Curator Dashboard

Software de novo adapter prediction algorithm for small RNA sequencing data.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This site has a dataset from a multicenter, double-blind, futility study of minocycline and creatine in subjects with early untreated Parkinson's Disease (PD) or FS-I (Futility Study I). There were 65 subjects/treatment arm with 195 total randomized subjects from approximately 42 sites in the US and Canada. A NINDS funded study. A Multicenter, Double-Blind, Futility Study of Minocycline and Creatine in subjects with early untreated Parkinson's Disease (PD) (FS-1).The primary objective of the study was to assess the impact of minocycline and creatine on the progression of PD in order to assess whether it was non-futile to proceed with further study of these agents. The progression of PD was measured by the change in total UPDRS score between the baseline visit and month 12 or the time of sufficient disability to require symptomatic therapy (last visit before subject goes on dopaminergic therapy), whichever occurs first. The additional follow-up of subjects until 18 months addressed the secondary objectives. The FS-1 study was conducted by the NINDS funded Neuroprotection Exploratory Trials in PD (NET-PD).

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• SciCrunch
• 17 years ago - by Anonymous

Software for automated structure calculation of biological macromolecules on basis of conformational constraints from nuclear magnetic resonance. Program for automated NMR protein structure calculation. CYANA requires a sufficient list of assigned chemical shifts and lists of cross-peak positions and columns from 2D, 3D, or4D NOESY spectra in order to calculate the assignment of the NOESY cross-peaks and the 3D structure of the protein in solution.

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• SciCrunch
• 11 years ago - by Anonymous

Software tool for reading and writing data stored by some versions of 'Epi Info', 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', and for reading and writing some 'dBase' files.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Application that provides users an interface to design analysis protocols combining one or more normalization and filtering steps. In this way, data from many individual hybridizations can be treated in a uniform and reproducible manner.

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• SciCrunch
• 13 years ago - by Anonymous

Open source software suite for processing and analyzing human brain MRI images. Used for reconstruction of brain cortical surface from structural MRI data, and overlay of functional MRI data onto reconstructed surface. Contains automatic structural imaging stream for processing cross sectional and longitudinal data. Provides anatomical analysis tools, including: representation of cortical surface between white and gray matter, representation of the pial surface, segmentation of white matter from rest of brain, skull stripping, B1 bias field correction, nonlinear registration of cortical surface of individual with stereotaxic atlas, labeling of regions of cortical surface, statistical analysis of group morphometry differences, and labeling of subcortical brain structures.Operating System: Linux, macOS.

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• SciCrunch
• 17 years ago - by Anonymous

Software tool as sequencing simulator producing realistic Illumina reads. Primarily intended for simulating metagenomic samples, it can also be used to produce sequencing data from a single genome.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package for analysis of de novo copy number variants in trios from high-dimensional genotyping platforms.

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• SciCrunch
• 13 years ago - by Anonymous

A research consortium with the long term goal of developing and testing measurement tools to describe symptoms of lower urinary tract dysfunction (LUTD) in women and men. The group plans to study targeted populations of patients with LUTD in order to expand our understanding of the causes of symptoms and common ways that symptoms change over time. The researchers will also collect biosamples from patients for current and future study of LUTD.

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• dkNET
• 11 years ago - submitted by Ko-Wei Lin

Software provides an interface to the ACEDB object-oriented database. Both read and write access is provided, and ACE objects are returned as similarly-structured Perl objects. Multiple databases can be opened simultaneously.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package to detect different methylation levels (DMR) that gives the exact p-value and q-value of MeDIP-seq and MRE-seq data for different samples comparison.

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• SciCrunch
• 13 years ago - by Anonymous

A database of experimentally-validate transcription factor binding sites (TFBS) in the Bacteria domain. CollecTF places special emphasis on providing a curation process that captures the experimental support for sites as reported by authors in peer-reviewed publications. Reported binding sites are mapped to NCBI RefSeq complete genome records. The database can be browsed by transcription factor families, NCBI taxonomy or experimental support, or through customized searches integrating these three elements.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Relational database schema that underlies many GMOD installations. It is capable of representing many of the general classes of data frequently encountered in modern biology such as sequence, sequence comparisons, phenotypes, genotypes, ontologies, publications, and phylogeny. It has been designed to handle complex representations of biological knowledge and should be considered one of the most sophisticated relational schemas currently available in molecular biology. The price of this capability is that the new user must spend some time becoming familiar with its fundamentals.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package using the GASSCO method for correcting for slide-dependent gene-specific dye bias.

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• SciCrunch
• 13 years ago - by Anonymous

A toolkit for mapping brain entropy using fMRI. It uses several functions from ASLtbx. At its core, the toolkit is a collection of batch scripts that implement a pipeline for processing fMRI data in order to get Sample entropy for each voxel.

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• RRID-Legacy
• 11 years ago - submitted by Maryann Martone

SIMD Smith-Waterman C/C++ library for use in genomic applications. SSW is a fast implementation of the Smith-Waterman algorithm, which uses the Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the instruction level. SSW library provides an API that can be flexibly used by programs written in C, C++ and other languages.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package for Data Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays.

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• SciCrunch
• 13 years ago - by Anonymous

Identity-by-descent (IBD) association testing software for genome-wide association study analysis. It requires an IBD detection method such as Beagle FastIBD to run first. GraphIBD then builds upon the IBD information to test if the IBD segments show association to the traits.

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• SciCrunch
• 13 years ago - by Anonymous

Software tool for analysis of genome alignments. It parses and manipulates MAF files as well as more simple fasta files. Despite various filtering options and format conversion tools, MafFilter can compute a wide range of statistics including phylogenetic trees, nucleotide diversity, inferrence of selection, etc.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

A regression based software package to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray experiments.

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• SciCrunch
• 13 years ago - by Anonymous