Search Results for "linux tool" - Page 2
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Showing 225 open source projects for "linux tool"
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PhiPsi
An eXtended Finite Element Method (XFEM) Software.
PhiPsi is a 2D and 3D computational solid mechanics program, which involves the extended finite element method (XFEM), as well as the finite element method (FEM). PhiPsi is written in Fortran and compiled using the GNU Fortran compiler (gfortran). PPView is a visualization tool for PhiPsi. PPView can be used to import Abaqus inp file, view the model defined in the PhiPsi keywords file (*.kpp), edit PhiPsi keywords file, perform a PhiPsi simulation, and view the simulation result files... -
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CAMPARI
Software for molecular simulations and trajectory analysis
We are proud to introduce version 5 of CAMPARI. We have added a number of new features, most notably a Python interface for interpreting user-supplied code (with the help of ForPy), a novel trajectory storage standard (with the help of libpqxx/PostgreSQL), and a module for performing transition path theory. Naturally, CAMPARI continues to provide the reference implementation of the ABSINTH force field paradigm and implicit solvation model. CAMPARI is a joint package for performing and... -
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IP-XACT 2009/2014 Platform
Smart GUI/Commandline tools to create IP-XACT( 2009/2014) files
Smart GUI to create or update IP-XACT often needed for the IP packaging. It has capability create Bus Definitions from scratch to populate BusDef library. One can create IP-XACT Component, Design or Registers by importing Ip in System Verilog/Verilog-95/VHDL, instantiate Bus Interfaces with proper port maps and attributes as needed. Smart GUI to create IP-XACT Registers, Memory Maps, Address Blocks for IP- has feature to import XLS or Verilog . It has Tcl/Python API... -
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Tokenized Text Aligner
Aligns tokens in two versions of a text with differing tokenization.
This tool performs token-by-token alignment of two versions of a text with differing tokenization by interpreting the results of a file diff (https://docs.python.org/3/library/difflib.html). It is intended for use in the preparation of annotated linguistic corpora, where differences in tokenization may arise (i) following corrections or modifications to the source text or (ii) through the creation of different layers of annotation (part-of-speech, treebank) requiring different tokenization.... -
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Baya - SoC Integration Platform
Best in class SoC Integration Platform, IP-XACT, Verilog VHDL, UPF
1. Comes with 200+ high level Tcl commands around SoC platform assembly 2. Easy to start - use the verilog2baya tool to convert existing SoC/SS into Baya 3. Adhoc and Interface based connections 4. Autoconnections 5. Rule based connections between component ports 6. A variety of SoC integration Methodologies 6.a. XLS/CSV Based connections 6.b. Port-to-Port Adhoc connections 6.c. IP-XACT and System Verilog Interface based connections 6.d. ... 7. Maintains a connectivity... -
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LabRPS
Random phenomena generator
This is an official mirror of LabRPS. Code and release files are primarily hosted on https://github.com/LabRPS/LabRPS and mirrored here LabRPS aims to be a tool for the numerical simulation of random phenomena such as stochastic wind velocity, seismic ground motion, sea surface ... etc. It can be in a wide range of uses around engineering, such as random vibration or vibration fatigue in mechanical engineering, buffeting analysis in bridge engineering.... LabRPS is mainly to assist... -
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CPAT
RNA coding potential assessment tool
Using RNA-seq, tens of thousands of novel transcripts and isoforms have been identified (Djebali, et al Nature, 2012 , Carbili et al, Gene & Development, 2011) The discovery of these hidden transcriptome rejuvenate the need of distinguishing coding and noncoding RNA. However, Most previous coding potential prediction methods heavily rely on alignment, either pairwise alignment to search for protein evidence or multiple alignments to calculate phylogenetic conservation score (such as CPC ,... -
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Argo
ARGO is a program for analysis of electronic structure calculations
The `Argo' program draws its name from ancient Greek, referencing the vessel of the same name commissioned for Jason's renowned Argonauts expedition. This choice symbolizes the pursuit of making the best use of quantum chemical calculation results. ARGO facilitates the analysis of results obtained from quantum chemistry codes, specifically Gaussian. This task is achieved through a set of Python scripts. Our code is freely available throughout the academic community with the ambition to... -
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Sezioni
Python tool for section property evaluation and stress calculation
This software is a basic tool for section property evaluation and stress calculation, written in python. The section can be imported or input by points and then can be modified moved, rotated etc.. Area and section inertia can be exported. Loads can be applied (multiple load cases can be imported) and the related stresses are calculated by mean of De Saint Venant formulas. Results are plot with selectable color maps. Point results are listed and may be exported. Section can be also... -
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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... -
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pyntcloud
pyntcloud is a Python library for working with 3D point clouds
This page will introduce the general concept of point clouds and illustrate the capabilities of pyntcloud as a point cloud processing tool. 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... -
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miRPV
miRPV: An automated pipeline for miRNA Prediction and Validation in si
miRPV is an Automated tool that allows users to predict and validate microRNA from genome/gene sequence. System Requirement CPU: AMD64 (64bit) Memory: 2Gb RAM Storage: 5Gb Ubuntu 18.04 -
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XISMuS
X-Ray Imaging Software for Multiple Samples
ATTENTION: Cumulative update 2.5.0 has been released!! The update works for any previous 2.x.x version. If upgrading from version v1.x.x, please download and install v2.0.0 first. 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... -
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MAGeCK
Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout
Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. For instructions and documentations, please refer to the wiki page. MAGeCK is developed by Wei Li and Han Xu from Dr. Xiaole Shirley Liu's lab at Dana-Farber Cancer Institute/Harvard School of Public Health, and is maintained by Wei Li lab at Children's National Medical Center. We thank the support... -
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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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QuCAT
Quantum Circuit Analyzer Tool
QuCAT stands for Quantum Circuit Analyzer Tool. This open source python library provides standard analysis tools for superconducting electronic circuits, built around Josephson junctions. QuCAT features an intuitive graphical or programmatical interface to create circuits, the ability to compute their Hamiltonian, and a set of complimentary functionalities such as calculating dissipation rates or visualizing current flows in the circuit. QuCAT currently supports quantization in the basis of... -
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Pytorch Points 3D
Pytorch framework for doing deep learning on point clouds
Torch Points 3D is a framework for developing and testing common deep learning models to solve tasks related to unstructured 3D spatial data i.e. 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... -
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This application is intended to be a tool for easy, almost automatic, creation and calculation of gear transmission finite element models. It consists of a geometry and mesh generator based on GMSH and a finite element model based on GETFEM++.
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ccplot
CloudSat and CALIPSO plotting tool
ccplot is an open source command-line program for plotting profile, layer and earth view data sets from CloudSat, CALIPSO and Aqua MODIS products. -
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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. MToolBox provides pathogenicity scores, profiles of genome... -
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Neural Networks Collection
Neural Networks Collection
This project implements in C++ a bunch of known Neural Networks. So far the project implements: LVQ in several variants, SOM in several variants, Hopfield network and Perceptron. Other neural network types are planned, but not implemented yet. The project can run in two modes: command line tool and Python 7.2 extension. Currently, Python version appears more functional, as it allows easy interaction with algorithms developed by other people. -
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OpenFrames
Real-time interactive 3D graphics API for scientific simulations
OpenFrames has moved its primary development repository to GitHub! Everything else will follow. Get it at https://github.com/ravidavi/OpenFrames/wiki OpenFrames is an Application Programming Interface (API) that allows developers to provides the ability to add interactive 3D graphics to any scientific simulation. A simulation developer can use OpenFrames to specify what they want to visualize, without having to know any details of computer graphics programming. OpenFrames is currently... -
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PythonToolkit (PTK) is an interactive environment for python. It was designed to provide a python based environment similiar to Matlab for scientists and engineers however it can also be used as a general purpose interactive python environment.
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LymPHOS2
LymPHOS2 Web-App
LymPHOS2 is a web-based Application at www.LymPHOS.org containing peptidic and protein sequences and spectrometric information on the PhosphoProteome of human T-Lymphocytes. - Nguyen, TD., Vidal-Cortes, O., Gallardo, Ó., Abian, J., Carrascal, M., LymPHOS 2.0: an update of a phosphosite database of primary human T cells. Database 2015, 2015. DOI: 10.1093/database/bav115 - Carrascal, M., Ovelleiro, D., Casas, V., Gay, M., Abian, J., Phosphorylation analysis of primary human T lymphocytes...
