Search Results for "can" - Page 11
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Showing 514 open source projects for "can"
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Maximum Common Genome Alignment (MCGA)
Pipeline for creating core genome alignments for phylogenetic analysis
Maximum Common Genome Alignment (MCGA) Tool MCGA is a bioinformatics analysis tool written in Python for generating core genome alignment for bacterial whole genome sequences which can be used to construct phylogenetic trees. -
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QuickNXS
Polarized ToF reflectivity raw data analysis tool
Data evaluation tool for the magnetism reflectometer at the spallation neutron source (BL-4A@SNS). Reads raw nexus files (HDF5) of histogrammed or event mode data to create reflectivity curves and 2D Q-maps. -
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Phobos Application
Software for recording rodents' behavior during behavioral tests
...Phobos provides the possibility to easily calculate all possible experimental parameters at once immediately after the evaluation of the fear/anxiety level of each animal. All extracted files can be readily combined to one in order for statistical analyses to be performed. If you use Phobos for your research, please cite: Telonis AG, Margarity M.Phobos: a novel software for recording rodents' behavior during the thigmotaxis and the elevated plus-maze test. Neurosci Lett (2015) doi: 10.1016/j.neulet.2015.05.045 Paper link: http://www.sciencedirect.com/science/article/pii/S0304394015004103 For support, questions or feedback: atelonis@users.sourceforge.net -
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scipion-xmipp
Image processing framework to integrate EM software packages.
...It integrates several software packages and presents an unified interface for both biologists and developers. Scipion allows to execute workflows combining different software tools, while taking care of formats and conversions. Additionally, all steps are tracked and can be reproduced later on. Xmipp is a well-known package in the EM image processing. It is integrated into Scipion and contains the algorithms in the core libraries and command line programs. -
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binana
BINANA (BINding ANAlyzer) is a python-implemented algorithm for analyz
...The program identifies key binding characteristics like hydrogen bonds, salt bridges, and pi interactions. As input, BINANA accepts receptor and ligand files in the PDBQT format. PDBQT files can be generated from the more common PDB file format using the free converter provided with AutoDockTools. As output, BINANA describes ligand binding. NOTE: The latest version of BINANA is now hosted at http://git.durrantlab.com/jdurrant/binana . Versions on SourceForge are not up to date. -
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GASiC
Genome Abundance Similarity Correction
...GASiC is a method to correct read alignment results for the ambiguities imposed by similarities of genomes. It has superior performance over existing methods. You can find the accompanying paper here: http://nar.oxfordjournals.org/content/41/1/e10.short Thanks to the great work of the SeqAn team, you can now use GASiC as a Knime workflow: https://github.com/seqan/knime_seqan_workflows/tree/master/metagenomics_gasic_workflow -
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pipasic
pipasic: Protein Abundance Correction in Metaproteomic Data
Metaproteomic analysis allows studying the interplay of organisms or functional groups and has become increasingly popular also for diagnostic purposes. However, difficulties arise due to the high sequence similarity between related organisms. Further, the state of conservation of proteins between species can be correlated with their expression level which can lead to significant bias in results and interpretation. These challenges are similar but not identical to the challenges arising in the analysis of metagenomic samples and require specific solutions. pipasic (peptide intensity-weighted proteome abundance similarity correction) is a tool which corrects identification and spectral counting based quantification results using peptide similarity estimation and expression level weighting within a non-negative lasso framework. pipasic has distinct advantages over approaches only regarding unique peptides or aggregating results to the lowest common ancestor. -
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...ADOMA is a commandline program that can easily be used in pipelines. For more information check the README.md in the Files section. How to cite ADOMA: Zaal, D. and Nota, B. (2016), ADOMA: A Command Line Tool to Modify ClustalW Multiple Alignment Output. Mol. Inf., 35: 42–44. doi: 10.1002/minf.201500083 http://onlinelibrary.wiley.com/doi/10.1002/minf.201500083/abstract
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RPy is a very simple, yet robust, Python interface to the R Programming Language. It can manage all kinds of R objects and can execute arbitrary R functions (including the graphic functions). RPy has been superseded by the RPy2 project: https://rpy2.github.io/
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fitGCP
Fitting genome coverage distributions with mixture models
...While the average genome coverage is frequently used within algorithms in computational genomics, the complete information available in coverage profiles (i.e. histograms over all coverages) is currently not exploited to its full extent. Thus, biases such as fragmented or erroneous reference genomes often remain unaccounted for. Making this information accessible can improve the quality of sequencing experiments and quantitative analyses. fitGCP is a framework for fitting mixtures of probability distributions to genome coverage profiles. Besides commonly used distributions, fitGCP uses distributions tailored to account for common artifacts. The mixture models are iteratively fitted based on the Expectation-Maximization algorithm. ... -
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**(9 march 2016) this project is continued on github : http://jaapkroe.github.io/polypy ** Python script to analyze (shortest-path) rings in structures read from xyz-files. It can be useful for example to identify defects in crystal structures or molecules.
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irit_diff_sequences
Python tool to create lifespan sequences from Wikipedia edits history
A Python tool which produced lifespan sequences from edits history. The tool is first developed for the Wikipedia edits history but can easily be adapted for others applications. From a database containing for each article its list of revisions, produce one csv file per article containing authored sequences and lifespans. Output format: i,j,lifespan,author with - i : begining of the chars sequence - j : end of the chars sequence - lifespan : number of edits the sequence has survives until the lattest revision - author : author id of the sequence. -
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This project provides a Fortran90 library and a python module for singular spectrum analyses such as PCA/EOF or MSSA. It is intended for people interested, for example, in analysing climate or financial variability.
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SCaVis
Scientific Computation and Visualization Environment
SCaVis is an environment for scientific computation, data analysis and data visualization for scientists, engineers and students. The program is fully multiplatform (100% Java) and integrated with Java and a number of scripting languages: Jython (Python), Groovy, JRuby, BeanShell. SCaVis can be used to plot functions and data in 2D and 3D, perform statistical tests, data mining, numeric computations, function minimization, linear algebra, solving systems of linear and differential equations. Linear, non-linear and symbolic regression are also available. Elements of symbolic computations using Octave/Matlab scripting are supported. ... -
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Multiplication Station
Grid based multiplication, add, sub including (-)ve #s
Multiplication Station will teach your child to add, subtract and multiply. All parameters configurable, like grid size and number ranges fonts and colors. Countdown timer keeps attention focused. High scores too. -
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Quadcontrol
Quadcopter Remote Control by RaspberryPi
...The goal is to be able to command and view what is in front of the quadcopter with a camera. This is allready working using a python Webserver and streaming video from Raspberry Camera. You can play also without camera support from command line with remote access. -
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iMir
Integrated pipeline for HT miRNA-Seq data analysis
Processing of smallRNA-Seq data to gather biologically relevant information requires application of multiple statistical and bioinformatics tools from different sources, each focusing on a specific step of the analysis pipeline. The analytical workflow can be challenging for the continuous interventions by the operator, a critical factor when large numbers of datasets need to be analyzed at once. To allow a flexible and comprehensive analysis of smallRNA-Seq data we designed a novel modular pipeline, called iMir, integrating multiple open source modules and resource in an automated workflow, devising different statistical approaches to analyze data rigorously. iMir comprises also a Graphical User Interface (GUI), so that the pipeline is particularly suited for biologist and early stage bioinformaticians and produces both graphics and text outputs. -
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This script can convert raw diffraction images to JPEG files. Support ADSC, MarCCD, Mar345, RAXIS and PILATUS, and can be run on Windows, Linux and Mac OS X.
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FingerID
Metabolite identification via machine learning.
...FingerID since version 1.4 will be hosted on github: https://github.com/icdishb/fingerid A metabolite identification software using tandem mass spectrometry and kernel methods. The related paper can be found at http://bioinformatics.oxfordjournals.org/content/early/2012/07/18/bioinformatics.bts437.abstract. Now it supports unix/linux like system. -
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FABS
Fluorescence and absorption spectroscopy made easy
...Accompanying this software is a hardware design, which can be used as a bare-bones spectrometer that will provide quantitative absorption and fluorescence emission spectra at an extremely low cost. It uses only materials that many people can find around their home. -
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MDcons(Molecular Dynamics consensus)
Interpretation of Biomolecular MD simulations
MDcons is a tool to analyze conserved contacts during Molecular Dynamics (MD) simulations of Protein, Rna, Dna & Ligand based complexes. The input is either a Molecular Dynamics trajectory or a set of snapshots. The input can also be a single snapshot. The outputs are (1) map of most/less frequently conserved contacts during MD (2) a list of most/less frequently conserved contacts during MD. -
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Vibeplot presents a new and attractive way to visualize vibrational analysis from density functional calculations (DFT). It is especially targeted at the chemists. The interface can either be scripted or used interactively with QVibeplot.
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Research Master
wxpython research organization tool with LaTeX flashcards
ResearchMaster is a tool that you can trust to help with organization, multitasking, and research. ResearchMaster provides a place to capture your fleeting thoughts and ideas, and it allows you to hit-the-ground-running on projects. -
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diCal-IBD
diCal-IBD predicts identical by descent tracts using sequence data
diCal-IBD can be used for predicting identical by descent (IBD) tracts in sequence data. It provides means for calculating the accuracy of the prediction, if the true tracts are available, plotting of the predicted tracts, their TMRCA (time to the most recent common ancestor) and corresponding posterior probabilities, and identification of putative recent positive selection through investigation of average IBD sharing -
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ReorJS
Distributed Computing with JavaScript
Create your own distributed computer that can distributed javascript based applications to any computer with a web browser, headless browser or node.js installation. For more information and updates please see our website - http://reorjs.com.
