Search Results for "command line" - Page 7
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Showing 449 open source projects for "command line"
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This (Python) tool allows you to easily create FPGA bitfiles for your embedded system, from several Open Source IPs (compatibles with the OpenCores Wishbone bus) . It will also generates the corresponding drivers (currently only Linux ones).
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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... -
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scipion-xmipp
Image processing framework to integrate EM software packages.
...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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**(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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fitGCP
Fitting genome coverage distributions with mixture models
Genome coverage, the number of sequencing reads mapped to a position in a genome, is an insightful indicator of irregularities within sequencing experiments. 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.... -
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ccwatcher
A computational chemistry monitoring, parsing and plotting application
ccwatcher monitors the progress of computational chemistry calculations during runtime. It has both a GUI and a "Command Line Interface" to which it parses important output and plots SCF energies. -
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KEMP
A FDTD solver for electromagnetic wave simulations on a GPU cluster
KEMP is a fast FDTD solver on a GPU-based cluster. The FDTD (Finite-Difference Time-Domain) method is a popular numerical method for electromagnetic field simulations. KEMP enables hardware accelerations suitable for multi-GPU, multi-core CPU and GPU cluster. KEMP also provide easy configuration by using Python scripting language. -
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Quadcontrol
Quadcopter Remote Control by RaspberryPi
An application to control remotely a Quadcopter throught a Raspberry Pi. 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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psignifit is a toolbox to fit psychometric functions and test hypotheses on psychometric data. This is version 3 which will now predominantly support python.
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LipidWrapper
Create lipid-bilayer models of arbitrary geometry.
LATEST VERSION NOW LOCATED AT http://git.durrantlab.com/jdurrant/lipidwrapper As ever larger and more complex biological systems are modeled in silico, approximating physiological lipid bilayers with simple planar models becomes increasingly unrealistic. When building large-scale models of whole subcellular environments, models of lipid membranes with carefully considered, biologically relevant curvature are essential. LipidWrapper, written by Jacob Durrant in the lab of Rommie E. Amaro,... -
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ADTEx
Aberration detection in tumour exome
Aberration Detection in Tumour Exome (ADTEx) is a tool for copy number variation (CNV) detection for whole-exome data from paired tumour/matched normal samples. -
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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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C++, Matlab and Python library for Hidden-state Conditional Random Fields. Implements 3 algorithms: LDCRF, HCRF and CRF. For Windows and Linux, 32- and 64-bits. Optimized for multi-threading. Works with sparse or dense input features.
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Pugsly
Command-line, PubChem PUG client, written in Python
Command-line, PubChem PUG client, written in Python; developed for Linux -
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Pyntrez
Command-line, Entrez, NCBI e-utilities client, written in Python
Command-line, Entrez, NCBI e-utilities client, written in Python; developed for Linux -
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Pyntrez NCBI Database Client
Command-line, Entrez, NCBI e-utilities client, written in Python
Comman-line client to Entrez, e-utilities, written in Python, developed for Linux -
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Pugsly PubChem Client
Command-line, PubChem PUG client, written in Python
Client to the PubChem Tool (PCT), The Power User Gateway (PUG). Written in Python and developed for use with Linux. -
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wreport has moved to: https://github.com/ARPA-SIMC/wreport dballe has moved to: https://github.com/ARPA-SIMC/dballe bufr2netcdf has moved to: https://github.com/ARPA-SIMC/bufr2netcdf
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Cospace Dance
Robot for cospace dance
A complete set of code to build your own robot for cospace dance using: raspberry pi, arduino, xbee and blender, -
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mitoMaker
mitoMaker - a mitochondria assembly and annotation script
mitoMaker is a pipeline script developed to simplify the assembly and automatic annotation of mitochondrial genomes, based on raw NGS reads and an optional target reference. mitoMaker calls well known assemblers and algorithms, such as SOAPdenovo, MIRA and blast+ and parses their results providing easily readable outputs, such as FASTA, GENBANK, SEQUIN, PNG and others. General pipeline: 1-iterative De Novo assembly, with different k-mer values, trying to assemble a build that matches... -
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Aelius Brazilian Portuguese POS-Tagger
Python, NLTK-based package for shallow parsing of Brazilian Portuguese
Aelius is an ongoing open source project aiming at developing a suite of Python, NLTK-based modules and interfaces to external freely available tools for shallow parsing of Brazilian Portuguese. It also includes language resources such as language models, sample texts, and gold standards. Presently, Aelius already offers facilities for POS-tagging and chunking corpora and outputting annotations in different formats, such as in XML in the TEI P5 encoding scheme. -
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Larch: Data Analysis for X-ray Spectra
Data Processing and Analysis for X-ray Spectroscopy and More
Larch is a scientific data processing language that is designed to be easy to use for novices and complete enough for advanced data processing and analysis. Larch provides a wide range of functionality for dealing with arrays of scientific data, and basic tools to make it easy to use and organize complex data. Larch has been primarily developed for dealing with x-ray spectroscopic and scattering data, especially the kind of data collected at modern synchrotrons and x-ray sources. ... -
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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.
