Curator Dashboard

Software that provides visualization tools for flow cytometry data.

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• SciCrunch
• 12 years ago - by Anonymous

NeuronJ is an ImageJ plugin to facilitate the tracing and quantification of elongated structures in two-dimensional (2D) images (8-bit gray-scale and indexed color), in particular neurites in fluorescence microscopy images. Sponsors: The development of NeuronJ started while the primary developer ( Dr. Erik Meijering, PhD) was with the Biomedical Imaging Group (collaborating with people from the Laboratory of Cellular Neurobiology) of the Swiss Federal Institute of Technology in Lausanne (EPFL), Switzerland, and was finished while Dr. Meijering was with the Biomedical Imaging Group Rotterdam in the Netherlands.

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• SciCrunch
• 17 years ago - by Anonymous

A software program to call short indels and SNPs for Ion Torrent and 454 data.

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• SciCrunch
• 13 years ago - by Anonymous

Warping tool for intersubject registration of brain images consisting of C functions for Unix systems plus Matlab visualization utility functions. Apart from warping there are also (command line) functions for ANALYZE header information, mirroring, translation, subsampling. The package cannot only be used as a preprocessing step in function neuroimaging but also as a step in deformation-based morphometry.

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• SciCrunch
• 17 years ago - by Anonymous

Privately held company that develops and produces antibodies, ELISA kits, ChIP kits, proteomic kits, and other related reagents used to study cell signaling pathways that impact human health.

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• SciCrunch
• 17 years ago - by Anonymous

Cell signaling pathways can be explored using PathFinder, the interactive, online graphical representation of cell signaling pathways. The user can use PathFinder to explore the relationships between different cell signaling pathway components while being presented with our high quality small molecules, antibodies, enzymes, siRNA for gene knockdown and qPCR components to aid them in their research.

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• SciCrunch
• 17 years ago - by Anonymous

Free, downloadable Cell Signaling and Neuroscience Pathway Slides with an overview of the pathway and its links to Your Favorite Gene. There you can explore dynamic pathways and locate products in the context of your research. Each overview contains helpful links to the biological pathways, interaction networks, gene details and related products. Slide Categories: *Apoptosis and Cell Cycle *Cytokines, Growth Factors and Hormones *Cytoskeleton and Extracellular Matrix *Gene Regulation and Expression *G Proteins and Cyclic Nucleotides *Immune Cell Signaling and Blood *Ion Channels *Lipids in Cell Signaling *Multi-Drug Resistance *Neurobiology *Neurotransmission *Nitric Oxide and Cell Stress *Protein Phosphorylation

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• SciCrunch
• 16 years ago - by Anonymous

An MCMC-based algorithm that uses next-generation sequencing data to estimate tumor purity and clonality for paired tumor-normal data.

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• SciCrunch
• 12 years ago - by Anonymous

Automatic prediction tool to infer protein-protein interaction networks, it is applicable for lots of species using orthology and known interactions. The interoPORC method is based on the interolog concept and combines source interaction datasets from public databases as well as clusters of orthologous proteins (PORC) available on Integr8. Users can use this page to ask InteroPorc for all species present in Integr8. Some results are already computed and users can run InteroPorc to investigate any other species. Currently, the following databases are processed and merged (with datetime of the last available public release for each database used): IntAct, MINT, DIP, and Integr8.

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• SciCrunch
• 14 years ago - by Anonymous

Software to visualize electrocorticographic (ECoG) and possibly also other kinds of neural activity (EEG / EMG/ DOT) on a 3D model of the cortical surface. The tool has been used to produce cortical activation images and image sequences in several recent studies using ECoG. The tool is written in matlab. The package is thoroughly documented and includes a demo.

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• SciCrunch
• 12 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database of orthologous exon regions in the genomes of human, chimpanzee, and rhesus macaque. It can be used in analysis of multi-species RNA-seq expression data, allowing for comparisons of exon-level expression across primates, as well as comparative examination of alternative splicing and transcript isoforms.

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• SciCrunch
• 13 years ago - by Anonymous

A protein-protein interaction (PPI) database intending to bridge between the two communities most active in their characterization: structural biology and functional genomics researchers. It offers users access to binary subcomplexes, (i.e. physical direct interactions between proteins) that are either structurally characterized or modellable entries in the main functional genomics PPI databases BioGRID, IntAct and HPRD. Selected web services are available to further investigate the validity of postulated PPI by inspection of their hypothetical modelled interfaces., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 13 years ago - by Anonymous

Curated database of core pathways and reactions in plant biology that covers biological pathways ranging from the basic processes of metabolism to high-level processes such as cell cycle regulation. While it is targeted at Arabidopsis pathways, it also includes many biological events from other plant species. This makes the database relevant to the large number of researchers who work on other plants. Arabidopsis Reactome currently contains both in-house curated pathways as well as imported pathways from AraCyc and KEGG databases. All the curated information is backed up by its provenance: either a literature citation or an electronic inference based on sequence similarity. Their ontology ensures that the various events are linked in an appropriate spatial and temporal context.

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• SciCrunch
• 17 years ago - by Anonymous

Graphics software for a real-time approach to creating 3D graphics that offers a variety of intuitive, powerful design tools to create your 3D masterpiece. The graphics engine allows for a completely interactive environment, where all operations occur on solid objects in real time. A rendering engine allows you to produce stunning 3D imagery at virtually any resolution for Web, print, digital video, and film. Advanced capabilities include Radiosity rendering for photo-realistic scenes, Raytracing for true-to-life surface reflections and refractions, as well as variable smoke and lighting effects.

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• SciCrunch
• 12 years ago - by Anonymous

Statistical software tool for calling common and rare variants in analysis of pool or individual next-generation sequencing data. This software is optimized for analysis of whole-exome sequencing data and whole-genome sequencing data.

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• SciCrunch
• 13 years ago - by Anonymous

A database of brain neuroanatomic volumetric observations spanning various species, diagnoses, and structures for both individual and group results. A major thrust effort is to enable electronic access to the results that exist in the published literature. Currently, there is quite limited electronic or searchable methods for the data observations that are contained in publications. This effort will facilitate the dissemination of volumetric observations by making a more complete corpus of volumetric observations findable to the neuroscience researcher. This also enhances the ability to perform comparative and integrative studies, as well as metaanalysis. Extensions that permit pre-published, non-published and other representation are planned, again to facilitate comparative analyses. Design strategy: The principle organizing data structure is the "publication". Publications report on "groups" of subjects. These groups have "demographic" information as well as "volume" information for the group as a whole. Groups are comprised of "individuals", which also have demographic and volume information for each of the individuals. The finest-grained data structure is the "individual volume record" which contains a volume observation, the units for the observation, and a pointer to the demographic record for individual upon which the observation is derived. A collection of individual volumes can be grouped into a "group volume" observation; the group can be demographically characterized by the distribution of individual demographic observations for the members of the group.

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• SciCrunch
• 17 years ago - by Anonymous

Organization portal for neuromuscular disease community and contains comprehensive listing of biological and clinical aspects of neuromuscular disorders.This knowledge base contains information on the physiology, structure of ion channels, neurotransmitters, neuroreceptors, and associated diseases. Major categories include DISORDERS & SYNDROMES, INDEXES, NEUROMUSCULAR EVALUATION, ANTIBODY TESTING and NEUROMUSCULAR DIVISION.

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• SciCrunch
• 16 years ago - by Anonymous

A manually curated database of protein-protein interactions (PPIs) for mammalian transient receptor potential (TRP) channels. The detailed summary of PPI data, fits into 4 categories: screening, validation, characterization, and functional consequence. These categorizations give answers for four basic questions about PPIs: how to identify PPIs (screening); how to confirm PPIs (validation); what are biochemical properties of PPIs (characterization); what are biological meaning of PPIs (functional consequence). Users can find in-depth information specified in the literature on relevant analytical methods, gene constructs, and cell/tissue types. The database has a user-friendly interface with several helpful features, including a search engine, an interaction map, and a function for cross-referencing useful external databases.

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• SciCrunch
• 13 years ago - by Anonymous

Software program for developing probabilistic models for the analysis of microarray data.

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• SciCrunch
• 17 years ago - by Anonymous

Interactive digital atlas and movies comprising 3-D reconstructions at all stages of human development from Carnegie Stage 12 (CS12; ~26 days post conception (dpc)) to CS23 (~ 56 dpc) and anatomical annotations of the 3-D models linked to an anatomical database. The 3D models are generated using Optical Projection Tomography (OPT; Sharpe et al 2002). The digital atlas is also linked to a gene expression database that has been developed from the Edinburgh Mouse Atlas Project gene expression database (EMAGE). In the future, the HUDSEN EADHB aims to provide the wider scientific and medical communities with a dynamic tool for documenting and analyzing gene expression patterns and morphological changes in the developing human brain.

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• SciCrunch
• 14 years ago - by Anonymous