Curator Dashboard

A metabolomics database which contains GC/MS metabolomics datasets. General users can search a curated annotated metabolite database, a metabolite response statistics database, experimental datasets, and uncurated repositories. Registered users can use Metabolome Express for data processing and management.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Open source Python software package designed to perform azimuthal integration and, correspondingly, two-dimensional regrouping on area-detector frames for small- and wide-angle X-ray scattering experiments.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Randomized, double blind, nationwide clinical trial to compare the efficacy and safety of three interventions to treat adolescents and youth with type 2 diabetes (T2D): (1) metformin alone, (2) metformin plus rosiglitazone, and (3) metformin plus an intensive lifestyle intervention called the TODAY Lifestyle Program (TLP). The secondary aims are to: compare and evaluate the safety of the three treatment arms; compare the effects of the three treatments on the pathophysiology of type 2 diabetes (T2D) with regards to beta cell function and insulin resistance, body composition, nutrition, physical activity and aerobic fitness, cardiovascular risk factors, microvascular complications, quality of life, and psychological outcomes; evaluate the influence of individual and family behaviors on treatment response; and compare the relative cost effectiveness of the three treatment arms. The study recruits patients over a three-year period and follows patients for a minimum of two years. Patients are randomized within two years of the diagnosis of T2D. Materials that were used for the study are made publicly available: * The TODAY Standard Diabetes Education (TSDE) program, developed especially for youth with type 2 diabetes. (All participants received the TSDE program) * The TODAY Lifestyle Program (TLP) that was among the treatments tested.

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• dkNET
• 14 years ago - by Anonymous

An R package that creates publishable-quality plots of p-values using single SNP and/or haplotype data. Main features of the package include options to display a linkage disequilibrium (LD) plot and the ability to plot multiple sets of results simultaneously. Plots can be created using global and/or individual haplotype p-values along with single SNP p-values. Images are created as either Portable Document Format (PDF) or Encapsulated (EPS) files. (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

Software Python library and associated set of scripts for rapid implementation of genome scale analyses.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Database of information on amphibian declines, natural history, conservation, and taxonomic information for every recognized species of amphibian in the world. Species accounts are being added regularly by specialists and volunteers and they contain species descriptions, life history information, conservation status, literature references, photos and range maps for many species. Some species have complete accounts; others as yet have only photographs or distributions. But all species can be queried for taxonomic, distributional and exact specimen data. AmphibiaWeb offers a powerful mapping tool by combining museum specimen data (via HerpNET) with expert opinion range maps (from Global Amphibian Assessment/IUCN) and overlaying these onto larger maps, allowing visualization in political, satellite, hybrid, or terrain map format. AmphibiaWeb currently (Aug 13, 2013) contains 7,160 species. They have 2,966 species accounts for 2,363 species, 6,517 literature references, 558 sound files, 109 video files, and 28,218 photos of 3,887 different amphibian species. These data come from numerous individuals--see acknowledgements. They have the ambitious goal of establishing a home page for every species of amphibian in the world. In order to accomplish this goal they encourage volunteers and specialists to help prepare species accounts. If you have special interest in a particular species, please contact them.

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• SciCrunch
• 14 years ago - by Anonymous

An object-oriented language for modeling large-scale neural systems, along with an IDE for writing and simulating models. N2A represents neural systems in a parts-relations framework combined with dynamics where each part has as set of equations that define its state variables and how they evolve over time. Each part is a pattern for a population of instances, and each instance has its own unique copy of the state variables.

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• RRID-Legacy
• 10 years ago - submitted by Fred Rothganger

Software R package defines many S4 generic functions used in Bioconductor.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Book with a downloadable version of the second edition of a practical introduction to the interdisciplinary field of computational neuroscience through the use of the GENESIS simulator. It is designed to be a step-by-step tutorial for professionals, researchers and students working in fields ranging from neuroscience to bioengineering, medicine, artificial neural networks and the cognitive sciences. Part I of the book teaches concepts in neuroscience and neural modeling by means of interactive computer tutorials on subjects ranging from neuronal membrane properties to cortical networks. These chapters, written by several contributors, allow the student to perform realistic simulations and experiments on model neural systems and provide the necessary background for understanding and using the tutorials. The simulations are user-friendly with on-line help and may be used without any prior knowledge of the GENESIS simulator or computer programming. Part II is intended to teach the use of the GENESIS script language for the construction of one's own simulations. This part will be useful for self-study by researchers who wish to do neural modeling, as well as students. It follows approximately the same sequence of topics as Part II, and uses parts of the tutorial simulations as examples of GENESIS programming. Several of these are based on recent research simulations which have been published in the neuroscience literature, but which have not been previously available for use outside the laboratories of the original researchers. Thus, the reader may modify these simulations and use them as a starting point for the development of original simulations. In addition to many revisions and additions to existing chapters, this second edition includes two new chapters on the modeling of biochemical signaling pathways and on the use of GENESIS on parallel computers and networks of workstations. Other new additions include a section describing ways to implement synaptic modification (learning), a section describing uses of a new method for modeling of a wide variety of voltage and ionic concentration dependent channels, a description of improvements in the procedure for implementing fast implicit numerical methods in GENESIS simulations, and descriptions of many new GENESIS commands and simulation components.

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• SciCrunch
• 14 years ago - by Anonymous

A function which allows users to generate two biological conditions synthetic microarray datasets. The user provides a subset of parameters, but default parameter settings can be modified.

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• SciCrunch
• 10 years ago - submitted by Jamie Li

Software R package implements filtering procedure for replicated transcriptome sequencing data based on global Jaccard similarity index in order to identify genes with low, constant levels of expression across one or more experimental conditions.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Geospatial software for monitoring and modeling the Earth system. Includes tools for GIS, image processing, surface analysis, vertical applications for land change analysis and earth trends exploration, and more.

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• SciCrunch
• 13 years ago - by Anonymous

The free Segway software package contains a novel method for analyzing multiple tracks of functional genomics data. The method uses a dynamic Bayesian network (DBN) model, which enables it to analyze the entire genome at 1-bp resolution even in the face of heterogeneous patterns of missing data. This method is the first application of DBN techniques to genome-scale data and the first genomic segmentation method designed for use with the maximum resolution data available from ChIP-seq experiments without downsampling. Segway uses the Graphical Models Toolkit (GMTK) for efficient DBN inference. The software has extensive documentation and was designed from the outset with external users in mind.

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• SciCrunch
• 16 years ago - by Anonymous

Software R package to parse Illumina Sequence Analysis Viewer files, access data, and generate QC plots.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Online portal of the software resources provided by Hanchuan Peng's lab. Program functions include 3D image rendering, MATLAB toolboxs, image annotator, and cell explorer atlas and building tools.

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• SciCrunch
• 16 years ago - by Anonymous

Core Facility provides support for short or long-term projects requiring expertise the analysis of biological datasets. The services provided include the analysis of large-scale datasets (e.g. next-gen sequencing data, microarrays, etc.), the development of customized databases and reusable analysis pipelines, guidance on experimental design, support with technical sections of manuscripts and grants, and training on analysis software packages. All services are charged at our hourly rate.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Software R package extends fitdistr function to help the fit of parametric distribution to non-censored or censored data.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Open-source set of tools to detect and report SNP genotypes, common Copy-Number Polymorphisms (CNPs), and novel, rare, or de novo CNVs in samples processed with the Affymetrix platform. While most of the components of the suite can be run individually (for instance, to only do SNP genotyping), the Birdsuite is especially intended for integrated analysis of SNPs and CNVs.

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• SciCrunch
• 14 years ago - by Anonymous

Core provides the infrastructure for cell-based gain-of-function (ORF, CRISPRa and CRISPRon) and loss-of-functioning (siRN, miRNA, shRNA, CRSIPRko, CRISPRi and CRISPRoff), libraries screening services, starting with assay development and carrying all the way through verification of identified targets. The large scale screens is accomplished via ready-to-use genome-wide or pathway-specific library platforms with choice of arrayed or pooled libraries. The FG core facility is equipped to perform custom CRISPR gene activation, knock-down, knock-out and editing services. We also adopt CRISPR nucleotide base editing technology and offer custom built CRISPR domain libraries. This approach can reveal the specific domain of a target protein interacting with another molecule, such as protein, IncRNA or drug in a native cell cellular environment.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Software R package provides interface to Nexus Class Library which allows parsing of NEXUS, Newick and other phylogenetic tree file formats. Provides elements of file that can be used to build phylogenetic objects such as ape's 'phylo' or phylobase's 'phylo4(d)'.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth