Curator Dashboard

Group of volunteer data scientists, machines learning experts, bioinformaticians and professional software developers who have joined together to offer their expertise for any data analysis problems that arise in context of ongoing coronavirus pandemic.

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• RRID-Legacy
• 7 years ago - submitted by Edyta Vieth

Software application to prepare figures for publication in reproducible way. This means you receive a figure representing your data and alongside a generated code file that can exactly reproduce the figure as you put them in the publication, without the need to readjust things in external programs. Offers interactive interface to find the best way to present your data in a figure for publication. Added formatting an styling can be saved by automatically generated code. To compose multiple figures to panels, pylustrator can compose different subfigures to a single figure.

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• RRID
• 1 year ago - by Anonymous

Web application that facilitates the management and analysis of high-throughput sequencing (HTS) data. In the back-end, it uses the Goby framework, BWA, STAR, Last, GSNAP, Samtools, VCF-tools, along with a cluster of servers to provide rapid alignment and efficient analyses. GobyWeb makes it possible to analyze hundreds of samples in consistent ways without having to use command line tools. GobyWeb provides tools that streamline frequent data analyses for RNA-Seq, Methyl-Seq, RRBS, or DNA-Seq datasets and to enable teams of investigators to share reads and results of analyses. GobyWeb can be extended for new analyses by developing plugins.

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• SciCrunch
• 13 years ago - by Anonymous

Collection of ontology of provisional cells determined by experimental methods.

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• NIF
• 7 years ago - submitted by Maryann Martone

Core facility primary mission is to provide access to advanced NMR spectroscopic methods and tools to students, postdoctoral fellows, and faculty of the University for the advancement of their research.

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• RRID
• 1 year ago - submitted by Edyta Vieth

There are a lot of fine blogs out there covering the avalance of current neuroscience research. With this blog Thomas Rams��y & Martin Skov want to highlight the many consequences of this growing understanding of the human brain. We are especially interested in two types of consequences: Tinkering with the brain and What is it like to be a human being? * Tinkering with the brain: First and foremost, with an understanding of how the brain works comes the possibility of tinkering with it. We already use billions of dollars every year on psychopharmocologia trying to treat depression, schizophrenia, obsessive-compulsive disorder and other mental diseases. But should we also use our knowledge of the brain to treat undesirable mental traits such as pedophilia or sociopathy? And what about enhancing normal brains? Clearly, evolution hasn''t endowed us with the most efficient brain imaginable. Shouldn''t we do something about its many shortcomings? * What is it like to be a human being?: Secondly, our view of human behavior is sure to change with our improved understanding of the human brain. Our knowledge of core human faculties such as language, social reasoning, aesthetics, and economics is already being challenged by modern neuroscience, yielding multiple hard questions. Do we have a free will? Is the mind innate or plastic? If people are not responsible for their actions (since all actions are caused by blind molecular processes) does our legal system still make sense? In short, will modern neuroscience come to completely redefine human nature? We try to discuss contemporary research literature, not just news reports. Although we will occasionally also target popular science reports, since we believe they play an important role in dissemining lessons from the lab. And in the future we plan to also post interviews with interesting researchers, as well as link to our own publications in journals and books. Additionally, the latest and most important books in the multidisciplinary field of neuroscience, cognition, psychology, ethics and economics are presented.

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• SciCrunch
• 15 years ago - by Anonymous

Assists University of Chicago investigators and research staff with medical imaging exams performed on human subjects for research purposes. Services include acquisition, analysis, collection, de-identification and distribution of image data for basic science research and clinical trials. Services ensure research-related imaging fulfills protocol requirements and allow investigators to obtain HIPAA- and IRB-compliant clinical research data. Provides services for all types of medical imaging, including x-ray, CT, MRI, ultrasound, nuclear medicine, PET, and most types of specialty imaging.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Laboratory is part of the Department of Nuclear Engineering and Radiological Sciences in the College of Engineering. MIBL is part of the National Nanotechnology Infrastructure Network. Services involve advancing our understanding of ion-solid interactions. Provides instruments for conducting ion beam surface modification and ion beam surface analysis under range of conditions. Experiments can be conducted at high or low temperature, in ultra-high vacuums, in reactive gas and in short turnaround times.

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• RRID
• 1 year ago - submitted by Edyta Vieth

A comparative pathology unit offering pathology support, training programs, and a Tissue Distribution Program (TDP). The TDP provides a wide variety of nonhuman primate tissues to investigative groups within and outside the Washington National Primate Research Center (WaNPRC). Tissue and pathology services (ACVP board certified Veterinary Pathologists), full histology services (including immunohistochemistry and frozen sectioning), and protocol development consultation are available. The Pathology and Tissue Program is an integration of comparative pathology activities occurring at the Washington National Primate Research Center and those occurring within the University of Washington Department of Comparative Medicine ((DCM). Using this model, Washington National Primate Research Center pathologists provide routine pathology support for Washington National Primate Research Center animals, with ancillary support, expertise, and guidance provided by DCM pathologists and mission-dedicated technicians and laboratories. This integrated comparative pathology unit also provides an excellent training opportunity for students such as those enrolled in the Department of Comparative Medicine post-doctoral training program, which offers training in laboratory animal medicine and comparative pathology. A particularly important function of this comparative pathology unit is support of the Tissue Distribution Program. The TDP provides a wide variety of nonhuman primate tissues to investigative groups within and outside the WaNPRC. This program is an extremely valuable method of conserving the nonhuman primate resource. NHP tissues and biological materials are collected in preparation for RNA/DNA isolation, cell culture, immunohistochemistry/histology, anatomic dissection, and cell sorting. Capabilities of the TDP include, but are not limited to flash frozen preservation, sterile preparation, perfusion, technical surgical dissections, and OCT embedding. In conjunction with the Histology and Imaging core of the University of Washington DCM, research capabilities post-collection include in situ hybridization, confocal and fluorescent microscopy, live cell imaging (DeltaVision), and whole slide scanning with image analysis (Visiopharm, Nikon Elements, and Image Pro). Centralized coordination of nonhuman primate tissue requests with animal availability allows support for a large number of biomedical programs with significantly decreased impact on the animal resource.

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• SciCrunch
• 15 years ago - by Anonymous

Software tool as composable cycle creator in python.

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• RRID-Legacy
• 6 years ago - submitted by Anita Bandrowski

Core offers instruments including Reichert-Jung Polycut microtome for decalcified or undecalcified samples, Reichert-Jung rotary microtomes for decalcified specimens, diamond band saws, cryostats for frozen sections with special features for bone section, slow speed diamond saws, high speed grinding cutoff wheel, precision grinding and polishing machines (Buehler Automet 300),complete embedding and preparation equipment and supplies for paraffin, methacrylate, epoxy, and other resins for embedding of biologic specimens, automated tissue processor for plastic and paraffin embedding preparation (Leica ASP 300S)

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• RRID
• 1 year ago - submitted by Edyta Vieth

Repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all kinds of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) representing all biotic taxa. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, book, conference proceedings, or thesis. Data used in publications that are in preparation or in review can be submitted to TreeBASE but will not be available to the public until they have passed peer review.

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• SciCrunch
• 17 years ago - by Anonymous

Interactive web application that depicts daily disease trends at level of US counties using time series plots and maps.

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• SciCrunch
• 6 years ago - submitted by Nathan Anderson

Software R package for full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac10, Feb. 2019) and stored in Biostrings objects.

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• RRID
• 1 year ago - by Anonymous

SIMBioMS (System for Information Management in BioMedical Studies) is a multi-module solution for data management in biomedical studies. Any research concerning human samples and/or utilizing high-throughput technologies yields such amount of information that conventional data storage solution might not be sufficient. We offer here three software modules: * Sample Information Management System (SIMS), * Assay Information Management System (AIMS) * Sample avAILability system (SAIL) * Emanta Administration tool (Emanta) All three software modules were developed as a part of the integrated EU project MolPAGE (Molecular Phenotyping to Accelerate Genomic Epidemiology) and the collaborative research project ENGAGE (European Network of Genomic and Genetic Epidemiology). SIMS and AIMS can work either as united system or as two completely independent components. In turn, SAIL is an independent web-based system for indexing of phenotypes availability in different cohorts and collections. All systems are packaged in such a way that they can easily be installed either as local (e.g. on a laptop) or as centralized databases (to be used by a group of people). SIMS and AIMS benefit from customizable interface, editable vocabularies and a choice of options for tackling data confidentiality issues. The systems provides a user with efficient means of control over data exchange process and at the same time helps to format the metadata in compliance with the standards accepted in functional genomics. Since SIMBioMS is an open source project, source files can be downloaded and changed by the user if needed.

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• SciCrunch
• 15 years ago - by Anonymous

Software program for spatial analysis for non geographic information systems specialists. Includes functionality ranging from simple mapping to exploratory data analysis, visualization of global and local spatial autocorrelation, and spatial regression.

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• RRID-Legacy
• 6 years ago - submitted by Nathan Anderson

Core provides mechanical and biomedical engineering expertise and services. Specializes in early-stage development and proof-of-concept prototypes. Utilizes 3D modeling, 3D printing, nitinol shape setting, and laser cutting to design and fabricate custom medical devices, test fixtures, and CT/MRI-based anatomy models.

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• RRID
• 1 year ago - submitted by Matthew Rudy

An integrated database of human maladies and their annotations, modeled on the architecture and richness of the popular GeneCards database of human genes. The database contains 17,705 diseases, consolidated from 28 sources.

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• SciCrunch
• 15 years ago - by Anonymous

Software R package for delineating temporal dataset shifts in electronic health records. Functions to delineate temporal dataset shifts in electronic health records through projection and visualization of dissimilarities among data temporal batches.Enables exploration and identification of dataset shifts, contributing to broadly examine and repurpose large, longitudinal datasets. Used to help ensure reliable data reuse to biomedical data users.

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• SciCrunch
• 6 years ago - by Anonymous

Core provides services and expert advice on routine and specialized molecular biology techniques including plasmid preps, genome editing, mutation detection, digital PCR and spatial transcriptomics.

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• RRID
• 1 year ago - submitted by Kym Delventhal