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on page 1 showing 20 out of 405 results from 1 sources

Cite this (Acquisition and Analysis for Electron Tomography, RRID:SCR_000192)

URL: http://www.biochem.mpg.de/en/rd/baumeister/research/ContentCEM/Software_development

Resource Type: Resource, software resource, software toolkit

A software platform for low dose electron tomography (ET) for all processing steps: acquisition, alignment, reconstruction, and analysis. Requires: Matlab R2008a and Image Processing Toolbox (V6.1)

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Cite this (ADAPT, RRID:SCR_006769)

URL: http://bmsr.usc.edu/software/adapt/

Resource Type: Resource, software resource, software application, simulation software, data processing software, data analysis software

Computational modeling platform developed for pharmacokinetic and pharmacodynamic applications. It is intended for basic and clinical research scientists and is designed to facilitate the discovery, exploration and application of the underlying pharmacokinetic and pharmacodynamic properties of drugs. Features in ADAPT 5
*Individual Analysis ** Estimation module (ID) includes weighted least squares, maximum likelihood (ML), generalized least squares (GLS), maximum a posterior Bayesian estimation (MAP) ** Simulation module (SIM) includes capabilities for single and multisubject simulations ** Sample schedule design module (SAMPLE) provides the ability to calculate D- and C-optimal designs * Population Analysis ** Parametric population PK/PD modeling using maximum likelihood estimation via the EM algorithm with sampling (MLEM), as introduced by Schumitzky (1995) and by Walker (1996), with extensions and enhancements by Bauer & Guzy (2004). ** Iterated two-stage (ITS) analysis as proposed by Prevost (1977) and Steimer, Mallet and colleagues (1984). ** Convenient standard two-stage (STS) and naive pooled data (NPD) modeling, each with WLS, ML, and MAP estimators. System Requirements * Operating System: Windows XP/Vista/7 * Other Software REQUIRED: Intel Visual Fortran 10.x XE2013

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Cite this (ADInstruments - Data Acquisition Systems for Life Science, RRID:SCR_001620)

URL: http://www.adinstruments.com/products/software/modules/neuro_explorer.php

Resource Type: Organization, material resource, instrument supplier

THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 19, 2018; A provider of computer-based data acquisition and analysis systems for life science. Products enable users to record and analyze life science data quickly and efficiently. ADInstruments product range is based on the PowerLab data acquisition system with LabChart software. The PowerLab system (also MacLab) is used in universities, hospitals, research institutes, pharmaceutical companies, contract research organizations and other private industry research sectors.

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Cite this (Advanced Neuroscience Imaging Research Laboratory Software Packages, RRID:SCR_002926)

URL: http://www.fmri.wfubmc.edu/cms/software

Resource Type: Resource, software resource, software toolkit

Research group based in the Department of Radiology of Wake Forest University School of Medicine devoted to the application of novel image analysis methods to research studies. The ANSIR lab also maintains a fully-automated functional and structural image processing pipeline supporting the image storage and analysis needs of a variety of scientists and imaging studies at Wake Forest. Software packages and toolkits are currently available for download from the ANSIR Laboratory, including: WFU Biological Parametric Mapping Toolbox, WFU_PickAtlas, and Adaptive Staircase Procedure for E-Prime.

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Cite this (Alacris Theranostics, RRID:SCR_003953)

URL: http://www.alacris.de/

Resource Type: Resource, portal, organization portal, service resource, commercial organization, data or information resource

Commercial organization that uses next generation sequencing technologies coupled with computational modeling of tumor and somatic tissues in order to identify individualized therapies for cancer patients. The company also uses these technologies to help pharmaceutical partners stratify patients for their clinical trials. Alacris has an exclusive worldwide commercial license for the computational modeling of tumors and somatic tissues using proprietary computational systems modeling technologies ModCell developed at the Max Planck Institute for Molecular Genetics (MPI-MG) in Berlin coupled with next generation sequencing and genotyping technology developed at Harvard Medical School in Boston. The company also is building up the first next generation sequencing center in Europe for clinical operations.

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Cite this (ALEA, RRID:SCR_006417)

URL: http://www.bcgsc.ca/platform/bioinfo/software/alea

Resource Type: Resource, software resource, software toolkit

A computational software toolbox for allele-specific (AS) epigenomics analysis. It incorporates allelic variation data within existing resources, allowing for the identification of significant associations between epigenetic modifications and specific allelic variants in human and mouse cells. It provides a customizable pipeline of command line tools for AS analysis of next-generation sequencing data (ChIP-seq, RNA-seq, etc.) that takes the raw sequencing data and produces separate allelic tracks ready to be viewed on genome browsers. ALEA takes advantage of the available genomic resources for human (The 1000 Genomes Project Consortium) and mouse (The Mouse Genome Project) to reconstruct diploid in-silico genomes for human or hybrid mice under study. Then, for each accompanying ChIP-seq or RNA-seq dataset, it generates two Wiggle track format (WIG) files from short reads aligned differentially to each haplotype.

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Cite this (AltAnalyze - Alternative Splicing Analysis Tool, RRID:SCR_002951)

URL: http://www.altanalyze.org/

Resource Type: Resource, software resource, software application

Software application for microarry, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), it will assess alternative exon (known and novel) expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, it provides comprehensive methods for the analysis of other data (RMA summarization, batch-effect removal, QC, statistics, annotation, clustering, network creation, lineage characterization, alternative exon visualization, gene-set enrichement and more). AltAnalyze can be run through an intuitive graphical user interface or command-line and requires no advanced knowledge of bioinformatics programs or scripting. Alternative regulated exons can be subsequently visualized in the context of proteins, domains and microRNA binding sites with the Cytoscape Plugin DomainGraph.

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Cite this (ALTER, RRID:SCR_015968)

URL: http://sing.ei.uvigo.es/ALTER/

Resource Type: Resource, image analysis software, data analysis software, data processing software, alignment software, software application, sequence analysis software, web application, software resource

Web application to perform program-oriented conversion of DNA and protein alignments and transform between multiple sequence alignment formats. ALTER focuses on the specifications of mainstream alignment and analysis programs rather than on the conversion among more or less specific formats.

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Cite this (Althia, RRID:SCR_003918)

URL: http://www.althia.es/

Resource Type: Resource, portal, organization portal, service resource, commercial organization, data or information resource

A biomedical company in Spain focused on the development of new tools for diagnosis and personalized treatment of oncological diseases and precancerous. It has three areas of activity in permanent innovation: Assistance in Diagnosis / Prognosis in solid and hematological tumors, Translational Research covering the gap between basic and clinical research and advanced radiotherapy treatments based image-guided single dose (SD-IGRT). Their objectives are: * Provide an integrated tissue and tumor molecular phenotype analysis using the most advanced technologies in diagnosis, to guide the most appropriate treatment for each patient. * Discover and validate molecular patterns by molecular systems and platforms including pathology, to generate predictive algorithms through computational biology, evolution and determining the response of patients with a particular tumor profile. Althia has laboratories equipped with the most advanced equipment and technologies in Barcelona and Granada Genyo Center, with offices in Madrid.

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Cite this (Ancient conserved untranslated sequences, RRID:SCR_008130)

URL: http://pbil.univ-lyon1.fr/acuts/ACUTS.html

Resource Type: Resource, data or information resource, database

THIS RESOURCE IS NO LONGER IN SERVICE, Documented on August 12, 2014. Database that identifies new regulatory elements in untranslated regions of protein-coding genes (5 prime flanks, 5 prime UTRs, introns, 3 prime UTRs and 3 prime flanks). The analyses is focused on genes from metazoan species (essentially vertebrates, insects and nematodes). Information on highly conserved regions (sequences, alignments, annotations, bibliographic references) are compiled. Currently 176 out of 326 detected highly conserved regions (HCRs) have been analyzed and incorporated in the database. You can also access the list of annotated conserved elements and the list of conserved elements that remain to be processed. Their approach is based on comparative sequence analysis, for the identification of phylogenetic footprints.

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Cite this (andi, RRID:SCR_015971)

URL: https://github.com/EvolBioInf/andi

Resource Type: Resource, image analysis software, data processing software, alignment software, software application, algorithm resource, software resource

Algorithm for rapidly computing and estimating the evolutionary distance between closely related genomes. Because andi does not compute full alignments it scales even up to thousands of bacterial genomes.

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Cite this (AnimalTracker, RRID:SCR_014397)

URL: http://animaltracker.elte.hu/

Resource Type: Resource, software resource, software application, data analysis software, data processing software

A universal tracking application specifically designed to support animal behavioral analysis. AnimalTracker consists of three main modules which can be used independently: Tracker is responsible for image processing and providing the coordinates of the identified object; Zone Designer provides tools to create custom-made investigation areas in order to design a maze-setup; and Tracking Analyzer module serves to define and obtain the parameters needed for the evaluation.

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Cite this (An Integrated Multiple Structure Visualization and Multiple Sequence Alignment Application, RRID:SCR_001646)

URL: http://ilyinlab.org/friend/

Resource Type: Resource, data analysis software, data processing software, software application, data visualization software, software resource, rendering software

Friend is a bioinformatics application designed for simultaneous analysis and visualization of multiple structures and sequences of proteins and/or DNA/RNA. The application provides basic functionalities such as: structure visualization with different rendering and coloring, sequence alignment, and simple phylogeny analysis, along with a number of extended features to perform more complex analyses of sequence structure relationships, including: structural alignment of proteins, investigation of specific interaction motifs, studies of protein-protein and protein-DNA interactions, and protein super-families. Friend is also useful for the functional annotation of proteins, protein modeling, and protein folding studies. Friend provides three levels of usage; 1) an extensive GUI for a scientist with no programming experience, 2) a command line interface for scripting for a scientist with some programming experience, and 3) the ability to extend Friend with user written libraries for an experienced programmer. The application is linked and communicates with local and remote sequence and structure databases.

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Cite this (ANNOgesic, RRID:SCR_016326)

URL: https://github.com/Sung-Huan/ANNOgesic

Resource Type: Resource, standalone software, data processing software, software application, data analysis software, software resource, software toolkit

Software tool for bacterial/archaeal RNA-Seq based genome annotations. Used for integrating, detecting, predicting, and grouping RNA-Seq data.

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Cite this (ARACHNE, RRID:SCR_000351)

URL: http://www.broadinstitute.org/science/programs/genome-biology/computational-rd/computational-research-and-development

Resource Type: Resource, software resource

A software for genome assembly, and is specifically designed to analyze long Sanger-chemistry reads.

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Cite this (ARB project, RRID:SCR_000515)

URL: http://www.arb-home.de/

Resource Type: Resource, software resource

A software environment for maintaining databases of molecular sequences and additional information, and for analyzing the sequence data, with emphasis on phylogeny reconstruction. The programs have primarily been developed for ribosomal ribonucleic acid (rRNA) sequences and, therefore, contain special tools for alignment and analysis of these structures. However, other molecular sequence data can also be handled. Protein gene sequences and predicted protein primary structures as well as protein secondary structures can be stored in the same database. The ARB package is designed for graphical user interface. Program control and data display are available in a hierarchical set of windows and subwindows. The majority of operations can be controlled using the mouse for moving the pointer and the left mouse button for initiating and performing operations.

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Cite this (ArcGIS for Desktop Basic, RRID:SCR_011081)

URL: http://www.esri.com/software/arcgis/arcgis-for-desktop

Resource Type: Resource, software resource, commercial organization

Geographical information system software produced by Esri.

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Cite this (Ariba, RRID:SCR_015976)

URL: https://github.com/sanger-pathogens/ariba

Resource Type: Resource, data analysis software, data processing software, software application, sequence analysis software, software resource, software toolkit

Analysis software that identifies antibiotic resistance genes by running local assemblies. It can also be used for MLST calling.

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Cite this (Artfastqgenerator, RRID:SCR_015979)

URL: https://sourceforge.net/projects/artfastqgen/

Resource Type: Resource, data analysis software, data processing software, software application, sequence analysis software, software resource, software toolkit

Software to evaluate and improve the accuracy of sequencing error under different experimental conditions. It can identify which components of a system may be suboptimal and which regions of the genome may be problematic.

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Cite this (AS-Peak, RRID:SCR_000380)

URL: http://sourceforge.net/projects/as-peak/

Resource Type: Resource, software resource

A software that utilizes a peak detection algorithm to identify RNA-protein binding sites.

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