Curator Dashboard

Software tool to model population dynamics as discrete, sequential events that occur according to probabilities that are random variables following user-specified distributions.Simulation of deterministic forces as well as demographic, environmental and genetic stochastic events on wildlife populations.Can model many of extinction vortices that can threaten persistence of small populations.

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• RRID-Legacy
• 6 years ago - by Anonymous

Software tool as SPM extension for longitudinal and repeated measures data. Modelling of longitudinal and repeated measures neuroimaging data.Implemented as Matlab toolbox for SPM8 or SPM12.

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• RRID-Legacy
• 6 years ago - by Anonymous

Electrophysiological recording software for use with RHD USB Interface Board by Intan Technologies.

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• RRID-Legacy
• 6 years ago - by Anonymous

Software tool for accurate cell type quantification from gene expression data. Uses gene expression data to estimate cell type abundances. Allows user to supply custom reference matrices.

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• SciCrunch
• 6 years ago - by Anonymous

An R package that automatically identifies and extracts indicators of transparency (data availability, code availability, statements of conflicts of interest, statements of funding, statements of protocol registration) from TXT and PMC XML versions of published research articles in biomedicine.

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• RRID-Legacy
• 6 years ago - by Anonymous

CD44 is a 80-95 kD glycoprotein also known as Hermes, Pgp1, H-CAM, or HUTCH. It is expressed on all leukocytes, endothelial cells, hepatocytes, and mesenchymal cells. As B and T cells become activated or progress to the memory stage, CD44 expression increases from low or mid levels to high levels. Thus, CD44 has been reported to be a valuable marker for memory cell subsets. High CD44 expression on Treg cells has been associated with potent suppressive function via high production of IL-10. CD44 is an adhesion molecule involved in leukocyte attachment to and rolling on endothelial cells, homing to peripheral lymphoid organs and to the sites of inflammation, and leukocyte aggregation.

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• SciCrunch
• 6 years ago - submitted by Min Cao

The 37.51 monoclonal antibody specifically reacts with mouse CD28 molecule, a 45 kDa homodimer. It is expressed on most thymocytes, at low density on most of the CD4+ and CD8+ peripheral T lymphocytes, and on the natural killer cells. It is additionally found on activated splenocytes, mast cells, and thymocytes. CD 28 is a costimulator of T lymphocytes and a ligand for CD80 (B7-1), and CD86 (B7-2). The CD28 signaling stimulates the expression of IL-2 and IL-2 receptor and the cytotoxicity of CD3-activated T lymphocytes. The 37.51 antibody stimulates the proliferation of T lymphocytes and natural killer cells and their respective cytokine production.

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• SciCrunch
• 6 years ago - submitted by Min Cao

The 17A2 monoclonal antibody specifically reacts with the mouse T lymphocytes receptor (TCR) associated CD3 complex, resulting in cellular activation and proliferation. CD3 is expressed by thymocytes and mature lymphocytes, and contains γ, δ, and ε subunits, involved in the assembly, trafficking, and surface expression of T-cell receptor complex. The interaction between the T lymphocytes and the 17A2 antibody can be blocked by the 145-2C11 anti-CD3e antibody, demonstrating that the 17A2 antibody recognizes the CD3 ε chain.

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• SciCrunch
• 6 years ago - submitted by Min Cao

Software tool as molecular structure drawing application by ACD Labs. Allows user to Draw chemical structures, reactions, and schema, and access variety of graphical tools and templates, Generate names from molecular structure and vice versa, Calculate molecular properties from chemical structure, Create professional reports, presentations, and publication ready figures, Communicate scientific information with clarity and ease.

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• SciCrunch
• 6 years ago - submitted by Jeffrey Grethe

Standalone application for 3D visualisation and manipulation of mathematical field models. Cmgui is part of Continuum Mechanics, Imaging, Signal processing, System identification mathematical modelling environment. Generic open source modelling and visualisation package used to enable researchers to visualise biomedical images alongside dynamic geometry fields from computer models of cells, tissues and organs.

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

Neural Module by Axion BioSystems Inc, provides simplified approach to set up, execution and analysis of neural experiments. Enables Maestro Pro and Edge to record and analyze key parameters of neural network function, including activity, synchrony, and network oscillations.

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• RRID-Legacy
• 6 years ago - by Anonymous

Software tool for rapid and comprehensive quality assessment of raw sequence reads. It generates comprehensive list of QC statistics, including ancestry and contamination estimation.

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• SciCrunch
• 6 years ago - by Anonymous

Cloud comparison for transcript annotation data analysis pipeline. Workflow for comparing transcriptome annotation pipelines.

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• SciCrunch
• 6 years ago - by Anonymous

Website to visualize and share anatomical labels. Franklin and Paxinos (FP) based anatomical labels in Allen Common Coordinate Framework (CCF). Cell type specific transgenic mice and MRI atlas were used to adjust and further segment labels. New segmentations were created in dorsal striatum using cortico-striatal connectivity data. Anatomical labels were digitized based on Allen ontology, and web-interface was created for easy visualization. These labels provide resource to isolate and identify mouse brain anatomical structures. Open source data sharing will facilitate further refinement of anatomical labels and integration of data interpretation within single anatomical platform.

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

Describes number, types, and positions of cells in all areas of mouse brain. Provides densities and positions of all excitatory, inhibitory and neuromodulatory neurons, as well as astrocytes, oligodendrocytes and microglia in each of brain regions defined in Allen Mouse Brain Atlas. Users can download cell numbers for statistical analysis, cell positions and types for modeling and visualizing brain areas. Underlying workflow uses imaging data from Allen Institute Common Coordinate Framework to generate cell positions and assign their type using API for data access.

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

Software tool that extends WholeBrain framework in R for segmenting and registering experimental images to Allen Mouse Common Coordinate Framework (CCF). Streamlines processing of large volumetric LSFM datasets and solves issues with non-uniform morphing across anterior-posterior axis with interactive “choice game.” Accounts for duplicate cell counts in adjacent z images and presents new ways to easily parse apart and interactively visualize final mapped datasets.

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

Open source and multi-platform pinning software tool to facilitate mapping samples into common 3D spaces. Desktop application based on 3D Slicer that displays Allen Institute for Brain Science CCF or MNI atlas, color segmented by structure of brain, and allows user to create planar polyline annotation to facilitate mapping samples into corresponding atlas.

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

Software tool that integrates histology reconstruction, MRI co-registration, and manual segmentation tools in easy-to-use and intuitive interface. Permits real-time interaction with complex and large histology datasets during co-registration steps of histology reconstruction. Software tool for interactively mapping 2D and 3D molecular and anatomical histology into Common Coordinate Frameworks. Has simple, interactive registration workflows that connect user images with CCFs.

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• SciCrunch
• 6 years ago - submitted by Anita Bandrowski

Free software algorithms for forward and inverse modelling for Electrical Impedance Tomography (EIT) and Diffusion based Optical Tomography, in medical and industrial settings, and to share data and promote collaboration between groups working these fields.

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• NIF
• 6 years ago - submitted by Maryann Martone

Software reproducible, continuously updating platform which benchmarks performance of spike sorting codes across large curated database of electrophysiological recordings with ground truth. Website and open source computing framework for evaluating and comparing spike sorting algorithms for neurophysiology data analysis. Project of Center for Computational Mathematics at Flatiron Institute.

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• NIF
• 6 years ago - submitted by Maryann Martone