Curator Dashboard

A brain bank which has obtained brains from individuals who suffered from some form of dementia. Clinical records and a family history are obtained for each donor in order to better understand each dementing illness and to work towards the improvement of diagnosing, treating, and preventing these diseases.

• Resource
• SciCrunch
• 15 years ago - by Anonymous

Software tool for rapid large scale prokaryote pan genome analysis. Builds large scale pan genomes, identifying core and accessory genes. Makes construction of pan genome of thousands of prokaryote samples on standard desktop without compromising on accuracy of results. Not intended for meta genomics or for comparing extremely diverse sets of genomes.

• Resource
• RRID-Legacy
• 7 years ago - submitted by Chao Yang

Core Facility houses 600 MHz Bruker Avance Neo NMR spectrometer available for both collaborative and fee-for-service use. The facility is equipped with a 14.1 T Bruker system and a nitrogen-cooled Prodigy probe, enabling a range of 3D experiments on isotopically labeled biomolecules with enhanced sensitivity for challenging samples. Services include biomolecular structure determination, characterization of biomolecular motions, and stable isotope-resolved metabolomics for studying metabolic pathways.

• Resource
• RRID
• 1 year ago - submitted by Mike Sabo

Software that characterizes coexisting subpopulations (SPs) in a tumor using copy number and allele frequencies derived from exome- or whole genome sequencing input data. The model amplifies the statistical power to detect coexisting genotypes, by fully exploiting run-specific tradeoffs between depth of coverage and breadth of coverage. ExPANdS predicts the number of clonal expansions, the size of the resulting SPs in the tumor bulk, the mutations specific to each SP and tumor purity. The main function runExPANdS provides the complete functionality needed to predict coexisting SPs from single nucleotide variations (SNVs) and associated copy numbers. The robustness of the subpopulation predictions by ExPANdS increases with the number of mutations provided. It is recommended that at least 200 mutations are used as an input to obtain stable results.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

GenomeRNAi is a database of phenotypes from systematic RNA interference (RNAi) screens in cultured Drosophila cells. The phenotype database can be searched by keywords, RNAi identifiers or Drosophila gene sequences. Searches with homologous sequences from human or C. elegans are also possible. Integrated tools evaluate the specificity of long double-stranded RNAs (RNAi probes) by similarity searches against all predicted Drosophila transcripts. This site can also be used to identify pre-designed RNAi probes from available Drosophila RNAi libraries. Caenorhabditis elegans genome, human genome

• Resource
• SciCrunch
• 17 years ago - by Anonymous

Integrated Cell Browser features integrated single-cell RNA sequencing (scRNA-seq) and single cell ATAC-seq data from human donor-specific pancreatic islet cells. The browser enables detailed interrogation of single cell RNA-seq and single cell ATAC-seq data through intuitive visualizations. Within the single-cell browser, users can first identify and filter single-cell datasets and dataset collections. Users can visualize interactive plots of cell type clusters, gene expression, cell type abundance, and marker gene expression. Donors and their data were provided by external programs described here.

• Resource
• dkNET
• 1 year ago - submitted by Ko-Wei Lin

Software focusing on calling indels from the next-generation paired-end sequencing data.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

Software tool to select particular records in file and perform operations upon them. awk utility interprets special purpose programming language that makes it possible to handle simple data reformatting jobs with few lines of code. Source code for latest release of GNU awk is available from GNU project ftp server and its many mirrors.

• Resource
• RRID-Legacy
• 7 years ago - submitted by Anita Bandrowski

Software Python package to optionally compute statistical test and add statistical annotations on plots generated with seaborn. Used to add statistical significance or custom annotations on seaborn plots.

• Resource
• RRID
• 1 year ago - by Anonymous

A database of bodily fluid proteome data. It contains information on proteins from humanplasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, seminal fluid, human milk, and amniotic fluid. Our body fluid protein database, Sys-BodyFluid, contains 11 body fluid proteomes, including plasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, seminal fluid, human milk, and amniotic fluid. Over 10,000 proteins are included in the Sys-BodyFluid. These body fluid proteome data come from 50 peer-review publications of different laboratories all over the world. Protein annotation are provided including protein description, Gene ontology, Domain information, Protein sequence and involved pathway. User can access the proteome data by protein name, protein accession number, sequence similarity. In addition, user could perform query cross different body fluids to get more comprehensive understanding. The difference and similarity between these 11 body fluids are also analyzed. Thus , the Sys-BodyFluid database could serve as a reference database for body fluid research and disease proteomics. plasm, serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, seminal fluid, human milk, and amniotic fluid, protein, proteomics

• Resource
• SciCrunch
• 17 years ago - by Anonymous

Enables visualization, storage and sharing of large image data. Cloud based system by MBF Bioscience to help with data from 2D and 3D slide scanners, confocal Z-stacks, lightsheet whole brain images. System for data storage and management, data analysis and visualization. Data is stored in secure and permanent way. Available also is free application named Biolucida Viewer, for viewing public images or images shared by collaborators owning Biolucida.

• Resource
• RRID-Legacy
• 7 years ago - submitted by Maci Heal

Cloud-based lab animal colony management application with realtime ambient sensing. Platform for managing vivaria. It features cage management, user management, lab management, and real-time environmental monitoring with IoT sensors.

• Resource
• RRID
• 1 year ago - submitted by Jensen Palmer

A database of in situ gene expression data in the developing mouse embryo and an accompanying suite of tools to search and analyze the data. mRNA in situ hybridization, protein immunohistochemistry and transgenic reporter data is included. The data held is spatially annotated to a framework of 3D mouse embryo models produced by EMAP (e-Mouse Atlas Project). These spatial annotations allow users to query EMAGE by spatial pattern as well as by gene name, anatomy term or Gene Ontology (GO) term. The conceptual framework which houses the descriptions of the gene expression patterns in EMAGE is the EMAP Mouse Embryo Anatomy Atlas. This consists of a set of 3D virtual embryos at different stages of development, as well as an accompanying ontology of anatomical terms found at each stage. The raw data images can be conventional 2D photographs (of sections or wholemount specimens) or 3D images of wholemount specimens derived from Optical Projection Tomography (OPT) or confocal microscopy. Users may submit data using a Data submission tool or without.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

Guidelines for data deposition in any common data hub or platform to facilitate data sharing in public health emergencies for scientific research.

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

Fully-staffed, open access, analytical research facility at Penn State's Materials Research Institute. Provided services include Surface Analysis (XPS, AFM, AES), Electron Microscopy (TEM, SEM, FIB, EPMA), X-ray Scattering (XRD and SAXS), Molecular Spectroscopy (FTIR, Raman, UV-VIs-NIR), Electrical Testing, Optical Microscopy, Thermal Analysis, Mechanical Testing, and Sample Preparation.

• Resource
• SciCrunch
• 14 years ago - by Anonymous

The International Neuroinformatics Coordinating Facility (INCF) Neuroinformatics blog.

• Resource
• SciCrunch
• 15 years ago - by Anonymous

Portal to share hCoV-19 genome sequences. Collection of genome sequences and related clinical and epidemiological data associated with coronavirus hCoV-19. Global repository of SARS-CoV-2 genomes. Initiative involves public-private-partnerships between Freunde of GISAID and governments of Federal Republic of Germany, Singapore and United States of America, with support from private and corporate philanthropy.

• Resource
• rapid-viraldb
• 7 years ago - submitted by Mia Jeffris

Vector Core produces gene transfer vectors that facilitate transfer of specific genes into either normal or aberrant cells. Provides intellectual and technical advice to researchers regarding the optimal use of these systems.

• Resource
• RRID
• 1 year ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 2nd, 2023. Sequence composition based classifier for metagenomic sequences. It works by capturing signatures of each sequence based on the sequence composition. Each sequence is modeled as a walk in a de Bruijn graph with underlying Markov chain properties. ClaMS captures stationary parameters of the underlying Markov chain as well as structural parameters of the underlying de Bruijn graph to form this signature. In practice, for each sequence to binned, such a signature is computed and matched to similar signatures computed for the training sets. The best match that also qualifies the normalized distance cut-off wins. In the case that the best match does not qualify this cut-off, the sequence remains un-binned.

• Resource
• SciCrunch
• 15 years ago - by Anonymous

Web server for anisotropy of diffraction limit and Bayesian estimation of structure amplitudes by Global Phasing Limited. Server uses DEBYE and STARANISO software to perform anisotropic cut off of merged intensity data, to perform Bayesian estimation of structure amplitudes and to apply anisotropic correction to data.

• Resource
• RRID-Legacy
• 7 years ago - by Anonymous