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Showing 512 open source projects for "can="
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SBEVSL is a collaborative project between Dowling and RIT on the development of a Structural Biology Extensible Visualization Scripting Language, so that users can move freely among various molecular graphics tools, such as rasmol, pymol, raster3d, etc.
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Open source steam property routines in C. Implements the IAPWS-IF97 steam tables from the International Association for the Properties of Water and Steam. Includes two-way property solvers and test suite. Can be used from C/C++, Fortran, Python, LabVIEW, Octave and ASCEND.
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OmicSelector
Feature selection and deep learning modeling for omic biomarker study
OmicSelector is an environment, Docker-based web application, and R package for biomarker signature selection (feature selection) from high-throughput experiments and others. It was initially developed for miRNA-seq (small RNA, smRNA-seq; hence the name was miRNAselector), RNA-seq and qPCR, but can be applied for every problem where numeric features should be selected to counteract overfitting of the models. Using our tool, you can choose features, like miRNAs, with the most significant diagnostic potential (based on the results of miRNA-seq, for validation in qPCR experiments). -
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pyntcloud
pyntcloud is a Python library for working with 3D point clouds
...Point clouds are one of the most relevant entities for representing three dimensional data these days, along with polygonal meshes (which are just a special case of point clouds with connectivity graph attached). In its simplest form, a point cloud is a set of points in a cartesian coordinate system. Accurate 3D point clouds can nowadays be (easily and cheaply) acquired from different sources. pyntcloud enables simple and interactive exploration of point cloud data, regardless of which sensor was used to generate it or what the use case is. Although it was built for being used on Jupyter Notebooks, the library is suitable for other kinds of uses. pyntcloud is composed of several modules (as independent as possible) that englobe common point cloud processing operations. -
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TheoDORE
Theoretical Density, Orbital Relaxation and Exciton analysis
...Wavefunction analysis is based on state and transition density matrices, which provides a unified formalism applicable independent of the wavefunction model. TheoDORE is interfaced to a number of quantum chemical programs (Q-Chem, Columbus, Turbomole, ...) and can be used for a wide range of excited state methods (MR-CI, ADC, CC, TDDFT). It is written in a modular fashion to allow for an easy extension of these capabilities. Code development moved to github: https://github.com/felixplasser/theodore-qc -
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QuickPlot
Simple user interface for gnuplot aimed for reflectometry data
...It supports templates for fast formatting of graphics, different plot styles, insets, axis and label options. One important feature is storing metadata in png and pdf files that can be used to reload any graph saved with QuickPlot. -
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remove the temporary files using Temp manager, and automate the operation (remove the files every 5 seconds). Built with python. Interface : Tkinter.
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XRD CUBIC
Simulate crystal cell length (a), Miller indices {h, k, l}, d-spacing
This is a basic computer program (coded in Python) to simulate possible unit crystal cell length (a), Miller indices - {h, k, l} and interplanar spacing (d) for cubic crystals from observed (experimental) X-ray diffraction (XRD) angle, 2-theta. It can simulate all these possible crystal lattice parameters for cubic crystal systems between the given 2–theta values within the range of specified cell length (a) limits. 1. Enter wavelength of X-ray (in Angstroms) 2. Enter minimum and maximum diffraction angle as 2-theta (in Degrees) 3. Enter minimum and maximum unit cell length (in Angstroms) All the possible cubic crystal parameters, as well as diffraction angle with reference to d-spacing between the given Miller indices (h k l planes), will be simulated. ... -
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XISMuS
X-Ray Imaging Software for Multiple Samples
...IMPORTANT FIXES in respect to base v2.0.0 version: v.2.5.0 introduces the Differential Attenuation and Cube Viewer utilities, and migrates user database to *.json files v2.4.3 fixes a with K element in the fit-approx method v2.4.3 fixes and issue where saving plots with fit-approx or a auto-wizard could freeze the software v2.4.2 introduces Image Viewer to Mosaic v2.4.1 fixes an issue in merging H5 or EDF datasets with Mosaic Full changelog at https://linssab.github.io/history X-Ray Fluorescence Imaging Software for Multiple Samples is an open source software to manipulate and study macro-X-Ray Fluorescence (MA-XRF) datasets. XISMuS also works as a sample management tool, where you can easily change between datasets (samples) and compare, cross-interact and normalize them. -
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pyModSlave
Modbus TCP/RTU Slave Software.
pyModSlave is a free python-based implementation of a ModBus slave application for simulation purposes. You can install the python module or use the precompiled (for Windows only) stand alone GUI (Qt based) utility (unzip and run). pyModSlave also includes a bus monitor for examining all traffic on the bus. You can also download it from pypi <https://pypi.org/project/pyModSlave/>. pyModSlave is based on modbus-tk <http://code.google.com/p/modbus-tk/>, pySerial <https://github.com/pyserial/pyserial> and pyQt5 <http://www.riverbankcomputing.co.uk>. ... -
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StreamAlert
StreamAlert is a serverless, realtime data analysis framework
...Computer security teams use StreamAlert to scan terabytes of log data every day for incident detection and response. Incoming log data will be classified and processed by the rules engine. Alerts are then sent to one or more outputs. Rules are written in Python; they can utilize any Python libraries or functions. Merge similar alerts and automatically promote new rules if they are not too noisy. Ingested logs and generated alerts can be retroactively searched for compliance and research. Serverless design is cheaper, easier to maintain, and scales to terabytes per day. Deployment is automated, simple, safe and repeatable for any AWS account. ... -
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MITRE Annotation Toolkit
A toolkit for managing and manipulating text annotations
...It can be customized for specific tasks (e.g., named entity identification, de-identification of medical records). The goal of MAT is not to help you configure your training engine (in the default case, the Carafe CRF system) to achieve the best possible performance on your data. MAT is for "everything else": all the tools you end up wishing you had. -
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Argos Translate
Open-source offline translation library written in Python
Argos Translate uses OpenNMT for translations and can be used as either a Python library, command-line, or GUI application. Argos Translate supports installing language model packages which are zip archives with a ".argosmodel" extension containing the data needed for translation. LibreTranslate is an API and web-app built on top of Argos Translate. Argos Translate also manages automatically pivoting through intermediate languages to translate between languages that don't have a direct translation between them installed. ... -
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FilmQADog
Program for analysis of radiochromic films
This is Python based program for analysis of radiochromic films. Similar to filmQAPro, but free. It can be used to study Gafchromic EBTX films. -
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HistogramsApp
Application that generates KDE-PDP plots from geochronological data
HistogramsApp is a Python 3.6 application that generates (KDE and PDP) from geochronological data .HistogramsApp allows to interactively setup plot parameters such as the bandwidth and the peak detection sensibility. To cite the application please refer to: 1) https://www.tandfonline.com/doi/abs/10.1080/00206814.2021.1954556?journalCode=tigr20 Rodriguez-Corcho, A. F., Rojas-Agramonte, Y., Barrera-Gonzalez, J. A., Marroquin-Gomez, M. P., Bonilla-Correa, S., Izquierdo-Camacho, D.,... -
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Xmaldi
Viewing collections of MALDI spectra and perform PCA and DFA analyses
Xmaldi is an application for viewing collections of MALDI spectra and perform PCA and DFA analyses on them (Python 3 version). For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/xmaldi3/code/ci/default/tree/README.md -
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Celestial Precomputation
Sight Reduction for Air Navigation with Python
...This Python TK application calculates a good set of stars for a 3 star fix, makes all calculations similar to the FAAs Celestial Computation Sheet (see FAA doc FAA-H-8083-18). Also, you can create a PDF file that generates Pub 249 Vol 1 for any epoch you specify. The PUB249 as PDF is found under "Files". I wrote this for my aircraft bubble octant :-) It is mainly useful for air navigation as it assumes a bubble sextant but may be used for normal sextants as well. Requires Ephem and ReportLab (optional for PDF output) Not to be used for real-world navigation! -
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JSONVisor
Visor for mass spectrometry JSON files generated by Integrator
Visor for mass spectrometry JSON files generated by the Integrator program (Python 3 version). For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/jsonvisor3/code/ci/default/tree/README.md - Gallardo, Ó., Ovelleiro, D., Gay, M., Carrascal, M., & Abian, J. (2014). A collection of open source applications for mass spectrometry data mining. PROTEOMICS, 14(20), 2275–2279. https://doi.org/10.1002/pmic.201400124 -
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LaiaMotifs
Search for MHC-like motifs in peptide collections
Search for MHC-like motifs in peptide collections (Python 3 version). For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/laiamotifs3/code/ci/default/tree/README.md -
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KimBlast
Blast+ the easy way
KimBlast GUI formats and indexes Fasta databases for Blast, performs Blast searches and analyzes results. Python 3.x version. For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/kimblast3/code/ci/default/tree/README.md -
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MutaNET
NGS Pipeline and Automated Mutation Analysis
MutaNET comes with a next generation sequencing (NGS) pipeline that calls mutations based on paired-end NGS reads, an automated mutation analysis tool and various file converters and mergers. The mutation analysis feature considers the coding region, protein domains, regulation and transcription factor binding site information, and can be used to analyse the potential impact of mutations on antibiotic resistance. -
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U-Net Fusion RFI
U-Net for RFI Detection based on @jakeret's implementation
...Additional work is being done to add custom layers to this model for further experimentation, including Squeeze/Excitation layers (unimplemented.) Sum Threshold (in fusion as an expert, and in testing as a comparison) requires the use of AOFlagger by Andre Offringa. You can find this code at https://gitlab.com/aroffringa/aoflagger. This project will use the aoflagger program within the code, so you may need to ensure that any environment variables are set for aoflagger before use. cite: https://sourceforge.net/p/u-net-fusion-rfi/wiki/cite/ -
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Pytorch Points 3D
Pytorch framework for doing deep learning on point clouds
...The framework currently integrates some of the best-published architectures and it integrates the most common public datasets for ease of reproducibility. It heavily relies on Pytorch Geometric and Facebook Hydra library thanks for the great work! We aim to build a tool that can be used for benchmarking SOTA models, while also allowing practitioners to efficiently pursue research into point cloud analysis, with the end goal of building models which can be applied to real-life applications. Task driven implementation with dynamic model and dataset resolution from arguments. Core implementation of common components for point cloud deep learning - greatly simplifying the creation of new models. 4 Base Convolution base classes to simplify the implementation of new convolutions. ... -
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OpenNum
OpenNum lets you distribute solvers with a nice graphical interface
...More specifically, OpenNum lets you · to collect a hierarchical dataset, · to call any executable file and · to visualize scalar and vector fields, plot graphs or show simple plain text files. It also has other useful utilities specifically designed for numerical simulation packages: · it allows managing a centralized materials dataset; · it can read several finite element mesh formats and several field formats. -
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PS-Drone
Programming a Parrot AR.Drone 2.0 with Python - The Easy Way
...The video function is not restricted to mere viewing, it is also possible to analyze video images data using OpenCV2. Obviously, the PS-Drone is perfect for teaching purposes; however, even the requirements for professional purposes can be satisfied. PS-Drone comes with a tutorial, explaining its most important commands and the drone's most important sensor values. The examples are easy to understand for people with little programming experience. A full list of commands and a description of all sensor data is available in a detailed documentation. It took several months to create PS-Drone, so it would be nice to get some donations for further development (e.g. ...
