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on page 1 showing 20 out of 194 results

    PiMS

Cite this (PiMS, RRID:SCR_011816)

URL: http://www.pims-lims.org/

Resource Type: Resource, software resource

Software for a Laboratory Information Management System (LIMS) developed to support the unpredictable workflows of Molecular biology and Protein production labs of all sizes.

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Cite this (Genboree Workbench, RRID:SCR_011864)

URL: http://www.genboree.org/java-bin/EpigenomeAtlas/workbench.jsp?isPublic=yes&context=EpigenomeAtlas

Resource Type: Resource, service resource

Service where users are able to upload and store data, access bioinformatics tools, and perform analyses.

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Cite this (PARalyzer, RRID:SCR_001208)

URL: http://www.genome.duke.edu/labs/ohler/research/PARalyzer/

Resource Type: Resource, software resource

Software tool to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. The algorithm utilizes the deep sequencing reads generated by the newly developed PAR-CLIP (Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) protocol. The use of photoactivatable nucleotides in the PAR-CLIP protocol results in a more efficient crosslinking between the RNA-binding protein and its target relative to other CLIP methods; in addition a nucleotide substitution occurs at the site of crosslinking during Illumina library preparation. PARalyzer utilizes this nucleotide substition in a kernel density estimate classifier to generate the high resolution set of Protein-RNA interaction sites.

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Cite this (Plantagora, RRID:SCR_001227)

URL: http://www.plantagora.org/

Resource Type: Resource, software resource, data set, data or information resource

A web-based plant genome assembly simulation platform whose resources include out of the box scripts for analyzing assembly data, an on-demand web graphing tool to model your experiment, and a downloadable database with metrics and parameters from over 3,000 simulated genome assemblies.

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    GenNav

Cite this (GenNav, RRID:SCR_000147)

URL: http://mor.nlm.nih.gov/perl/gennav.pl

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

GenNav searches GO terms and annotated gene products, and provides a graphical display of a term's position in the GO DAG. Platform: Online tool

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Cite this (TFmodeller, RRID:SCR_015715)

URL: http://www.ccg.unam.mx/tfmodeller

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

Web application that scans a library of protein-DNA complexes and builds comparative models of proteins bound to DNA. Its results include complex coordinates, schematic interface diagrams, interface alignments and DNA motifs.

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    LSQMAN

Cite this (LSQMAN, RRID:SCR_015751)

URL: http://xray.bmc.uu.se/usf/lsqman_man.html

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

Software for alignment, comparison of macromolecules, and performing least-squares superpositioning of biomacromolecules. The program offers a superset of the LSQ- functionality inside O and removes some of the limitations and irritations of the LSQ-commands.

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    Genesis

Cite this (Genesis, RRID:SCR_015775)

URL: https://genome.tugraz.at/genesisclient/genesisclient_description.shtml

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

Software for cluster analysis of microarray data. Genesis is a platform independent Java package of tools to simultaneously visualize and analyze a whole set of gene expression experiments.

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Cite this (UCSF ChimeraX, RRID:SCR_015872)

URL: https://www.cgl.ucsf.edu/chimerax/

Resource Type: Resource, data processing software, software application, data visualization software, 3d visualization software, 4d visualization software, software resource

Software for 3D/4D image reconstruction. UCSF ChimeraX is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera.

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    easyGV

Cite this (easyGV, RRID:SCR_016260)

URL: https://www.phc.ox.ac.uk/research/technology-outputs/easygv

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

Software for calculating different measures of glycaemic variability (GV). It analyzes continuous glucose monitoring data using a simple interface.

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    iHOMA2

Cite this (iHOMA2, RRID:SCR_016259)

URL: https://www.phc.ox.ac.uk/research/technology-outputs/ihoma2

Resource Type: Resource, model, dynamic model, data or information resource

Model of assessment with the baseline default characteristics of the HOMA2 computer model of fasting insulin glucose interaction. iHOMA2 enables the mathematical functions describing the organs and tissues involved in the glucose and hormonal compartments to be modified using simple visual analogue controls.

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    OVAL

Cite this (OVAL, RRID:SCR_016261)

URL: https://www.phc.ox.ac.uk/research/technology-outputs/oval-calc

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

Software that allows you to quantify glucose homeostasis in type 2 diabetes and control subjects. OVAL also has the capacity to quantify sequential deterioration and monitor effects of intervention.

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    BaSiC

Cite this (BaSiC, RRID:SCR_016371)

URL: https://www.helmholtz-muenchen.de/icb/research/groups/quantitative-single-cell-dynamics/software/basic/index.html

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

Software plugin for Fiji/ImageJ that performs retrospective image correction for optical microscopy. It is based on low rank and sparse decomposition, which corrects both shading in space and background bleaching in time.

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    DnaSP

Cite this (DnaSP, RRID:SCR_003067)

URL: http://www.ub.edu/dnasp/

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

A software package for the analysis of nucleotide polymorphism from aligned DNA sequence data. DnaSP can estimate several measures of DNA sequence variation within and between populations (in noncoding, synonymous or nonsynonymous sites, or in various sorts of codon positions), as well as linkage disequilibrium, recombination, gene flow and gene conversion parameters. DnaSP can also carry out several tests of neutrality: Hudson, Kreitman and Aguad (1987), Tajima (1989), McDonald and Kreitman (1991), Fu and Li (1993), and Fu (1997) tests. Additionally, DnaSP can estimate the confidence intervals of some test-statistics by the coalescent. The results of the analyses are displayed on tabular and graphic form.

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    HYDEN

Cite this (HYDEN, RRID:SCR_003126)

URL: http://acgt.cs.tau.ac.il/hyden/

Resource Type: Resource, software resource

Software program for designing pairs of degenerate primers for a given set of DNA sequences. It works well for large input sets of genomic sequences (e.g., hundreds of sequences of length 1Kbp). It is a batch (i.e., command-line, as opposed to graphical interface) program, available for Windows XP (downloadable version) and Linux (upon request).

  • From Current Category

    GENO3D

Cite this (GENO3D, RRID:SCR_003183)

URL: http://geno3d-pbil.ibcp.fr

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

An automatic web server for protein molecular modelling. Starting with a query protein sequence, the server performs the homology modelling in six successive steps: (i) identify homologous proteins with known 3D structures by using PSI-BLAST; (ii) provide the user all potential templates through a very convenient user interface for target selection; (iii) perform the alignment of both query and subject sequences; (iv) extract geometrical restraints (dihedral angles and distances) for corresponding atoms between the query and the template; (v) perform the 3D construction of the protein by using a distance geometry approach and (vi) finally send the results by e-mail to the user. The strategy used in Geno3D is comparative protein structure modelling by spatial restraints (distances and dihedral) satisfaction.

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Cite this (resExomeDB, RRID:SCR_003224)

URL: http://resexomedb.bioinf-dz.org/

Resource Type: Resource, service resource, data or information resource, data repository, storage service resource, database

An online catalog for whole-exome sequencing (WES) results including mutations and gene-disease associations identified by WES. It is browsable and searchable by mutation, gene, study or publication. In addition, it centralizes all publications, software, platforms related to exome / whole genome sequencing.

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    Osprey

Cite this (Osprey, RRID:SCR_003627)

URL: http://osprey.ucalgary.ca/

Resource Type: Resource, software resource

Oligonucleotide design software that calculates optimal oligonucleotides for a range of tasks: sequence assembly, differential expression, and microarrays (cDNA and spotted oligos).

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    X-Tile

Cite this (X-Tile, RRID:SCR_005602)

URL: http://www.tissuearray.org/rimmlab/xtile.html

Resource Type: Resource, software resource

A bio-informatics tool for biomarker assessment and outcome-based cut-point optimization.

  • From Current Category

Cite this (IsoformEx, RRID:SCR_005235)

URL: http://bioinformatics.wistar.upenn.edu/isoformex

Resource Type: Resource, software resource

Software that estimates transcript expression levels and gene expression levels from mRNA-Seq data. Technically speaking, IsoformEx parses bowtie alignment files in a project directory (e.g. ~yourid/isoformex/xxx, where xxx is the project name) and generates two files: (1) xxx/xxx_transcript_1.txt: expression levels of all transcripts, (2) xxx/xxx_gene_1.txt: expression levels of all genes.

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