Curator Dashboard

Software Snakemake workflow for bacterial genome assembly plus polishing for Oxford Nanopore sequencing using multiple tools.

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• RRID
• 3 years ago - by Anonymous

A comprehensive characterization of expression patterns of genetically-controlled markers or tool genes in the brains of transgenic mice generated by the Allen Institute as well as the broad scientific community. Providing standardized, detailed, anatomical profiling of transgene expression throughout the brain, this dataset is intended to reveal the potential of each transgenic mouse line and help researchers choose the appropriate tools for their studies. Transgenic mice are valuable tools to label selective neuronal or non-neuronal populations, modulate gene expression in these cells or manipulate activity of these cells for the study of neural circuits and brain function. The Allen Institute has launched a project to generate a variety of transgenic mouse lines, mainly using the Cre/lox system, to express fluorescent probes or neuronal activity manipulating tools in a variety of cell types in the brain. At the same time, utilizing Allen Institute's unique high-throughput capability, a pipeline is set up to characterize the ability in directing cell type specific expression in the brains of various transgenic mice generated by the Allen Institute as well as the broad scientific community. Through standardized, detailed, anatomical profiling of the transgene expression in the entire mouse brain, this dataset is intended to provide a comprehensive evaluation of the potential of each transgenic mouse line and help researchers choose the appropriate transgenic tools to study the function of different regions and/or cell types of the brain. This data release adds additional data to the existing set of new Cre-reporter lines generated at the Allen Institute that have stronger expression than other commonly used reporter lines are used to characterize approximately a dozen Cre-driver lines. The types of characterization data include digitized images (of sections sampling the entire brain) of colorimetric in situ hybridization (CISH), double fluorescent in situ hybridization (DFISH), native fluorescence of XFP (generic term for fluorescent proteins of different colors), and immunohistochemical (IHC) labeling of marker genes.

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• SciCrunch
• 17 years ago - by Anonymous

Software to orchestrate the distribution of computational work units (data and applications) to volunteers and have results collected back. It supports diverse applications, including those with large storage or communication requirements, and addresses unsolved issues in biology, medicine, physics, astronomy and computer science.

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• SciCrunch
• 9 years ago - by Anonymous

Comprehensive, semi-manually curated crowdsourcing database of biomolecular condensates and their constituents as well as encyclopedia for scientific terms used to describe them.

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• RRID
• 2 years ago - by Anonymous

Software for differential expression analysis of RNA-seq using the Poisson-Tweedie family of distributions.

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• SciCrunch
• 12 years ago - by Anonymous

Software toolkit for multivariate pattern analysis (MVPA) of event-related potentials. This software is written in MATLAB.

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• RRID-Legacy
• 9 years ago - by Anonymous

Core facility is dedicated to structural characterization of biological samples and microcrystals using cryo-electron microscopy. CryoEM workflows including, single-particle CryoEM, Cryo-electron tomography , and Micro crystal electron diffraction. Instrumentation includes TFS 200kV Glacios CryoTEM, equipped with zero-loss Selectris Energy Filter, Flacon 4i Direct Electron Detector, and Ceta-D camera, Pelco Easy Glow Discharger, TFS Vitrobot Mark IV, and Leica EM GP2. We also present all the capacities for storing and shipping samples. Facility has Data storage Server and Live processing workstation for our users� convenience, including data processing suites RELION and CryoSPARC available at our campus supercomputer Swan cluster at the Holland Computer Center.

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• SciCrunch
• 2 years ago - submitted by Edyta Vieth

Computational biology resource for investigating candidate functional sites in eukarytic proteins. Functional sites which fit to the description linear motif are currently specified as patterns using Regular Expression rules. To improve the predictive power, context-based rules and logical filters are being developed and applied to reduce the amount of false positives. The current version of the ELM server provides core functionality including filtering by cell compartment, phylogeny, globular domain clash (using the SMART/Pfam databases) and structure. In addition, both the known ELM instances and any positionally conserved matches in sequences similar to ELM instance sequences are identified and displayed (see ELM instance mapper). Although the ELM resource contains a large collection of functional site motifs, the current set of motifs is not exhaustive.

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• SciCrunch
• 14 years ago - by Anonymous

Statistical software that provides classes and functions for the estimation of many different models, as well as for conducting statistical tests, and statistical data exploration. The results are tested against existing statistical packages to ensure that they are correct. http://conference.scipy.org/proceedings/scipy2010/seabold.html

• RRID-Legacy
• 9 years ago - submitted by Marin Manuel

Software R package provides intuitive interface for working with competing risk endpoints. Used for competing risks estimation.

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• RRID
• 2 years ago - by Anonymous

International Symposium on Objective Measures in Auditory Implants to explore what unique measures help us to achieve the best hearing outcome for each person who needs an auditory prosthesis.

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• SciCrunch
• 13 years ago - by Anonymous

Software for a statistical multiple sequence alignment algorithm which uses a "distance-based" approach to align homologous protein, RNA or DNA sequences. The GUI, MAD (Multiple Alignment Display), can display the intermediate alignments produced by FSA, where each character is colored according to the probability that it is correctly aligned.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software R package for calculation of standard and bootstrap confidence intervals.

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• RRID
• 2 years ago - by Anonymous

Tools for researchers to connect their data, code and computational methods to their published or soon to be published research in a convenient and easily citeable form. ResearchCompendia provides the tools to publish digital scholarly objects by hosting data, code, and methods in a form that is accessible, trackable, and persistent. They provide hosting and computational cloud resources for all researchers. Data and code should be citable and linked to the original publication.

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• SciCrunch
• 13 years ago - by Anonymous

Music composition and manipulation software.

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• RRID-Legacy
• 9 years ago - by Anonymous

Core supports fabrication and characterization of nanoscale materials and structures, and integration of devices at all length scales. Houses advanced equipment with core nano-level capability for fabrication and characterization, including electron-beam lithography system, dual-beam system, plasma etching, thin film deposition, TEM, multifunctional scanning probe station, modular XRD, and more.

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• SciCrunch
• 2 years ago - submitted by Edyta Vieth

A database of nuclear localization signals (NLSs) and of nuclear proteins targeted to the nucleus by NLS motifs. NLSs are short stretches of residues mediating transport of nuclear proteins into the nucleus. The database contains 114 experimentally determined NLSs that were obtained through an extensive literature search. Using "in silico mutagenesis" this set was extended to 308 experimental and potential NLSs. This final set matched over 43% of all known nuclear proteins and matches no currently known non-nuclear protein. NLSdb contains over 6000 predicted nuclear proteins and their targeting signals from the PDB and SWISS-PROT/TrEMBL databases. The database also contains over 12 500 predicted nuclear proteins from six entirely sequenced eukaryotic proteomes (Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana and Saccharomyces cerevisiae). NLS motifs often co-localize with DNA-binding regions. This observation was used to also annotate over 1500 DNA-binding proteins. From this site you can: * Query NLSdb * Find out how to use NLSdb * Browse the entries in NLSdb * Find out if your protein has an NLS using PredictNLS * Predict subcellular localization of your protein using LOCtree

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• SciCrunch
• 17 years ago - by Anonymous

Consortium that is an independent research initiative of the Human Research Information Network (HIRN). It is investigating methods to increase or maintain functional beta cell mass in T1D through targeted manipulation of islet plasticity or engineered protection of beta cells from immune-mediated destruction.

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

Core is self service facility that provides access to specialized instrumentation for phenotyping and genotyping of immune cells. Offers single cell next generation sequencing and quality control technologies. All instruments are located in the laboratories of four different CIIC investigators (KCBD 10220E and 10220C), and are available for use by the larger UChicago community.

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• SciCrunch
• 2 years ago - submitted by Edyta Vieth

The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase.

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• SciCrunch
• 13 years ago - by Anonymous