Results 1 - 10 of 56

Pybedtools: a flexible Python library for manipulating genomic datasets and annotations

by Ryan K. Dale, Brent S. Pedersen, Aaron R. Quinlan - Bioinformatics , 2011
"... Summary: pybedtools is a flexible Python software library for manipulating and exploring genomic datasets in many common formats. It provides an intuitive Python interface that extends upon the popular BEDTools genome arithmetic tools. The library is well-documented and efficient, and allows researc ..."
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Summary: pybedtools is a flexible Python software library for manipulating and exploring genomic datasets in many common formats. It provides an intuitive Python interface that extends upon the popular BEDTools genome arithmetic tools. The library is well-documented and efficient, and allows

PyClimate 1.2: Python tools for the climate variability analysis

by Juan Zubillaga , 2002
"... (a) In module bpcca.py, if the second field was not two-dimensional, the program crashed. It is already corrected. (b) The last character in the last line of a file could be missed by readdat.py if the last line did not end in a new line. It is corrected now. 2. Added a netCDF iterator. This is an o ..."
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is that under some systems (Linux, for instance), files larger than 2 Gb may produce errors in the filesystem. This way, they may be processed as smaller chunks and, still, give the user the impression of a single object that can be traversed by means of a single iteration. 3. Huge dataset EOFs (hdseofs.py

The CMS Dataset Bookkeeping Service

by Anzar Afaq , Andrew Dolgert , Yuyi Guo , Chris Jones , Sergey Kosyakov , Valentin Kuznetsov , Lee Lueking , Dan Riley , Vijay Sekhri
"... Abstract. The CMS Dataset Bookkeeping Service (DBS) has been developed to catalog all CMS event data from Monte Carlo and Detector sources. It provides the ability to identify MC or trigger source, track data provenance, construct datasets for analysis, and discover interesting data. CMS requires p ..."
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Abstract. The CMS Dataset Bookkeeping Service (DBS) has been developed to catalog all CMS event data from Monte Carlo and Detector sources. It provides the ability to identify MC or trigger source, track data provenance, construct datasets for analysis, and discover interesting data. CMS requires

Weaver: Integrating Distributed Computing Abstractions into Scientific Workflows using Python

by Peter Bui, Li Yu, Douglas Thain
"... Weaver is a high-level framework that enables researchers to integrate distributed computing abstractions into their scientific workflows. Rather than develop a new workflow language, we built Weaver on top of the Python programming language. As such, Weaver takes advantage of users ’ familiarity wi ..."
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with Python, minimizes barriers to adoption, and allows for integration with existing software. In this paper, we introduce Weaver’s programming model, which consists of datasets, functions, and abstractions that users combine to organize and specify large-scale scientific workflows. We also explain how

Classifying Unsolicited Bulk Email (UBE) using Python Machine Learning Techniques

by Sabah Mohammed, Osama Mohammed, Jinan Fiaidhi, Simon Fong, Tai Hoon Kim
"... Email has become one of the fastest and most economical forms of communication. However, the increase of email users has resulted in the dramatic increase of spam emails during the past few years. As spammers always try to find a way to evade existing filters, new filters need to be developed to cat ..."
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. There are a plethora of options when it comes to deciding how to add a machine learning component to a python email classification. This article describes an approach for spam filtering using Python where the interesting spam or ham words (spam-ham lexicon) are filtered first from the training dataset

Gene expression BackCLIP: a tool to identify common background presence in PAR-CLIP datasets

by P H Reyes-Herrera , C A Speck-Hernandez , C A Sierra , S Herrera
"... Abstract Motivation: PAR-CLIP, a CLIP-seq protocol, derives a transcriptome wide set of binding sites for RNA-binding proteins. Even though the protocol uses stringent washing to remove experimental noise, some of it remains. A recent study measured three sets of non-specific RNA backgrounds which ..."
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. It is possible to identify the presence of common backgrounds in a dataset and identify differences in datasets for the same protein. This method is the first step in the process of completely removing such backgrounds. Availability: The tool was implemented in python. The common background set

Rätsch G: Optimal spliced alignments of short sequence reads

by Fabio De Bona, Stephan Ossowski, Korbinian Schneeberger, Gunnar Rätsch - BMC Bioinformatics 2008, 9(Suppl 10):O7
"... Motivation: Next generation sequencing technologies open exciting new possibilities for genome and transcriptome sequencing. While reads produced by these technologies are relatively short and error prone compared to the Sanger method their throughput is several magnitudes higher. To utilize such re ..."
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results and a stand-alone alignment tool implemented in C++ and python are available at

GENERALIZATION EXPERT SYSTEM (GES): A KNOWLEDGE- BASED APPROACH FOR GENERALIZATION OF LINE AND POLYLINE SPATIAL DATASETS

by Sharon Kazemi, Samsung Lim, Hye-young Paik
"... Current map production systems provide reasonably complex tools and procedural cartographic protocols, however, cartographers ’ interactions are essential for selecting information, symbolizing features, maintaining topological relationships, and visualizing graphical conflicts. Although an efficien ..."
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Current map production systems provide reasonably complex tools and procedural cartographic protocols, however, cartographers ’ interactions are essential for selecting information, symbolizing features, maintaining topological relationships, and visualizing graphical conflicts. Although

Generalization Expert System (GES): a Knowledge-Based Approach for Generalization of Line and Polyline Spatial Datasets

by Sharon Kazemi, Samsung Lim, Hye-young Paik
"... Current map production systems provide reasonably complex tools and procedural cartographic protocols, however, cartographers ’ interactions are essential for selecting information, symbolizing features, maintaining topological relationships, and visualizing graphical conflicts. Although an efficien ..."
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Current map production systems provide reasonably complex tools and procedural cartographic protocols, however, cartographers ’ interactions are essential for selecting information, symbolizing features, maintaining topological relationships, and visualizing graphical conflicts. Although

Praaline: Integrating Tools for Speech Corpus Research

by George Christodoulides
"... This paper presents Praaline, an open-source software system for managing, annotating, analysing and visualising speech corpora. Researchers working with speech corpora are often faced with multiple tools and formats, and they need to work with ever-increasing amounts of data in a collaborative way. ..."
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, to produce aggregated data-sets. Praaline is extensible using Python or C++ plug-ins, while Praat and R scripts may be executed against the corpus data. A series of visualisations, editors and plug-ins are provided. Praaline is free software, released under the GPL license.
Results 1 - 10 of 56