Curator Dashboard

Designed for use in an MRI simulator, MoTrak software uses Ascension Technology?s Flock of Birds. The sensor attaches to the subject?s head and determines the position of the head in space relative to the transmitter. The sensor records angular rotations as well as positional displacements from an initially calibrated position. This information is displayed and logged by the program in real-time, allowing observation of head motion in an MRI simulator. In the simulator, the participant can simultaneously be habituated to the MRI environment, while being trained to remain still via feedback from the MoTrak system.

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• SciCrunch
• 14 years ago - by Anonymous

Software Computer Assisted Medical Intervention Tool Kit helps researchers and clinicians to easily and rapidly collaborate in order to prototype CAMI applications, that feature medical images, surgical navigation and biomechanical simulations.Open source, cross-platform generic tool, written in C++, which can handle medical images, surgical navigations and biomechanical simulations.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Johns Hopkins University School of Medicine is a medical graduate institution that provides physician, clinical fellowship and residency programs.

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• SciCrunch
• 17 years ago - submitted by Andrea Stagg

Spm-toolbox that performs region of interest (ROI)-level and voxel-level between-subjects analyses of functional MRI data, restricting the analyses to those areas identified using subject-specific functional localizers. Methods: The toolbox implements ROI-level and voxel-level analyses, and it implements an automatic cross-validation procedure when the localizers are not orthogonal to the effects-of-interest. ROI-level analyses allow manually defined parcels of interest, as well as automatically-defined ones (GcSS procedure, Fedorenko et al. 2010). General linear model second-level analyses are implemented, including ReML and OLS estimation of population level effects. Hypothesis testing includes standard univariate tests as well as multivariate tests for mixed within- and between-subject designs (T, F, and Wilks' lambda statistics) This toolbox requires Matlab and SPM5/SPM8.

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• SciCrunch
• 14 years ago - by Anonymous

Software Python library and software package for fast parsing and querying of VCF and BCF files and illustrate its speed, simplicity and utility. Used for variant analysis.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package written in Perl and C++ that provides a computational pipeline for identifying gene fusions from RNA-seq data.

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• SciCrunch
• 13 years ago - by Anonymous

A tool for analysis of Magnetic Resonance Spectroscopy (MRS) data by registering it to anatomical images. BrainCSI imports LCModel results to calculate absolute metabolite concentrations using tissue water. Corrections to LCModel metabolite concentrations for partial volume of tissues are accomplished by tissue classification of the anatomical images.

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• SciCrunch
• 14 years ago - by Anonymous

Software Python library aimed at making the simulation of metapopulation models. Software tool to study disease spread in complex networks.Used to help designing and simulating network-epidemic models with any kind of node behavior.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

A tool for creating logos representing both sequence alignments and profile hidden Markov models. The interactive logos enable scrolling, zooming, and inspection of underlying values. Skylign can avoid sampling bias in sequence alignments by down-weighting redundant sequences and by combining observed counts with informed priors. It also simplifies the representation of gap parameters, and can optionally scale letter heights based on alternate calculations of the conservation of a position.

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• SciCrunch
• 13 years ago - by Anonymous

Project portal dedicated to understand animal and machine intelligence and repository of data and tools. Suite of tools to analyze and graph imaging data. Image and data repository for large, publicly available neuro-specific data files and images. Contains tools for analytics, databases, cloud computing, and Web-services applied to both big neuroimages and big neurographs.

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• SciCrunch
• 11 years ago - submitted by Anita Bandrowski

Software tool as time efficient progressive Multiple Sequence Alignment algorithm. Sequence distance estimation step is determined by the natural grammar present in nucleotide and amino acid sequences.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

A k-mer counting software that can count k-mers of large Illumina datasets on laptops and desktop computers.

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• SciCrunch
• 13 years ago - by Anonymous

Free Pascal is a 32, 64 and 16 bit professional Object Pascal compiler targeting multiple processor architectures and operating systems. Documentation, including guides and manuals, are available on the website.

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• SciCrunch
• 11 years ago - submitted by Johannes W. Dietrich

Software tool as bibliography editor for KDE. Used in conjunction with Kile. BibTeX editor for KDE. KBibTeX's primary file format is BibTeX as known from LaTeX, but other formats such as RIS, PDF, or RTF can be imported and exported.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Non-profit organization based out of Seattle, Washington that conducts medical research on autoimmune disease.

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• SciCrunch
• 15 years ago - submitted by Stephen Larson

A database of domain-centric ontologies on functions, phenotypes, diseases and more. As a biomedical ontology resource, dcGO integrates functional, phenotypic, disease, and drug information. As a protein domain resource, it includes annotations to both the individual domains and supra-domains. Domain classifications and ontologies are organized in hierarchies, and dcGO includes the facility to browse the hierarchies: SCOP Hierarchy for browsing domains, GO Hierarchy for browsing GO terms, and BO Hierarchy for browsing other terms (mostly phenotypes). Users can mine and browse through resources.

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• SciCrunch
• 11 years ago - by Anonymous

Software package which interacts with and retrieves data from NCBI's eUtils. This distribution encompasses low-level API for interacting with (and storing) information from NCBI's eUtils interface. See Bio::DB::EUtilities for the query API to retrieve data from NCBI, and Bio::Tools::EUtilities for the general class storage system. Note this may change to utilize the XML schema for each class at some point, though we will attempt to retain current functionality for backward compatibility unless this becomes problematic.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Model-based software package for processing microarray images so as to estimate foreground and background intensities. The method starts with a very simple but effective automatic gridding method, and then proceeds in two steps. The first step applies model-based clustering to the distribution of pixel intensities, using the Bayesian Information Criterion (BIC) to choose the number of groups up to a maximum of three. The second step is spatial, finding the large spatially connected components in each cluster of pixels. The method thus combines the strengths of the histogram-based and spatial approaches. It deals effectively with inner holes in spots and with artifacts. It also provides a formal inferential basis for deciding when the spot is blank, namely when the BIC favors one group over two or three.

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• SciCrunch
• 13 years ago - by Anonymous

An independent committee established to improve visibility of cell lines and promote awareness and authentication testing to combat false or misidentified cell lines. It contains a databases of cross-contaminated or otherwise misidentified cell lines, as well as resources to familiarize users of cell lines and the problem of misidentification. Their Terms of Reference defines false or misidentified cell lines and other commonly used terms, as well as sets out the committee goals and ground rules.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Software C++ class library for interpreting data files in NEXUS format. NEXUS Class Library software package is collection of C++ classes designed to simplify interpreting data files written in the NEXUS format used by many computer programs for phylogenetic analyses.NEXUS format allows different programs to share the same data files, even though none of the programs can interpret all of the data stored.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth