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http://rgd.mcw.edu/rgdCuration/?module=portal&func=show&name=nuro

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Portal that provides researchers with easy access to data on rat genes, QTLs, strain models, biological processes and pathways related to neurological diseases. This resource also includes dynamic data analysis tools.

Proper citation: Rat Genome Database: Neurological Disease Portal (RRID:SCR_008685) Copy   

•   Source: SciCrunch Registry

http://www.blogmydata.org/

Software tool for data sharing, incorporating blogs and spatial registration of data. Mainly used in geological data sets. A Virtual Research Environment (VRE) aims to combine the capabilities of two existing technologies that have already seen wide adoption among scientists: - The Godiva2 data visualization system provides a means for scientists to browse interactively in a ''Google Maps-like'' fashion through large environmental datasets, including numerical model outputs and high-resolution satellite imagery, using only a web browser. - The LabBlog is a web-based blogging tool specifically designed for the practising scientist to record, disseminate and evaluate their research. The Blog can also be used as a collaboration tool that allows secure discussion between colleagues. Although initially designed for the use of laboratory chemists, the LabBlog is being adapted in this project to meet the needs of environmental scientists. The BlogMyData VRE will allow scientists to explore data visually using Godiva2, then make comments about features in the data on a blog. Colleagues will discover these blog entries and offer further information, providing answers to research questions through comments. Through RSS and GeoRSS feeds, colleagues, investigators and other interested parties can be notified of research activity, and scientists can discover hitherto-unknown colleagues working with similar data in similar geographic regions. Sponsors: BlogMyData is a collaboration between the Reading e-Science Centre and the University of Southampton and is one of the JISC VRERI projects.

Proper citation: BlogMyData (RRID:SCR_008697) Copy   

•   Source: SciCrunch Registry

http://openii.sourceforge.net/

OpenII (pronounced open-eye-eye) is a freely downloadable, open source information integration (II) tool suite. It includes 1) an extensible, plug-and-play platform for II tools and 2) several tools that assist with common integration tasks, including fully- or semi-automated support in the following scenarios: :- An integration engineer building a data warehouse must determine how diverse component data schemas map to the schema of the warehouse. :- An XML document that conforms to one schema needs to be converted into an equivalent document that conforms to a second (different) schema. :- To support data exchanges, a community needs to create a shared data model based on the models of its members. When a new member joins, the community needs to identify promising data exchange partners, and to what extent its shared model needs to be extended. Similarly, a chief information officer must identify data integration opportunities and make level-of-effort estimates after an acquisition or merger. To support these scenarios, OpenII provides a schema repository into which diverse data models can easily be imported. It also provides tools that 1) assist with identifying semantic correspondences across data models (Harmony), 2) compare a set of data models against a common reference model (Proximity), 3) visually organize a set of data models into clusters of related data models (Affinity), and 4) establish a common data model for a set of inter-related data models (Unity). Why should You use OpenII? Here are some reasons: :- OpenII is the only open-source platform for information integration tools. OpenII and its source code are freely available using the Apache 2.0 license, so you are free to borrow, extend or resell any portions of OpenII. :- The OpenII schema and mapping repository is based on a neutral modeling language. Thus, all of the OpenII tools can be used regardless of the underlying modeling language. For example, Harmony can identify correspondences among an XML schema, a relational database, and an OWL ontology. By comparison, most commercial tools are tied to a particular modeling language. :- OpenII is based on the Eclipse framework. As a result, the environment is already familiar to many programmers. Non-programmers can choose, instead, to use OpenII off-the-shelf without needing to first install Eclipse. :- OpenII is fully extensible. If needed components do not exist, they can be readily added. For example, adding a new importer or exporter is a straightforward task that can be completed in only a few hours. Moreover, each of the tools supports the introduction of new algorithms. And, programmers familiar with the Eclipse environment can add new views with moderate effort. Sponsors: This resource is supported by the MITRE Corporation.

Proper citation: Open Information Integration (RRID:SCR_008699) Copy   

•   Source: SciCrunch Registry

http://neuro-information.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. The International Observatory on Neuro-Information is the central source of knowledge, research and data on all skills and issues for Neuroscience applied in Information Sciences. It is an initiative of the Documentation Sciences Foundation, from Spain, which aims to gather information, express opinions, prepare documents, make comparative research, support and promote policy-making, evaluate trends, and take other appropriate action relating to the Neuroscience and its application to the Information Sciences (Libraries, Archives, Documentation centers), and how the traditional knowledge of Information Sciences can bring expertise in data visualization and retrieval techniques, records management, quality assurance and usability in Neuroscience. The Observatory may work together, or in agreement with other national or international organizations pursuing similar or compatible aims.

Proper citation: International Observatory on Neuro-Information (RRID:SCR_008690) Copy   

•   Source: SciCrunch Registry

https://www.brainproducts.com/

Commercial organization for hardware and software for neurophysiological research. Provides EEG and ERP amplifier systems, EEG recording caps, Data recording and analysis software, TMS Stimulator for combined EEG/TMS coregistrations and more.

Proper citation: Brain Products (RRID:SCR_009443) Copy   

•   Source: SciCrunch Registry

http://wbiomed.curtin.edu.au/genepop/

Population genetic data analysis software package. Used to perform exact Hardy Weinberg Equilibrium test. Used for population differentiation and for genotypic disequilibrium among pairs of loci. Computes estimates of F-statistics, null allele frequencies, allele size-based statistics for microsatellites, etc. and performs analyses of isolation by distance from pairwise comparisons of individuals or population samples., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GENEPOP (RRID:SCR_009194) Copy   

•   Source: SciCrunch Registry

http://www.mitre.org/news/digest/archives/2002/neuroinformatics.html

This resource''s long-term goal is to develop informatics methodologies and tools that will increase the creativity and productivity of neuroscience investigators, as they work together to use shared human brain mapping data to generate and test ideas far beyond those pursued by the data''s originators. This resource currently has four major projects supporting this goal: * Database tools: The goal of the NeuroServ project is to provide neuroscience researchers with automated information management tools that reduce the effort required to manage, analyze, query, view, and share their imaging data. It currently manages both structural magnetic resonance image (MRI) datasets and diffusion tensor image (DTI) datasets. NeuroServ is fully web-enabled: data entry, query, processing, reporting, and administrative functions are performed by qualified users through a web browser. It can be used as a local laboratory repository, to share data on the web, or to support a large distributed consortium. NeuroServ is based on an industrial-quality query middleware engine MRALD. NeuroServ includes a specialized neuroimaging schema and over 40 custom Java Server Pages supporting data entry, query, and reporting to help manage and explore stored images. NeuroServ is written in Java for platform independence; it also utilizes several open source components * Data sharing: DataQuest is a collaborative forum to facilitate the sharing of neuroimaging data within the neuroscience community. By publishing summaries of existing datasets, DataQuest enables researchers to: # Discover what data is available for collaborative research # Advertise your data to other researchers for potential collaborations # Discover which researchers may have the data you need # Discover which researchers are interested in your data. * Image quality: The approach to assessing the inherent quality of an image is to measure how distorted the image is. Using what are referred to as no-reference or blind metrics, one can measure the degree to which an image is distorted. * Content-based image retrieval: NIRV (NeuroImagery Retrieval & Visualization) is a work environment for advanced querying over imagery. NIRV will have a Java-based front-end for users to issue queries, run processing algorithms, review results, visualize imagery and assess image quality. NIRV interacts with an image repository such as NeuroServ. Users can also register images and will soon be able to filter searches based on image quality.

Proper citation: MITRE Neuroinformatics (RRID:SCR_006508) Copy   

•   Source: SciCrunch Registry

http://cytoscape.org

Software platform for complex network analysis and visualization. Used for visualization of molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.

Proper citation: Cytoscape (RRID:SCR_003032) Copy   

•   Source: SciCrunch Registry

http://platform.visiome.neuroinf.jp/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023.Analytical tools. Archive files may be written in any format and may include explanatory figures, program sources, readme files, and other related files. The readme file describes the purpose and usage of the archive file. This data sharing framework allows users to improve the reproducibility of simulations. Users can browse the platform contents via branch sites (A catalogue of illusions, Visitope), which introduce user friendly view of items such as basic images and original artworks of visual illusions with high resolution. The items in Visiome Platform are useful not only for reproducing the published results, but also for advancing and expanding the research in Vision Science.

Proper citation: Visiome Platform (RRID:SCR_003049) Copy   

•   Source: SciCrunch Registry

https://bioimagesuiteweb.github.io/webapp/index.html

Web applications for analysis of multimodal/multispecies neuroimaging data. Image analysis software package. Has facilities for DTI and fMRI processing. Capabilities for both neuro/cardiac and abdominal image analysis and visualization. Many packages are extensible, and provide functionality for image visualization and registration, surface editing, cardiac 4D multi-slice editing, diffusion tensor image processing, mouse segmentation and registration, and much more. Can be intergrated with other biomedical image processing software, such as FSL, AFNI, and SPM.

Proper citation: BioImage Suite (RRID:SCR_002986) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/gsea/

Software package for interpreting gene expression data. Used for interpretation of a large-scale experiment by identifying pathways and processes.

Proper citation: Gene Set Enrichment Analysis (RRID:SCR_003199) Copy   

•   Source: SciCrunch Registry

http://www.ime.fraunhofer.de/en.html

Provides assistance with consulting on experimental design, training on bioinformatics tools and databases, data quality assessment, data processing, data visualization, data interpretation, data mining of published datasets, and assistance with preparation of manuscripts and grant proposals.

Proper citation: Mainz Institute of Molecular Biology Bioinformatics Core Facility (RRID:SCR_011244) Copy   

•   Source: SciCrunch Registry

https://alleninstitute.org/

Non profit bioscience research organization in Seattle, Washington dedicated to accelerating research globally and sharing that data within the science community. Allen Institute for Brain Science, Allen Institute for Cell Science, Allen Institute for Immunology, and The Paul G. Allen Frontiers Group are four divisions of this Institute with commitment to open science model within its research institutes.

Proper citation: Allen Institute (RRID:SCR_005435) Copy   

•   Source: SciCrunch Registry

https://datadryad.org

International, curated, digital repository that makes the data underlying scientific publications discoverable, freely reusable, and citable. Particularly data for which no specialized repository exists. Provides the infrastructure for, and promotes the re-use of, data underlying the scholarly literature. Governed by a nonprofit membership organization. Membership is open to any stakeholder organization, including but not limited to journals, scientific societies, publishers, research institutions, libraries, and funding organizations. Most data are associated with peer-reviewed articles, although data associated with non-peer reviewed publications from reputable academic sources, such as dissertations, are also accepted. Used to validate published findings, explore new analysis methodologies, repurpose data for research questions unanticipated by the original authors, and perform synthetic studies.UC system is member organization of Dryad general subject data repository.

Proper citation: Dryad Digital Repository (RRID:SCR_005910) Copy   

•   Source: SciCrunch Registry

http://ucsd.researchaccelerator.org/

Software platform that allows researchers to easily collaborate on research and share reagents, antibodies, cell lines and more. It is designed to increase scientific collaboration across disciplines and geographical boundaries. Among the institutions now using the platform include Yale University, U of Pennsylvania, U of Chicago, Washington U, Cambridge University, University College London. The platform is licensed to select institutions. ResearchAccelerator.org allows researchers to form targeted, data driven collaborations. Researchers can search for data based on gene, disease and pathway, and they can post data which would otherwise be orphaned. The resulting collaborations, which are likely to be transdisciplinary, can greatly amplify impact and research productivity.

Proper citation: Research Accelerator (RRID:SCR_006051) Copy   

•   Source: SciCrunch Registry

http://web.bioinformatics.ic.ac.uk/eqtlexplorer/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. eQTL Explorer was developed as a computational resource to visualize and explore data from combined genome-wide expression and linkage studies is essential for the development of testable hypotheses. This visualization tool stores expression profiles, linkage data and information from external sources in a relational database and enables simultaneous visualization and intuitive interpretation of the combined data via a Java graphical interface. eQTL Explorer also provides a new and powerful tool to interrogate these very large and complex datasets. eQTLexplorer allows users to mine and understand data from a repository of genetical genomics experiments. It will graphically display eQTL information based on a certain number of selection criteria, including: tissue type, p-value, cis/trans, probeset Affymetrix id and PQTL type. Sponsors: This work was funded by the MRC Clinical Sciences Centre and the Wellcome Trust programme for Cardiovascular Functional Genomics.

Proper citation: eQTL Visualization Tool (RRID:SCR_013413) Copy   

•   Source: SciCrunch Registry

https://www.fieldtriptoolbox.org

Software toolbox for analysis of MEG, EEG, and other electrophysiological data. Used by experimental neuroscientists.

Proper citation: FieldTrip (RRID:SCR_004849) Copy   

•   Source: SciCrunch Registry

http://blast.ncbi.nlm.nih.gov/Blast.cgi

Web search tool to find regions of similarity between biological sequences. Program compares nucleotide or protein sequences to sequence databases and calculates statistical significance. Used for identifying homologous sequences.

Proper citation: NCBI BLAST (RRID:SCR_004870) Copy   

•   Source: SciCrunch Registry

http://alt.kompetenznetz-parkinson.de/englisch/englisch.html

A medical network comprised of university clinics, special clinics, and special practices working together to collect data, gene samples, and execute clinical trials in order to bring about diagnoses and therapy methods. Research projects are done in cure research, diagnostic and therapeutic research. The care network includes university clinics, town clinics, special clinics for Parkinson's disease, specialists, and general practitioners.

Proper citation: Competence Network on Parkinson's Disease (RRID:SCR_005013) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/

Non profit research organization for genome sequences to advance understanding of biology of humans and pathogens in order to improve human health globally. Provides data which can be translated for diagnostics, treatments or therapies including over 100 finished genomes, which can be downloaded. Data are publicly available on limited basis, and provided more extensively upon request.

Proper citation: Wellcome Trust Sanger Institute; Hinxton; United Kingdom (RRID:SCR_011784) Copy   

•   Source: SciCrunch Registry