Search Results for "extraction"

Turku Event Extraction System (TEES) is a free and open source natural language processing system developed for the extraction of events and relations from biomedical text. It is written mostly in Python, and should work in generic Unix/Linux environments. Currently, the TEES source code repository still remains on GitHub at http://jbjorne.github.com/TEES/ where there is also a wiki with more information.

...Collection of tools to help generate artificial Whole Slide Images (WSIs). A WSI is stored as a ZIP archive of JPG tiles, and this software contains a tool to visualize this format. SVS files can be used directly for texture extraction (thanks to the included Bio-Formats library). Main source files in package fr.unistra.wsi.synthetic.

This space is not maintained anymore. If you want to get the latest updates on fpocket refer to https://github.com/Discngine/fpocket. Fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level.

Information System "Supercritical Fluid Extraction" has developed as tool for collecting and analyzing the experimental data from various supercritical fluids experiments. The final target is to help to scientists who worked with supercritical fluids to predict some useful properties such as density, solubility etc. In order to calculate molecular descriptors, parse SMILES and another applied purposes is used Chemistry Development Kit (https://sourceforge.net/projects/cdk).

GeneNetWeaver (GNW) is an open-source tool for in silico benchmark generation and performance profiling of network inference methods. GNW was used to generate the community-wide DREAM3, DREAM4 and DREAM5 In Silico Challenges.

EToS (Efficient Technology of Spike sorting; Extracellular recording To Spike trains) is an open-source system for spike sorting. EToS contains the programs of spike detection, feature extraction and clustering.

...Extracting the data for individual SNP/CNV markers or individual samples was slow grep/awk'ing the text files exported from the genotyping run (e.g. Illumina final report files). bint converts the text representation of the intensity float data to into a IEEE754 indexed binary file for rapid extraction of subsets of the data. In theory bint could be used for any large tables of float data.

DASS-GUI is a graphical user interface for pattern search in non-sequential data.

The Hanalyzer is a tool designed to help biologists explain results observed in genome-scale experiments and to generate new hypotheses. It combines information extraction, semantic data integration, reasoning, and visualization.

User friendly PDB (Protein Data Bank) file editor with graphic user interface for protein crystallographers to expedite selective parallel edit / data extraction / analysis of their PDB files

Extraction of binding sites of ligands and search for unknown binding sites on apoproteins. Some call it docking. Some call it binding site detections. Some call it knowledge based.

MutationFinder is a biomedical natural language processing (NLP) system for extracting mentions of point mutations from free text. MutationFinder achieves high performance (99% precision, 81% recall on blind test data) as an information extraction system

BioEval, a web-based evaluation platform for one or multiple biomedical text extraction systems and the collaborative creation of gold standards. Handles evaluation of extraction of one to many related entities, plus supporting evidence and normalization

UIMA-compliant text analytics using a rule language in which to express context-sensitive constraints on syntactic and semantic text elements.

A web based tool that combines automatic extraction of gene and protein entities with manual curation done by the researchers who read and write the biomedical texts. The interface is loaded in web browser extensions and viewed along with the abstract.

GraphSpider is a pattern matcher which searches parsed text in phrase-structure tree or dependency graph format for syntactic structures matching a set of patterns in MPL, a regexp-like pattern language. Applications: information extraction, text mining.