Search Results for "analyze"
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Showing 54 open source projects for "analyze"
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BioNeMo
BioNeMo Framework: For building and adapting AI models
BioNeMo is an AI-powered framework developed by NVIDIA for protein and molecular generation using deep learning models. It provides researchers and developers with tools to design, analyze, and optimize biological molecules, aiding in drug discovery and synthetic biology applications. -
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OpenFermion
The electronic structure package for quantum computers
OpenFermion is an open source library for compiling and analyzing quantum algorithms to simulate fermionic systems, including quantum chemistry. Among other functionalities, this version features data structures and tools for obtaining and manipulating representations of fermionic and qubit Hamiltonians. For more information, see our release paper. Currently, OpenFermion is tested on Mac, Windows, and Linux. We recommend using Mac or Linux because the electronic structure plugins are only... -
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Airborne Data Processing and Analysis
Software to processing and analyze of airborne measurements.
The Airborne Data Processing and Analysis (ADPAA) package is an open-source software package containing a collection of programs and scripts to process and analyze data from in-situ instruments deployed on airborne platforms. The ADPAA package was started to process data on the North Dakota Citation Research Aircraft but has been used to process data on many airborne platforms. The software methodology used in ADPAA is provided in the peer-review publication: Delene, D. J., Airborne Data Processing and Analysis Software Package, Earth Science Informatics, 4(1), 29-44, 2011, URL: http://dx.doi.org/10.1007/s12145-010-0061-4, DOI: 10.1007/s12145-010-0061-4. -
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xrayutilities
a package with useful scripts for X-ray diffraction physicists
xrayutilities is a python package used to analyze x-ray diffraction data. It can support with performing diffraction experiments and used for common steps in the data analysis. It can read experimental data from several data formats (spec, edf, xrdml, ...); convert them to reciprocal space for arbitrary goniometer geometries and different detector systems (point, linear as well as area detectors); for further processing the data can be gridded (transformed to a regular grid). ... -
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Abacus software
Software to control and analyze Tausand Abacus coincidence devices
Abacus Software is a specialized tool for controlling and analyzing Tausand Abacus devices (AB1002, AB1004, AB1502, AB1504, AB2502, and AB2504). It enables precise measurement of temporal coincidences with up to 2-nanosecond resolution, and real-time visualization of count data from one, two, or three channels simultaneously. The software includes advanced features such as adjustable line width, sampling time configuration, direct device settings control, and the ability to save both raw... -
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Tellurium
Model, simulate, and analyze biochemical systems using one tool.
Tellurium (te.) is a Python environment supporting Spyder2 IDE and Jupyter Notebook aimed for large-scale systems and synthetic biology simulation. It combines a number of existing libraries, including libSBML, libRoadRunner (including libStruct), libAntimony, and is extensible via tePlugins. In addition other tools kits such as matplotlib and NumPy are used to provide additional analysis and plotting support. -
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Croizat
A software package for quantitative analysis in Panbiogeography
Croizat is a free, user-friendly, cross-platform desktop software package which biologists can use to integrate and analyze spatial data on species or other taxa and to explore geographical patterns in diversity under a panbiogeographic and graph-theoretic approach. -
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GromacsProSuite
Graphical User Interface for Gromacs
This tool is an integrated graphical interface that simplifies molecular dynamics simulations using Gromacs. It provides a structured, tab-based environment to set up, execute, and analyze simulations data without complex command-line operations. The software automates tasks such as topology generation, solvation, ion addition, minimization, equilibration, and production runs while executing GROMACS commands in the background. Built-in monitoring tracks CPU, RAM, and disk usage to ensure stable performance during parallel processing. ... -
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Tempico software
Software to control and analyze Tausand Tempico timing data
Tempico Software is designed to control the Tausand Tempico TP1004 and TP1204 devices, a time-to-digital converter that captures temporal differences from a common start signal across multiple channels. The software generates histograms from captured data, supports lifetime measurements via single-photon correlation (SPC), and displays real-time graphs with adjustable fitting options. It includes a 'Counts Estimation' panel to estimate count rates per channel over time, and a 'Time Stamping'... -
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CodonU
A python project for analysis of codon usage for gene or genome analys
With CodonU, you can now easily read, manipulate, and analyze various file formats used in this kind of analysis, and generate high-quality graphics suitable for publishing. This open-source project incorporates various statistical measures necessary for codon usage analysis, including codon adaptation index, codon bias index, Gravy score, and correspondence analysis for both nucleotide and protein sequences. -
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MiModD
Mutation Identification in Model Organism Genomes using Desktop PCs
...For most model organism genomes it lets the user carry out a complete analysis from unaligned genomic NGS read data to an annotated list of variants on a regular Desktop PC within a few hours. Its user-interface is beginner-friendly and designed to encourage geneticists to analyze NGS data themselves without the help of a trained bioinformatician. -
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StreamAlert
StreamAlert is a serverless, realtime data analysis framework
StreamAlert is a serverless, real-time data analysis framework that empowers you to ingest, analyze, and alert on data from any environment, using data sources and alerting logic you define. 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. ... -
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PS-Drone
Programming a Parrot AR.Drone 2.0 with Python - The Easy Way
...It was designed to be easy to learn, but it offers the full set of the possibilities of the AR.Drone 2.0, including Sensor-Data (aka NavData), Configuration and full Video-support. 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. ... -
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MToolBox
A bioinformatics pipeline to analyze mtDNA from NGS data
MToolBox is a highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from high throughput sequencing data. MToolBox includes an updated computational strategy to assemble mitochondrial genomes from Whole Exome and/or Genome Sequencing (PMID: 22669646) and an improved fragment-classify tool (PMID:22139932) for haplogroup assignment, functional and prioritization analysis of mitochondrial variants. -
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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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parent-map
Analyze parental contributions to evolved or engineered protein or DNA
Documentation: https://parent-map.readthedocs.io/ -
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Crystalsim - XRD hkl simulation
X-ray diffraction (XRD) analysis for hkl simulation of any crystal.
Crystalsim is a simple freeware program with a neat graphical user interface for X-ray diffraction (XRD) data analysis . It can simulates all possible {hkl} planes data for the selected crystal. Crystallographic Information File (.cif) can also be used. Analyze both powder diffraction and single crystal data . Indexed at International Union of Crystallography (IUCR). Crystalline lattice parameters such as ‘a’, ‘b’, ‘c’ as well as interfacial angles such as alpha, beta, gamma can also be entered manually. Processed data can be saved as .csv file format. Designed by M Kanagasabapathy, Associate Professor, Department of Chemistry, Rajus' College, Affiliated to Madurai Kamaraj University Rajapalayam (TN) India email: rrcmks(at)gmail.com -
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QMForge reads output from various quantum mechanical calculations and provides tools for analyzing these results. Specifically, population (Mulliken and C-squared), fragment, and charge decomposition analyses are available. See https://qmforge.net for more info.
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Arramooz Alwaseet Open Arabic Dictionary for morphological analyze. To be useful for Arabic language processing. This dictionary is derived from the Ayaspell Arabic spell checker.
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This project houses software to analyze data acquired from electrophysiology experiments. Currently, we have an Octave/MATLAB program to analyze electroneurogram traces of coupled oscillators, and a Perl library for the analysis of voltage trace data
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LOOS
Analyze molecular simulation data
LOOS is a light-weight object oriented software library for creating new tools for analyzing molecular simulation data, written in C++. The main design goal is to allow casual programmers to easily implement new analysis methods. THIS PAGE IS NO LONGER UPDATED. Please see https://github.com/GrossfieldLab/loos for all recent developments -
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Buildes
A designer’s program for describing parts of the building
Buildes is an integrated development environment that assists the user in creating building information. It reads a text (session) file from which it compiles the information. It then allows the user to browse, analyze and export the resulting building knowledge. The compilation system is written in pure Python. The building components created are rendered in PythonOCC. The GUI is written using PyQt. -
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Py3DN
Morphometric analysis and visualization of the 3D structure of neurons
Py3DN, is an open-source solution providing innovative tools to analyze 3D data collected with the widely used commercial system Neurolucida (MBF). It allows the construction of mathematical representations of neuronal topology, visualization and a variety of morphometric analysis on the neuronal structures. Above all, it provides a flexible environment where new types of analyses can be easily set up allowing total freedom to test new hypotheses. -
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pyMDMix
Molecular dynamics with aqueous-organic solvent mixtures
This python package aims to help people set up and analyze molecular dynamics simulations in aqueous-organic solvent mixtures. See D. Alvarez-Garcia et al. Journal of Medicinal Chemistry, 2014. -
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ExAM-Exome_Analysis_And_Mining
A whole exome sequencing analysis package and its graphical interface
...As a consequence of their power and of the rapidly decreasing cost of these technologies, massive amount of exome sequencing data are generated and becoming available to a broadening community of scientists. However, these data remain difficult to analyze and interpret by the general scientific community, due to the limited bioinformatics resources that are currently freely available for their analysis and the partial information that they provide. Here, we present an interactive and free analysis package, ExAM, dedicated to whole exome sequencing data analysis. It is accessible to non-computer scientists and provides a complete set of information, as well as decision support to prioritize candidate disease causing variants.
