Search Results for "using" - Page 2
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Showing 102 open source projects for "using"
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Drug Extraction
Drug name extraction
...Feature set: Word, Word-1, Word+1, Word-1_Word, Word_Word+1, DrugBankPresence, POS DrugBankPresence feature indicates the presence of the drug name in the DrugBank. Using CONLL-Evaluation: processed 32065 tokens with 3656 phrases; found: 3251 phrases; correct: 2786. accuracy: 95.25%; precision: 85.70%; recall: 76.20%; FB1: 80.67 Using GATE Corpus Benchmark: Strict: P: 0.65 R: 0.73 F1: 0.69 Lenient: P: 0.74 R: 0.84 F1: 0.78 The details of how to reproduce evaluation, see README. ... -
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SuRankCo
Supervised Ranking of Contigs in de novo Assemblies
...For more details about SuRankCo and its functioning, please see "SuRankCo: Supervised Ranking of Contigs in de novo Assemblies" Mathias Kuhring, Piotr Wojtek Dabrowski, Andreas Nitsche and Bernhard Y. Renard (http://www.biomedcentral.com/1471-2105/16/240/abstract) PLEASE NOTE, it is recommended to read the paper and the readme.txt file before using SuRankCo. Update Jun2015: * Minor changes to enable BAM support. Update Feb2014: * Added support for FASTA/SAM assemblies in addition to ACE/FASTQ(QUAL). NOTE: features of FASTA/SAM assemblies do not include BaseCount, BaseSeqmentCount and ContigQualities yet. -
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scipion-xmipp
Image processing framework to integrate EM software packages.
Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM). It integrates several software packages and presents an unified interface for both biologists and developers. Scipion allows to execute workflows combining different software tools, while taking care of formats and conversions. Additionally, all steps are tracked and can be reproduced later on. Xmipp is a well-known package in the EM image processing. -
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Exreco
EXperimental REplicator COllider
...It aims to support the exploration of genetically rooted phenomena like - aging (programmed cell death) - sexual and asexual reproduction - altruism of individuals - spread of diseases The typical way of using Exreco starts by defining the behavior of your replicators ( agents that can reproduce and evolve over time), and defining the environment of these replicators. If it is all done you can let it run observing what kind of genes prevail over time. The tool typically runs the same world (experiment scenario) over and over again to have a statistical understanding of the various replicator strategies. -
Find Hidden Risks in Windows Task SchedulerWindows Task Scheduler might be hiding critical failures. Download the free JAMS diagnostic tool to uncover problems before they impact production—get a color-coded risk report with clear remediation steps in minutes.
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TE-locate
a tool for calling transposons
TE-locate is a tool to locate all copies of sequences in a reference sequence using read-pairs. TE = Transposable Element Input is NGS-data. Please download all files first (including the demo data) and make your first run then. -
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LiDSiM
LImits of Detection SImulation for Microbes
...For more details about LiDSiM and its functioning, please see "Estimating the Computational Limits of Detection of Microbial Non-Model Organisms" Mathias Kuhring and Bernhard Y. Renard (http://onlinelibrary.wiley.com/doi/10.1002/pmic.201400598/abstract) PLEASE NOTE, it is recommended to read the paper and the readme.txt file before using LiDSiM. -
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cnvOffSeq
detecting & genotyping intergenic CNVs using off-target exome data
cnvOffSeq is a set of Java-based command-line tools for detecting and genotyping intergenic copy number variation (CNV) using off-target data from whole-exome sequencing experiments. -
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HomSI
Homozygous Stretch Identifier from next-generation sequencing data
...Recently, the advent of next generation sequencing enables the concurrent identification of homozygous regions and the detection of mutations relevant for diagnosis, using data from a single sequencing experiment. In this respect, we have developed a novel tool that identifies homozygous regions using deep sequence data. Using *.vcf files as an input file, our program identifies the majo -
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BioAnnote
Annotator Desktop application is able to annotate biomedical texts by
Annotator Desktop application is able to annotate biomedical texts by using different high-quality online resources, such as Medlineplus and Freebase. Users can introduce biomedical documents and obtain annotations for the relevant terms, such as diseases, symptoms and treatments. In addition, users can retrieve more detailed information for each recognized entity (making use of an integrated web browser), including related topics, external links, related bibliography and paper abstracts. -
Comet Backup - Fast, Secure Backup Software for MSPsComet is a flexible backup platform, giving you total control over your backup environment and storage destinations.
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BiMS
BiMS (biclustering for mass spectrometry data) is a Java application d
...Users can load their MS datasets and apply different clustering and biclustering algorithms (current version includes Bimax and BiBit). In adition, users can load raw datasets (in mzML or mzXML formats) and preprocess them using MALDIquant package and MassSpecWavelet. -
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Luscinia is a program for archiving and analyzing field sound recordings (especially of animals). It incorporates an interface to a database, spectrogram measurement algorithms, sound comparison algorithms, and statistical analysis.
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EDNA
Energy Based Multiple Sequence Alignment (MSA) for Binding Sites
Multiple Sequence Alignment for Transcription Factor Binding Sites using Di nucleotides dependencies and relying on Free Interaction energies between neighbouring DNA bases to stabilise substitution energy of the alignment. http://www.ncbi.nlm.nih.gov/pubmed/23990411 -
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DimerRemover
Remove adapter dimers from NGS data
This program can be used to count or remove adapter dimers in fastq files. Using a provided adapter sequence, it generates variations of this sequence and stores them in a hash table. The reads can then be directly matched against the hash. It is far more time efficient than doing alignment. -
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bioluminescence
A java library for polymorphic genome assembly.
...It then uses this information to partition the original input read set into two subsets, each of which has been enriched for one of the haplotypes. Initial results using this technique have dramatically improved de novo asseblies of such data. The implementation provided here remains partial, and under daily development, and is released as a daily "snapshot" as opposed to a static version. -
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Used to record and analyze some behavioural experiments in neuroscience (using usb webcam). it was developed in collaboration with neuropharmacology lab at Faculty of Medicine, Ain Shams University. it can use(JMF,OpenCV,JMyron & AGCamLib) for webcam
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ViSEN
Visualization tool for statistical epistasis networks
The objective of this project is to provide a graphical visualization for statistical epistasis. Pairwise and three-way epistatic interactions are measured using information gain and are represented using networks. -
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TFAST
Software for analysis of afSELEX-seq data
Transcription Factor Analysis using SELEX with High-Throughput Sequencing (TFAST) is software developed by the Mobley lab at the University of Michigan designed to assist with transcription factor binding site discovery using data generated from aptamer-free SELEX-seq (afSELEX-seq). -
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Cyrface
Cytoscape and R interface
A Cytoscape plug-in to interface with R language. The connection is established using Rserve library. -
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Face Recognition Based Login Assistant
Login to Websites Automatically Using Your Face as Password
Face detection can be regarded as a more general case of face localization. In face localization, the task is to find the locations and sizes of a known number of faces (usually one). In face detection, one does not have this additional information. Face detection is mostly used along with facial recognition feature to extract faces out of an image or video feed and identify the faces against a set of stored images. This feature can be used for tracking prisoners, attendance and signing in... -
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CytoCopteR
A Cytoscape plug-in for training logic models, based on CellNOptR.
Homepage: www.cellnopt.org Based on prior knowledge networks CellNOptR can derive functional information about the network using logic modeling. CytoCopteR is a friendly way to use CellNOptR taking advantage of the network visualization and analysis of Cytoscape and without requiring knowledge on R. -
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Bayesian Network tools in Java (BNJ) is an open-source suite of software tools for research and development using graphical models of probability. It is published by the Kansas State University Laboratory for Knowledge Discovery in Databases (KDD).
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...The first module in the project was the "ePrescribing application"; certified by RxHub and SureScripts back in 2007. New implementation needs to "re-certify" with SureScripts (which should not be much of a problem) Work on eLabs (using ELINCS, LOINC etc.) is being considered as participants join the project become available. The HL7 RIM allows for eImaging applications, eConsults applications, eReferrals applications, etc. Applications work independently, but through HIE, results come back to the provider to see it in its "CPOE Section or Module" Requires licensing of the MediSpan Drug Database for ePrescrib
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PathMEN
A Java tool for mining pathway mentions from literature
...PathNER is built upon the GATE embedded framework.It's based on soft dictionary matching and rules-based detection. The dictionary is generated from ConsensusPathDB and Pathway Ontology and the rules are implemented in JAPE. Using PathNER, you can identify all occurrences of informative pathway names (e.g. 'the Wnt pathway'). PathNER can be used to assist studies that aim at uncovering associations between disease and pathways. -
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This plugin allow to visualize several e.g. gene expression values simultanously using pie charts. * Please cite http://www.biomedcentral.com/1752-0509/4/164 *
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cnvHiTSeq
cnvHiTSeq is a set of tools for detecting CNVs using sequencing data.
cnvHiTSeq is a set of Java-based command-line tools for detecting Copy Number Variants (CNVs) using next-generation sequencing data. cnvHiTSeq uses standard BAM files as input.
