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A social visualization repository for the scientific workflow management system VisTrails providing a platform for sharing and executing computational tasks. It adopts the model used by social Web sites and that integrates a set of usable tools and a scalable infrastructure to provide an environment for scientists to collaboratively analyze and visualize data. crowdLabs aims to foster collaboration but was specifically designed to support the needs of computational scientists, including the ability to access high-performance computers and manipulate large volumes of data. By providing mechanisms that simplify the publishing and use of analysis pipelines, it allows IT personnel and end users to collaboratively construct and refine portals. This lowers the barriers for the use of scientific analyses and enables broader audiences to contribute insights to the scientific exploration process, without the high costs incurred by traditional portals. In addition, it supports a more dynamic environment where new exploratory analyses can be added on-the-fly.
Proper citation: crowdLabs (RRID:SCR_006294) Copy
A visualization hub displaying sequencing data from the Roadmap Epigenomics project. It hosts high volume of tracks from ENCODE and Roadmap Epigenomics projects, supports multiple organisms, visualizes chromatin-interaction data (e.g. Hi-C), performs gene set view, gene plot, and many others. All delivered on the web at high performance.
Proper citation: VizHub (RRID:SCR_006209) Copy
http://evolution.genetics.washington.edu/phylip.html
A free package of software programs for inferring phylogenies (evolutionary trees). The source code is distributed (in C), and executables are also distributed. In particular, already-compiled executables are available for Windows (95/98/NT/2000/me/xp/Vista), Mac OS X, and Linux systems. Older executables are also available for Mac OS 8 or 9 systems.
Proper citation: PHYLIP (RRID:SCR_006244) Copy
http://www.animalgenome.org/pig/genome/db/
Database facilitating information integration and mining within the pig and across species of all genomics / genetics research results accumulated over the years including pig gene expression, quantitative trait loci (QTL), candidate gene, and whole genome association study (WGAS) results. The key functions developed so far include pig gene pages (a centralized gene search tool), a local copy of Biomart (for customizable genome information queries), genome feature alignment tools (Pig QTLdb and Gbrowse), integrated gene expression information (ANEXDB and ESTdb), a dedicated pig genome and gene set BLAST server, and virtual comparative map database and tools (VCmap). By developing the PGD, it is our aim to collaboratively utilize existing databases and tools via networked functions, such as web services, database API, etc., to maximize the potential of all related databases through the PGD implementation.
Proper citation: Pig Genome Database (RRID:SCR_006367) Copy
Collection of chemical structures. Provides access to structures, properties and associated information from hundreds of data sources to find compounds of interest and provides services to improve this data by curation and annotation and to integrate it with users applications.
Proper citation: ChemSpider (RRID:SCR_006360) Copy
http://purl.bioontology.org/ontology/RETO
An application ontology for the domain of gene transcription regulation. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI, KEGG and orthology relations.
Proper citation: Regulation of Transcription Ontology (RRID:SCR_006238) Copy
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A public resource for sharing general proteomics information including data (Tranche repository), tools, and news. Joining or creating a group/project provides tools and standards for collaboration, project management, data annotation, permissions, permanent storage, and publication.
Proper citation: Proteome Commons (RRID:SCR_006234) Copy
Online repository of open access images including MR Sessions, MRI, Freesurfer APARC, Freesurfer ASEGs, Clinical Assessments, Atlas Scaling Factors, and Fast Segmentations data. CENTRAL currently contains 374 Projects, 3808 Subjects, and 5174 Imaging Sessions (June 2014). Central is powered by XNAT (The Extensible Neuroimaging Archive Toolkit), an open source software platform designed to facilitate management and exploration of neuroimaging and related data. XNAT includes a secure database backend and a rich web-based user interface.
Proper citation: XNAT Central (RRID:SCR_006235) Copy
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. Project to advance understanding of the neural mechanisms of vocal learning by providing a quantitative description of the relationship between physiological variables and vocal performance over the course of development in a songbird, the zebra finch. They propose to study vocal learning dynamically across neuronal and peripheral subsystems, using a novel collaborative approach that will harness the combined expertise of several investigators. Their proposed research model will 1) provide simultaneous measurements of acoustic, articulatory and electrophysiological data that will document the detailed dynamics of the vocal imitation process in a standardized learning paradigm; and 2) incorporate these measurements into a theoretical/computational framework that simultaneously provides a phenomenological description and attempts to elucidate the mechanistic basis of the learning process.
Proper citation: Zebra Finch Song Learning Consortium (RRID:SCR_006356) Copy
Web server to identify statistically enriched pathways, diseases, and GO terms for a set of genes or proteins, using pathway, disease, and GO knowledge from multiple famous databases. It allows for both ID mapping and cross-species sequence similarity mapping. It then performs statistical tests to identify statistically significantly enriched pathways and diseases. KOBAS 2.0 incorporates knowledge across 1327 species from 5 pathway databases (KEGG PATHWAY, PID, BioCyc, Reactome and Panther) and 5 human disease databases (OMIM, KEGG DISEASE, FunDO, GAD and NHGRI GWAS Catalog). A standalone command line version is also available, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: KOBAS (RRID:SCR_006350) Copy
An open-source, open-process, open-access scholarly authoring and publishing platform based on WordPress. Its objectives are to develop a simple, robust, easy-to-use authoring system to create and edit scholarly articles, and to deliver an editorial review and publishing system that can be used to submit, review, and publish scholarly articles. Software and source code are also available. Annotum will build upon the WordPress platform as a foundation, filling in the gaps by providing the following additional features: * Rich, web-based authoring and editing: ** What you see is what you get (WYSIWYG) authoring with rich toolset (equations, figures, tables, citations and references) ** coauthoring, comments, version tracking, and revision comparisons * Strict conformance to a subset of the NLM journal article publishing tag set * Multiple import and export formats ** Export to PDF and XML formats ** Import XML and WXR formats for round-tripping of content ** Articles can be cited, exported, imported across systems/sites * Simple editorial workflow for authoring and reviewer/editor approval * Features specific to scholarly publishing: ** Equations, figures, tables ** References including citation search features ** Auto-generation and registration of CrossRef DOIs
Proper citation: Annotum (RRID:SCR_006353) Copy
http://www.centropiaggio.unipi.it/software
Software to handle and process large numbers of optical microscopy image files of neurons in culture or slices in order to automatically run batch routines, store data and apply multivariate classification and feature extraction using 3-way principal component analysis (PCA). This freeware for semi automated quantitative and dynamic analysis of neuron morphometry incorporates the most important microstructural quantification methods, such as fractal and sholl analysis with statistical and classification tools to provide an integrated image processing environment which enables fast and easy feature identification. It includes: * Friendly interactive graphical user interface * Image pre-processing * Morphological analysis * Topological analysis * Cell counting * 3-way PCA analysis (also available as an ImageJ plugin) * Plot of variables Sequential images of labeled or unlabelled neurons or tissue slices can be uploaded batch-wise in order to create a 3 axis (time, image coordinate) data base and a datamatrix of variables for 3-way Principal Component Analysis*.
Proper citation: NEuronMOrphological analysis tool (RRID:SCR_006304) Copy
An ontology for the description of biological and clinical investigations built with international, collaborative effort. The ontology represents the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. This includes a set of universal terms that are applicable across various biological and technological domains, and domain-specific terms relevant only to a given domain. Currently OBI is being built under the Basic Formal Ontology (BFO). This project was formerly titled the Functional Genomics Investigation Ontology (FuGO) project.
Proper citation: Ontology for Biomedical Investigations (RRID:SCR_006266) Copy
The LBDA is a Lewy Body Disease (LBD) information resource for lewy body patients, caregivers, and medical professionals. It provides general information on LBD, including diagnosis, symptoms, treatments, etc., as well as providing links to support resources and an LBD online community. For professionals, the site also provides information on patient care, current LBD research and publications, and diagnostics information. LBDA offers many support resources for those affected by LBD and for their loved ones. These resources include local support group meeting information, online support groups, and user forums where users can find information or ask any questions they may have about the disease. A portion of the site is also dedicated to those who wish to help, either through participation in clinical trials, donations, or volunteering. LBDA also offers information on upcoming LBD-related events. LBDA is located Atlanta, GA. :NIF thanks the : :Parkinson''s Disease Foundation : : :for their referral of this resource to us.
Proper citation: Lewy Body Dementia Association (RRID:SCR_006421) Copy
Data and knowledge management infrastructure for the new Center for Clinical and Translational Science (CCTS) at the University of Utah. This clinical cohort search tool is used to search across the University of Utah clinical data warehouse and the Utah Population Database for people who satisfy various criteria of the researchers. It uses the i2b2 front end but has a set of terminology servers, metadata servers and federated query tool as the back end systems. FURTHeR does on-the-fly translation of search terms and data models across the source systems and returns a count of results by unique individuals. They are extending the set of databases that can be queried.
Proper citation: FURTHeR (RRID:SCR_006383) Copy
http://brainvis.wustl.edu/wiki/index.php/Caret:About
Software package to visualize and analyze structural and functional characteristics of cerebral and cerebellar cortex in humans, nonhuman primates, and rodents. Runs on Apple (Mac OSX), Linux, and Microsoft Windows operating systems.
Proper citation: Computerized Anatomical Reconstruction and Editing Toolkit (RRID:SCR_006260) Copy
A community building portal dedicated to understanding Alzheimer's disease and related disorders, it reports on the latest scientific findings from basic research to clinical trials, creates and maintains public databases of essential research data and reagents, and produces discussion forums to promote debate, speed the dissemination of new ideas, and break down barriers across disciplines.
Proper citation: Alzheimer's Research Forum (RRID:SCR_006416) Copy
A project that observes the processes of adaptive evolution in nature, and tests evolutionary hypotheses, by studying populations of guppies on the Caribbean island of Trinidad. Darwin thought that evolution by natural selection occurred very slowly, over hundreds if not thousands of years. Evolutionary biologists now know that evolutionary changes in species can happen very quickly, over a relatively few generations. The National Science Foundation (NSF), through its Integrative Biological Research (FIBR) program, is funding a 5-year study by 13 biologists from colleges, universities, and research institutions throughout the United States and Canada, to study the relationship of adaptive evolution and environmental circumstances. The Trinidadian guppy (Poecilia reticulata) is an excellent species for these purposes because: * It matures rapidly (one generation = 3-4 months) * It inhabits different ecological environments that can be easily manipulated On Trinidad, guppies live in streams, or portions of streams, that can differ in the species of predators that the guppies have to contend with. Some streams are high-predation environments, others low-predation. Different predation environments are often right next to one another, separated by a waterfall (which neither guppies nor predators can cross). Guppies from high-predation environments experience much higher mortality rates than do guppies in low-predation environments. High mortality is associated with the following characteristics, all of which have a genetic basis: * Earlier maturity * Greater investment of resources in reproduction * More and smaller offspring. We have found that mortality rates can be manipulated by: * Transplanting guppies from high-predation localities into sites from which they and their predators had previously been excluded by natural waterfalls, thus lowering mortality rates; * Introducing predators into low-predation sites, thus increasing mortality rates. Such experiments have shown that species evolve as predicted by theory. We have also found that evolution by natural selection can be remarkably fast, on the order of four to seven orders of magnitude faster than had been inferred from the fossil record.
Proper citation: Guppy Project (RRID:SCR_006255) Copy
An open-source natural language processing system for information extraction from electronic medical record clinical free-text. This is a system through which one creates one or more pipelines to process clinical notes and to identify clinical named entities. It processes clinical notes, identifying types of clinical named entities, drugs, diseases/disorders, signs/symptoms, anatomical sites and procedures. Each named entity that is found is given attributes for the text span, the ontology mapping code, the context (family history of, current, unrelated to patient), and negated/not negated. cTAKES is built on the UIMA framework. cTAKES 2.5 does not provide a GUI of its own for installation or processing. The cTAKES documentation shows how to use the GUIs provided by the UIMA framework, and how to run cTAKES from a command line. Before using cTAKES you need to know that cTAKES does not provide any mechanisms of its own to handle patient data securely. It is assumed that cTAKES is installed on a system that can process patient data, or that any data being processed by cTAKES has already been through a deidentification step in order to comply with any applicable laws. The tool has been developed and deployed at Mayo Clinic since early 2000.
Proper citation: cTAKES (RRID:SCR_006379) Copy
A publicly accessible database containing data on Affymetrix DNA microarray experiments, and Serial Analysis of Gene Expression, mostly on human and mouse stem cell samples and their derivatives to facilitate the discovery of gene functions relevant to stem cell control and differentiation. It has grown in both size and scope into a system with analysis tools that examine either the whole database at once, or slices of data, based on tissue type, cell type or gene of interest. There is currently more than 210 stem cell samples in 60 different experiments, with more being added regularly. The samples were originated by researchers of the Stem Cell Network and processed at the Core Facility of Stemcore Laboratories under the management of Ms. Pearl Campbell in the frame of the Stem Cell Genomics Project. Periodically, new expression data is submitted to the Gene Expression Omnibus (GEO) repository at the National Center for Biotechnological Information, in order to allow researchers to compare the data deposited in StemBase to a large amount of gene expression data sets. StemBase is different from GEO in both focus and scope. StemBase is concerned exclusively with stem cell related data. we are focused in Stem Cell research. We have made a significant effort to ensure the quality and consistency of the data included. This allows us to offer more specialized analysis tools related to Stem Cell data. GEO is intended as a large scale public archive. Deposition in a public repository such as GEO is required by most important scientific journals and it is advantageous for a further diffusion of the data since GEO is more broadly used than StemBase.
Proper citation: StemBase (RRID:SCR_006252) Copy
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