Search Results for "b-tree" - Page 2
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Showing 61 open source projects for "b-tree"
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CorNetMap
A tool for Gene Expression Correlation Network
...How to use and doccumentation: https://sourceforge.net/projects/cornetmap/files/Documentation_corNetMap.pdf Sample data for testing: https://sourceforge.net/projects/cornetmap/files/Test%20Data/ Citation: Cite CornetMap as " Khaund, A. Bose, B. CorNetMap. https://sourceforge.net/projects/cornetmap " Credit: Abhigyan Khaund, Biplab Bose, IIT Guwahati -
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FAST Simulations
An Open source Analysis and SImulation Toolbox for Fuel Cells
FAST is an Analysis and Simulation Toolbox (FAST) for Fuel Cells (FC) FAST-FC is the doctorate work of David B. Harvey and was developed with support from the U.S. DOE, Ballard, and Queen's University. Derivative works of FAST-FC include FC-APOLLO which is a forked branch of this project intended to capture the code state at the exit of the funded DOE project. FAST-FC is the open and active community branch. FAST-FC is developed and maintained by the original creator and developer, David B. ... -
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PyRate
Bayesian Estimation of Speciation and Extinction from Fossil Data
...*Please download the most up-to-date code from the "PyRate code" tab on this page or from: https://github.com/dsilvestro/PyRate * *An updated manual can be found here: https://github.com/dsilvestro/PyRate/tree/master/tutorials * -
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PyLogAnalyser
A Python multiplatform tool to filter, colorise and analyse logs
...These rules permit to detect an input line according to a regular expression (regex) or line number range, filter it, pass it, colorise in foreground and background, columnise the groups of the regex and enable or disable the rule. The final goal of this tool is to ameliorate reading long and difficult b/w logs, speed up the analysis and enhance day to day wearying activities. As common application, you can colorise adb logcat logs taking the example files and using them (and also, filter unnecessary lines). You can INSTALL it from PyPI: $ python -m pip install pyloganalyser -
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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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GASiC
Genome Abundance Similarity Correction
...You can find the accompanying paper here: http://nar.oxfordjournals.org/content/41/1/e10.short Thanks to the great work of the SeqAn team, you can now use GASiC as a Knime workflow: https://github.com/seqan/knime_seqan_workflows/tree/master/metagenomics_gasic_workflow -
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...ADOMA is a commandline program that can easily be used in pipelines. For more information check the README.md in the Files section. How to cite ADOMA: Zaal, D. and Nota, B. (2016), ADOMA: A Command Line Tool to Modify ClustalW Multiple Alignment Output. Mol. Inf., 35: 42–44. doi: 10.1002/minf.201500083 http://onlinelibrary.wiley.com/doi/10.1002/minf.201500083/abstract
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PhyloTrack
PhyloTrack, D3.js and JBrowse for phylogeny and positioning of samples
PhyloTrack is a JavaScript--based software tool that integrates the D3.js library for data visualization with the JBrowse tool for genome browser representation. It requires a phylogenetic tree of the common Newick data format as input, as well as three meta data files for samples, clade-defining nodes and clade color definitions - all in tab delimited format. Functionality within PhyloTrack shows the informative markers at each node in the phylogenetic tree, therefore highlighting clade-defining polymorphism. This functionality has been implemented using the tabix tool on the server side, providing simple and rapid access to the information at each tree node, including informative SNPs stored in VCF-similar files. ... -
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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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walterbot
walterbot: Virtual presence device www controlled with a raspberrypy
walterbot è un "virtual presence device" controllabile da remoto via interfaccia web. La distro Debian per architettura ARMhf6 è stata ottimizzata per "Raspberrypi B rev2". Il codice python scritto da Walter, controlla 2 motori DC tramite un TB6612FNG https://github.com/InformaticiTarantini/Pi-dro La distro è "out of the box" basta clonare l'immagine su una SD card (minimo 2Gb) proprio come si fa con raspbian. Tramite accesso ssh o direttamente dal raspberrypi, eseguire il comando "sudo ceni" per configurare la rete wireless (Si consiglia di creare una swap ed estendere il filesistem con raspi-config, ma non è indispensabile). ... -
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pyMantis is a data-management system for (systems) biology build on the web2py framework. It features: tree based file explorer, relational db table wizzard with automated creation of user interfaces, internal and external access management, wiki, ..
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Automatic Compound Processing (AuCoPro)
Automatic compound splitting and semantic analysis of compounds
...Specifically, we will explore the possibility to create new knowledge about closely-related languages, and efficiently develop additional, more advanced resources for (a) compound segmentation; and (b) the semantic analysis of compounds; as such, the project will be divided into two interrelated subprojects, to be executed simultaneously. The focus in this project will be on Afrikaans (with Dutch as the closely-related, well-sourced language), which will lay grounds for future work on other closely-related language pairs. -
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t2t-pipe
automatic alignment pipeline for parallel treebanks
The *Tree-to-Tree (t2t) Alignment Pipe* is a collection of python scripts, co-ordinating the process of automatic alignment of parallel treebanks from plain text files with a single call from a unix command line. Supported Languages: DE, FR, EN -
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Dosematic3
Software for aberration dosymetry
Objective: The program is being developed for three main purposes: A. Dose assessment after acute whole body exposure. B. Dose assessment in partial body exposure C. Dose assessment after protracted and fractioned exposure 2. Applicability The following DNA lesions can be investigated with the help of the program: A. Dicentrics B. γ-H2AX foci C. Micronuclei D. PCC fragments It is planned to include Comet assays as well RICA assays in the future. -
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A functional-structural model of tree growth based on carbon partitioning among individual organs that compete for resources.
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hrefinder
Detection of homologous recombination events from SNP data
...But if a series of SNP alleles differ from the ancestral pattern, then it may be more likely that an HRE has occurred, particularly if the allele pattern matches that from another part of the tree better than that of the ancestral node. -
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syphon is an extension for mod_openopc, to monitor telnet devices (serial devices) that sit on Serial -to- Ethernet bridges (such as barcode scanners) and export parsed data to an OPC compliant device (such as a PLC).
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CSST
Cascade and Sharing Survival Trees, an ensemble for survival analysis
Cascading and Sharing Survival Trees (CSST) is a tree-based enseble that allows to efficiently analize survival data. It is a strightforward extension of the CS4 method for lifetime collections of data. The CSST software comes along with its companion the CSST Prediction tool, to use the ensemble prediction in everyday life. Please, refer to the user's manual for further information. -
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Pysimony
A Pythonic Implementation of Parsimony Inference of Phylogeny
...Pysimony reads a FASTA file (only ATGC accepted) specified as its only argument. Basic testing has shown that it is slow, inaccurate and most definitely inefficient. An unlikely-to-be-the-most-parsimonious tree is printed upon completion in basic Newick tree format. As all parts of the program are the original work of a beginner programmer, this may represent one of the worst approaches to solving the phylogenetic problem. I have clearly avoided object-oriented programming. Nevertheless, I distribute this imagining it might someday be slightly educational or at least provide a laugh at the pathetic attempt it makes to reinvent the wheel -
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JBoost is a simple, robust system for classification. JBoost contains implementations of several boosting algorithms in an alternating decision tree framework. In addition, JBoost provides extensible software for adding more learning algorithms.
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Redundancy due to cut-paste operations in text creates bias in machine learning for NLP. This module takes a directory and produces a subset of the files in that directory (in a list) with an upper bound on similarity between two files.
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The SplitDB project gives practitioners of statistical tools for inferring phylogenies a way to store, retrieve and visualize important properties, like convergence, of the overwhelmingly large resulting tree-sets produced by these tools.
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General purpose discrete event simulation (DES) framework for the Python programming language. Khronos gathers ideas from other simulation software and tries to provide a simple and poweful toolset for simulation of discrete systems.
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H-mito is a mitochondrial DNA haplogroup prediction tool based on the phylogenetic tree http://www.phylotree.org/. Ancillary scripts: mitoP.py to extract mutation lists and clustal-2-fasta.zip to join, align through clustalw and convert data.
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This is a Python package designed to process Penn Treebank Release II-style combined trees (.mrg files) into useful objects for tree traversal, feature extraction, and statistical analysis. For more information, go to http://mrgutils.sourceforge.net
