Search Results for "python" - Page 2
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Showing 56 open source projects for "python"
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ProtPOS
Prediction of PROTtein Preferred Orientation on a Surface
... simulations. ProtPOS is implemented in Python, making use of the PyMOL library for generating protein conformations and calling GROMACS externally to calculate protein-surface interaction energies. https://cbbio.online/software/protpos/ -
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ChIP-RNA-seqPRO
ChIP-RNA-sequencing-processing (ChIP-RNA-seqPRO)
ChIP-RNA-seqPRO: A strategy for identifying regions of epigenetic deregulation associated with aberrant transcript splicing and RNA-editing sites. Runnable python scripts packaged together with customized annotation libraries, demo data input and README guide. 9/26 : v1.1 Updated MAIN_IV to debug error thrown by python pandas no longer supporting 'subset'. This code will no longer be actively maintained/updated here. A cloud-based resource for comparative analysis of epigenetic, sequence... -
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mwetoolkit
THIS PROJECT MIGRATED TO https://gitlab.com/mwetoolkit/mwetoolkit3/
... to virtually any text collection, language, and MWE type. It is a command-line tool written mostly in Python. Its development started in 2010 as a PhD thesis but the project keeps active (see the SVN logs). Up-to-date documentation and details about the tool can be found on the mwetoolkit website: http://mwetoolkit.sourceforge.net/ -
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memesa-tools
A collection of tools used in the enumeration of solution spaces
This collection of tools forms the basis of a pipeline for the complete enumeration of the number of solutions present in a model that maximizes a single objective function. -
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XMIPP is an image processing suite for 3D-reconstruction of biological specimens from transmission electron microscopy data. NOTE that stable releases (including binaries) are longer stored at Sourceforge, but are available at http://xmipp.cnb.csic.es
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ADOMA stands for: Alternative Display Of Multiple Alignment. ADOMA can create four different displays of a multiple sequence alignment: a ClustalW alignment in HTML format, a simplified ClustalW alignment in HTML and/or txt format and a colored ClustalW alignment in HTML format. For examples of these outputfiles check the screenshots. ADOMA uses ClustalW to create the multiple alignment from DNA or protein sequences and displays them slightly different than the normal output of ClustalW....
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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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openSEQ
NGS compute distro proloaded with pipeline analysis software
.... The first homepage tab links to our pipeline constructer. The second homepage tab links to a xterm session on the client. Software included (location - name): path - biobambam path - bwa path - bowtie2 path - bowtie path - cufflinks path - bcftools path - tophat path - scalpel path - samtools path - sra-toolkit path - bamtools path - delly path - delly-parallel path - picard-tools path - fastahack path - twoBitToFa ~/prog/java/ - mutect ~/prog/python/ - platypus ~/prog/java/ - gatk -
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Malware Analysis Network in Taiwan
MAN in Taiwan, MiT
Malware Analysis Network in Taiwan <Man in Taiwan, MiT> Welcome to contact us (TonTon@TWMAN.ORG) if you are interested in collaborating with us. This project is open source and distributed under the GNU General Public License version 3. Please feel free to add to or modify this source and propose changes or new converters. Developer & Copyrighted by : TonTon Hsien-De Huang Prompter: Jazz Yao-Tsung Wang, Figaro Chen-Ho Yang | Logo Desinger:Temaki Guo Community on... -
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RoboComp is a robotics framework providing a set of open-source, distributed, real-time robotic and artificial vision software components and the necessary tools to create and manage them.
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Ymap - Yeast Mapping Analysis Pipeline
Pipeline for large-scale genome changes analysis of genome datasets.
The active use repository has migrated over to: https://github.com/darrenabbey/ymap The repository here was errantly created with some large binary files included. Attempts to extract the files from the history here have failed. A copy of the history was successfully scrubbed and then hosted at github. -------- Eukaryotic pathogens have complicated and dynamic genomes. To facilitate analysis of copy number variations (CNV), single nucleotide polymorphisms (SNPs), and loss of... -
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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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That project aims at studying and comparing typical airline IT methods, for instance RM-related algorithms. It works from a Unix/Linux/Mac command-line, and exposes basic APIs. It is being developed in C++, with Python wrappers for some components.
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minder
Monitoring your infrastructure for free.
This software presents a flexible and configurable proposal for monitoring and management of real and virtual HPC infrastructures, compatible with paradigm of cloud computing. We help you to answer: 1) What is the performance of my resources? 2) What equipment and resources do we have already? 3) What do we need to upgrade or repair? 4) What can we consolidate to reduce complexity or reduce energy use? 5) What resources would be better reused somewhere else? Status: PreAlpha, so... -
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A set of Unix command line tools for quick and convenient batch processing of tabular text files (a.k.a., tab-delimited, csv, or flat file format) with a header line. Provides delimiter and compression detection, column reference by name. * tblmap: per-line ("map") computation: derive columns through an expression, delete, reorder, filter rows. * tblred: compute ("reduce") aggregations (e.g., sum, average) over groups defined by key columns. * tbldesc: Summarize columns in file...
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HPC cloud computing for OpenFOAM (R) users
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This project is for particle accelerator start-to-end simulation. The project contains software infrastructure for setting up model run as service/client mode.
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A collection of tools for working with the comparative data analysis ontology including import/export facilities for common phylogenetic file formats, and also a triple-store framework.
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A cooperative passive radar aimed to be used over commercial (and cheap) hardware.
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This project implements an algorithm for segmenting protein sequences into smaller meaningful blocks. The method is based on the pure statistical approach and it uses an analogy between proteins and natural language.
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MBDyn_sim_suite is a collection of free pre&post-processing tools and simulation models for the open-source multi-body analysis software MBDyn forming a general purpose simulation environment for structural dynamics with an emphasis on wind turbines.
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This project is for maintaining a linux system that concentrates on math, logic, and geometry related softwares.
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The WISDOM project is a Grid based production environment used to deploy bio-informatics large scale applications.
