Curator Dashboard

An extensible framework for data-driven model parameter optimization that wraps and standardizes several existing open-source tools. BluePyOpt abstracts the optimization and evaluation tasks into various reusable and flexible discrete elements according to established best-practices. It also provides methods for setting up both small- and large-scale optimizations on a variety of platforms.

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• NIF
• 10 years ago - submitted by Matt Travers

Stereotactic atlases with probabilistic values describing the location of the main cerebral arteries. The data collected are from the COBRA study as described in "COBRA: A prospective multimodal imaging study of dopamine, brain structure and function, and cognition" by Nevalainen et al.

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• NIF
• 10 years ago - submitted by Matt Travers

Web application search tool intended to help users find MRI data shared publicly on the Web, particularly from projects organized under the 1000 Functional Connectomes Project (FCP) and International Neuroimaging Data-sharing Initiative (INDI). Users can perform queries visually to select a cohort of participants with brain imaging data based on their demographics and phenotypic information and then link out to imaging measures.

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• NIF
• 10 years ago - submitted by Matt Travers

Web application which allows users to visualise and collaboratively segment and annotate any brain MRI dataset available online via URL. A list of brains are available for use on the main site. Segmentations are automatically saved and can be downloaded as Nifti files or triangular meshes. Users can point BrainBox to their own Nifti data, or try data catalogues created by the community.

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• NIF
• 10 years ago - submitted by Matt Travers

Web framework for collaborative applications for neuroimaging. It hosts various web applications for curation, editing, and analysis in conjunction with neuroimaging data available publicly online.

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• NIF
• 10 years ago - submitted by Matt Travers

Web application used to visualise and annotate collaboratively high resolution histology data. In short, it uses public ontologies to create collaborative, community-curated atlases. Annotations are vectorial, and users can use boolean operations to combine, subtract and split regions.

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• NIF
• 10 years ago - submitted by Matt Travers

A software add-on that builds upon GENESIS by adding a library to installed versions of GENESIS. It is useful for simulations that must be run many times independently and for large-scale network models.

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• SciCrunch
• 10 years ago - submitted by Jamie Li

Commercial software company that offers simulation technology for both simulation and PCB design. PSpice has integrated analog and event-driven digital circuit simulation and a focus on bringing the tools needed for simulation that will help bring customer products to market. The website contains resources, libraries, and a user forum to support use of PSpice technology.

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• SciCrunch
• 10 years ago - submitted by Jamie Li

Block diagram environment that contains a graphical editor, customizable block libraries, and solvers for multidomain simulation and model-based design in MATLAB. It supports simulation, automatic code generation, and continuous test and verification of embedded systems.

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• SciCrunch
• 10 years ago - submitted by Jamie Li

Analog circuit analyzer and approximator used as a pre-processor to find design formulas or as a post-processor to approximate design formulas. The program performs the .AC analysis in SPICE symbolically with optional numeric evaluation and user selected threshold approximation.

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• SciCrunch
• 10 years ago - submitted by Jamie Li

A software toolbox containing a symbolic linear circuit analysis program. It is a MATLAB application that helps set up and solve design equations of electronic circuits.

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• SciCrunch
• 10 years ago - submitted by Jamie Li

Software toolbox for deriving and solving circuit equations symbolically in MATLAB.

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• SciCrunch
• 10 years ago - submitted by Jamie Li

A webserver for the prediction of prokaryote promoter elements and regulons. DNA in FASTA or plain format serve as input. A gene table can be included with the run.

• RRID-Legacy
• 10 years ago - submitted by Ivan Erill

Software used to automatically trace single neurons. It supports VTK 3D visualization.

• RRID-Legacy
• 10 years ago - submitted by David Kennedy

MATLAB-based tool for use with NEURON network models. It supports the modeler with model design, organization, execution (including on supercomputers), analysis, and reproducibility.

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• RRID-Legacy
• 10 years ago - by Anonymous

Application that uses molecular sequence data to compute unrooted phylogenetic networks. Given an alignment of sequences, a distance matrix, or a set of trees, the program will compute a phylogenetic tree or network using methods such as split decomposition, neighbor-net, consensus network, super networks methods or methods for computing hybridization or simple recombination networks., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• RRID-Legacy
• 10 years ago - by Anonymous

Nucleotide sequence alignment and alignment cleaning based on amino acid information. Users can paste nt-sequences into the application and select the desired protein alignment method and the genetic code, and the option for alignment cleaning., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• RRID-Legacy
• 10 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for the rapid annotation of prokaryotic genomes. It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank/DDJB/ENA. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• RRID-Legacy
• 10 years ago - by Anonymous

Software tool to automatically improve draft assemblies and find variation among strains, including large event detection. FASTA files of genome along with one or more BAM files of reads aligned as input. Read alignment analysis is used to identify inconsistencies between input genome and evidence in reads, then attempts to make improvements to genome.

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• RRID-Legacy
• 10 years ago - by Anonymous

Open access repository for Johns Hopkins University researchers to share their research data. Data repository is administered by professional curators at JHU Data Services, who will work with depositors to enable future discovery and reuse of your data, and ensure your data is Findable, Accessible, Interoperable and Reusable (FAIR). Each dataset has citation and DOI, facilitating attribution, and connection to research publications.

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• SciCrunch
• 10 years ago - submitted by Yueling Li