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http://www-01.ibm.com/software/uk/analytics/spss/
Software package used for interactive, or batched, statistical analysis in social science, health sciences and marketing. Software platform offers advanced statistical analysis, a library of machine-learning algorithms, text analysis, open-source extensibility, integration with big data and deployment into applications.Versions that were produced by SPSS Inc. before the IBM acquisition (Versions 18 and earlier) would be given origin or publisher of SPSS Inc. in Chicago.
Proper citation: SPSS (RRID:SCR_002865) Copy
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
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
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
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
https://scicrunch.org/resolver/SCR_002250
THIS RESOURCE IS NO LONGER IN SERVICE. Documented Jul 19, 2024. Metadatabase manually curated that provides web accessible tools related to genomics, transcriptomics, proteomics and metabolomics. Used as informative directory for multi-omic data analysis.
Proper citation: OMICtools (RRID:SCR_002250) Copy
Independent international facilitator catalyzing and coordinating global development of neuroinformatics aiming to advance data reuse and reproducibility in global brain research. Integrates and analyzes diverse data across scales, techniques, and species to understand brain function and positively impact the health and well being of society.
Proper citation: International Neuroinformatics Coordinating Facility (RRID:SCR_002282) Copy
Collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.
Proper citation: Ensembl (RRID:SCR_002344) Copy
http://brainproducts.com/productdetails.php?id=17
Software to manage the daily work of analyzing various neurophysiological data. Features include a history tree, automated analysis, various data format readers, and more.
Proper citation: BrainVision Analyzer (RRID:SCR_002356) Copy
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 26, 2016; however, the URL provides links to associated projects and data. A suite of data query, download, upload, analysis and sharing tools serving the needs of the microbial ecology research community, and other scientists using metagenomics data.
Proper citation: Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (RRID:SCR_002676) Copy
A program that provides technical assistance for surveys that aim to advance global understanding of health and population trends in developing countries. The DHS program collects, analyzes, and disseminates accurate and representative data on population, health, HIV, and nutrition through more than 300 surveys in over 90 countries.
Proper citation: DHS Program (RRID:SCR_000905) Copy
Netherlands institute for permanent access to digital research resources. DANS encourages researchers to make their digital research data findable, accessible, interoperable and reusable. It does this by providing expert advice and certified services.
Proper citation: DANS (RRID:SCR_000904) Copy
http://www.bioconductor.org/packages/2.12/bioc/html/rGADEM.html
R package with tools for de novo motif discovery in large-scale genomic sequence data.
Proper citation: rGADEM (RRID:SCR_001091) Copy
THIS RESOURCE IS NO LONGER IN SERVICE, documented on December 02, 2011. Notice: This domain name expired on 10/29/11 and is pending renewal or deletion PD-DOC is a portal and a database resource, hosting a database and linking to other databases and data sets of clinical and translational data. PD-DOC functions to organize and facilitate clinical and translational research in Parkinson's disease. The PD-DOC Database contains standardized data collected by user institutions on large numbers of patients with Parkinsons disease and other parkinsonian disorders. In some cases, data is obtained at a single point in time, while in others data is collected repeatedly over time. The PD-DOC Database is composed of the Core Data Set (CDS) which consists of those variables required to be gathered for each subject whose data is entered into the PD-DOC database. In 2005, working groups of Udall Center and invited experts deliberated to establish the components of each CDS section (e.g. General Clinical, Cognitive/Behavioral, Postmortem Brain Neuropathological Findings). The PD-DOC CDS was established and designed to optimize data analyses and data mining for large numbers of subjects participating in a variety of research studies. In most cases corresponding DNA samples are available form the NINDS Human Genetic Repository (at Coriell). Much of the website is publicly available for viewing. To request access to sections of the website dealing with downloading or requesting data, requesting a consultation, or submitting data or other information you will need to register. Before registering, you should read the PD-DOC Policies. Note that PD-DOC data can be used for research purposes only. Once your registration is successfully completed you will be automatically logged into the website.
Proper citation: PD-DOC (RRID:SCR_001596) Copy
http://eddylab.org/software.html
Software library containing tools for statistical manipulations of data. Tools include profile hidden Markov models for biological sequence analysis, RNA structure analysis, and a prototype noncoding RNA genefinder.
Proper citation: Eddy Lab Software (RRID:SCR_001458) Copy
http://pubchem.ncbi.nlm.nih.gov/
Collection of information about chemical structures and biological properties of small molecules and siRNA reagents hosted by the National Center for Biotechnology Information (NCBI).
Proper citation: PubChem (RRID:SCR_004284) Copy
Repository for all data, figures, theses, publications, posters, presentations, filesets, videos, datasets, negative data in a citable, shareable and discoverable manner with Digital Object Identifiers. Allows to upload any file format to be made visualisable in the browser so that figures, datasets, media, papers, posters, presentations and filesets can be disseminated in a way that the current scholarly publishing model does not allow. Features integration with ORCID, Symplectic Elements, can import items from Github and is a source tracked by Altmetric.com. Figshare gives users unlimited public space and 1GB of private storage space for free. Data are digitally preserved by CLOCKSS. Supported by Digital Science, a division of Macmillan Publishers Limited, as a community-based, open science project that retains its autonomy.
Proper citation: FigShare (RRID:SCR_004328) Copy
EuPathDB integrates numerous database resources and multiple data types. The phylum Apicomplexa comprises veterinary and medically important parasitic protozoa including human pathogenic species of genera Cryptosporidium, Plasmodium and Toxoplasma. ApiDB serves not only as database but unifies access to three major existing individual organism databases, PlasmoDB.org, ToxoDB.org and CryptoDB.org, and integrates these databases with data available from additional sources. Through ApiDB site, users may pose queries and search all available apicomplexan data and tools, or they may visit individual component organism databases. EuPathDB Bioinformatics Resource Center for Biodefense and Emerging/Re-emerging Infectious Diseases is a portal for accessing genomic-scale datasets associated with eukaryotic pathogens.
Proper citation: Eukaryotic Pathogen Database Resources (RRID:SCR_004512) Copy
Intergovernmental organisation funded by public research money from its member states in Europe. Groups and laboratories perform basic research in molecular biology and molecular medicine, training for scientists, students and visitors. Provides development of services, new instruments and methods, data and technology in its member states.
Proper citation: European Molecular Biology Laboratory (RRID:SCR_004473) Copy
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
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
