Search Results for "text based"
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Showing 24 open source projects for "text based"
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QUAST
Quality Assessment Tool for Genome Assemblies
...QUAST computes several well-known metrics, including contig accuracy, the number of genes discovered, N50, and others, as well as introducing new ones, like NA50 (see details in the paper and manual). A comprehensive analysis results in summary tables (in plain text, tab-separated, and LaTeX formats) and colorful plots. The tool also produces web-based reports condensing all information in one easy-to-navigate file. QUAST and its three follow-up papers (MetaQUAST, Icarus, QUAST-LG) papers were published in Bioinformatics; the last paper (WebQUAST) is out in Nucl Acid Research. -
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PlateEditor
PlateEditor, a free web application to work with multi-well plates
PlateEditor is a free web application to work with multi-well plates, from creation of layouts to data visualization and aggregation. It is primarily designed as a tool to help scientists working in the field of biology to simplify and fasten the process of data analysis. It is fully client-side: files are never transferred to the server, ensuring complete security and privacy of research data. It doesn't require any installation. - PlateEditor is available at this... -
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TIES
A smart search engine for medical documents
TIES (Text Information Extraction System) is a clinical text search engine that uses Natural Language Processing techniques to extract medical concepts from free text clinical reports. It provides secure de-identified access to this information and has in built collaboration tools and honest broker functionality. It is licensed for academic use under the BSD license. For commercial use please contact Nexi at http://nexihub.com *** NOTICE: this software and forum are no longer... -
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@Note2
@Note2 - A workbench for Biomedical Text Mining
Biomedical Text Mining (BioTM) is providing valuable approaches to the automated curation of scientific literature. -
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GNAT
GNAT recognizes gene names in text and maps them to NCBI Entrez Gene
GNAT is a BioNLP/text mining tool to recognize and identify gene/protein names in natural language text. It will detect mentions of genes in text, such as PubMed/Medline abstracts, and disambiguate them to remove false positives and map them to the correct entry in the NCBI Entrez Gene database by gene ID. March 2017: We started to upload GNAT output on Medline. See files/results/medline/. -
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bsclient
An interactive FTP-like command-line BaseSpace download client
bsclient is an interactive text-based client for browsing and downloading files from Illumina BaseSpace. It has a simple interface simliar to FTP and can be used to easily download files onto a remote server or in any situation when the web-based interface is not accessible or desirable. Please note that current development on this project has moved to GitHub: https://github.com/jvolkening/bsclient -
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Java class libraries for structural biology development: includes protein format conversion tool, printf-based text formatting, Pred2ary secondary structure prediction, neural net library, Hooke-Jeeves global optimizer, and misc. math & statistics.
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Framework for text mining, data integration and data analysis. Keywords: ontology and graph alignment, relation mining, warehouse, semantic database integration, bioinformatics, systems biology, microarray, Java.
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BioDare
BioDare is Biological Data Repository focused on timeseries data
...The main features of BioDare are: - an online repository for experimental data accompanied by extensive metadata - generation of secondary data (normalized, detrended, averaged …) - graphical output of data, secondary data and rhythm analysis - simple text-based search throughout metadata - biology- and conditions-aware search for data - data aggregation and export - group-based privacy settings for collaborative research -
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CRIS-IE-Smoking
GATE based app to extract patient smoking status from free text
This application was developed by the NIHR Biomedical Research Centre at the Institute of Psychiatry and South London and Maudsley NHS Foundation Trust, in collaboration with the University of Sheffield. Its purpose is to identify the smoking status of a individual, based on text evidence in clinical notes. Currently, it classifies patients as 'current', 'past' or 'never'. It runs on the GATE infrastructure, available at http://gate.ac.uk/. Please contact richard.g.jackson@slam.nhs.uk for support/queries. -
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FFP (Feature frequency profile) is an alignment free comparison tool for phylogenetic analysis and text comparison. It can be applied to nucleotide sequences, complete genomes, proteomes and even used for text comparison.
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This is a Java-based project for complex event extraction from text and co-reference resolution. Currently the code can read BioNLP shared task format (http://2011.bionlp-st.org/) and i2b2 Natural Language Processing for Clinical Data shared task format (https://www.i2b2.org/NLP/DataSets/Main.php). Event extraction includes finding events and the parameters for an event in a text.
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coords-view
Graphically displays nucmer/mummer mapping results
Displays mummer/nucmer mappings and prints PNG to stdout via the "show-coords -lcdTH" output. The output file is <coords-output>.png. Command line options allow for different features when producing the image. Within the code there are comment blocks which give examples of how to further customize it i.e. grouping based on name similarity, color, etc. This program is aimed at providing full customization within the limits of the Bio-Graphics module. Current version supported is Bio-Graphics-2.25 -
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Skittle Genome Visualizer
Skittle Development MOVED to Github
Skittle is a 2D visualization of genome sequence files. The program assigns four colors to the four nucleotides and text wraps the sequence to create a 2D picture based on the DNA sequence. Great for researching tandem repeats and chromosome structure. Compiled downloads available at http://dnaskittle.com/ Source maintained at https://github.com/josiahseaman/skittle -
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Contextor is a light-weight simple-to-use Java based library to help developers and researchers working with the general concept of a resource; as examples, resources can be text resources, web resources, images and videos.
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Ruby Research Wiki (RRiki) can be used to keep notes and organize references for research. It uses a browser interface, an intuitive plain text formatting language (markdown), and facilities to cross-reference and hierarchically organize notes
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Moara is a biological text mining tool and consists of a Java library and some auxiliary MySQL databases for gene/protein training and extraction of mentions and its further normalization and disambiguation.
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LAITOR is a text mining software developed to find co-occurrence of biological entities (gene/protein terms) together with biointeractions and concepts term from customized dictionaries.
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BioNotate is an open-source web-based tool for the collaborative and distributed annotation of biomedical text with entities and facts of interest.
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@Note2 is now available in www.anote-project.org @Note is a Biomedical Text Mining workbench that integrates current Biomedical Text Mining (BioTM) methods and provides biologists with intuitive tools capable of supporting their bibliographic searches and further literature curation.
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SENTENSA Knowledge Miner is a platform independent tool for searching any text. SENTENSA uses robust methods of indexing and searching text, leveraging on experience from more than 20 years of information retrieval.
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cafetiere
Rule-based information extraction.
UIMA-compliant text analytics using a rule language in which to express context-sensitive constraints on syntactic and semantic text elements. -
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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
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The OBO-Annotator is a semantic NLP tool that is designed to give its end-users a great deal of flexibility to combine any number of OBO ontologies from the OBO foundry regardless of their format and use them to annotate text-bases.
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