequencing data, rather than relying on outside institutes. -
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Systems Glycobiology
Glycosylation Network Analysis Toolbox (GNAT)
GNAT is an open source, platform-independent MATLAB based toolbox. It is written in MATLAB and Java. It has been tested in Windows (Windows 7), Linux (Ubuntu), and Mac OS (X Lion) platforms. The original GNAT package (file GNAT.zip) provides functions for reading, writing, manipulation, visualization and simulation of glycan structures and glycosylation reaction networks (citation [1]). The second version of this software (GNATv2beta.zip) upgrades the original GNAT program with additional features that are geared towards incorporating glycan-structure experimental data into the simulation environment. ... -
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SBEToolbox
Systems Biology and Evolution Toolbox (SBEToolbox).
SBEToolbox (Systems Biology and Evolution Toolbox) is being developed in MATLAB as a menu-driven UI software to determine various statistics of the biological network. Some of its features include (but not limited to) algorithms to create random networks (small-world, ring lattice etc..), deduce clusters in the network (MCL, mCode, clusterOne) etc... ******************************************************************************************************************************** PROJECT... -
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DyMMM
Dynamic Multispecies Metabolic Modeling framework
The Dynamic Multispecies Metabolic Modeling (DyMMM [dĭm]) framework is a mathematical modeling tool that integrates multiple constraint-based metabolic models into a single dynamic community metabolic model. The DyMMM framework was formerly known as the DMMM framework. Please use the following citation for bibliographical purposes: Zhuang, K., Izallalen, M., Mouser, P., Richter, H., Risso, C., Mahadevan, R., & Lovley, D. R. (2011). Genome-scale dynamic modeling of the competition... -
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Tools for mass spectrometry, especially for protein mass spectrometry and proteomics: Quantification tools, converters for Applied Biosystems (Q Star and Q Trap), calculation of in-silico fragmentation spectra, converter for Mascot result files
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ISAD
Individual Synaptic Activity Detection (ISAD)
ISAD is a peak detection software that detects individual (pre-)synaptic activity in microscopy images from neuronal cultures transfected with pHluorin. It computes synaptic signals from automatically segmented regions of interest and detects peaks that represent vesicle fusion events, thus, pre-synaptic activity. ISAD is based on MWA, which is a continuous wavelet transform based algorithm that employs multiple wavelets and is published as: Sokoll, S., Tönnies, K., and Heine, M. Detection... -
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sigTOOL provides a user-extendable signal analysis environment for processing electrophysiological data within MATLAB. Neuron spike-train, + spectral and time-domain analyses are built in. See http://dx.doi.org/10.1016/j.jneumeth.2008.11.004
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Modern MATLAB-based modelling software for 13C metabolic flux analysis (MFA). Support available in Google group (https://groups.google.com/d/forum/13cmfa-openflux).
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(AB)² Simulation
Simulation for Physics / Bilogics Systems
Supports flow Simulation for Physics and Meso-Compartimental Simulations for Biological Systems. Uses a Container-Flow based System. -
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gfit creates an interface between computational models and experimental data and provides tools for their analysis
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This is a MATLAB toolbox for the quality control and scoring of EMAP and SGA genetic interaction data. It includes a graphical user interface and some automatic plot-generating tools.
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JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, conversion of file formats, 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available.
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Esra is a 100% pure java library for the interactive analysis of molecular mechanics data. Mangles your data in your favorite scripting language.
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