Tools   Select Another Resource Report Type

http://www.ebi.ac.uk/IPI

IPI provides a top level guide to the main databases (UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, RefSeq, Ensembl, TAIR, H-InvDB, Vega) that describe the proteomes of higher eukaryotic organisms. IPI: :1. effectively maintains a database of cross references between the primary data sources :2. provides minimally redundant yet maximally complete sets of proteins for featured species (one sequence per transcript) :3. maintains stable identifiers (with incremental versioning) to allow the tracking of sequences in IPI between IPI releases. IPI is updated monthly in accordance with the latest data released by the primary data sources. As previously announced, the closure of IPI has been proposed for some time. Replacement data sets are now available through UniProt for human and mouse; sets for the other species contained within IPI are expected to be included as part of the UniProt release 2011_07. To allow users time to transition to using the new UniProt data sets, IPI releases will continue to be produced throughout the summer. The final release will be made in September 2011. Thereafter, the IPI website will cease to be maintained, although previous releases of the dataset will continue to be available from the FTP site. We would like to thank our users for their support and interest in this service.

Proper citation: IPI (RRID:SCR_003012) Copy   

•   Source: SciCrunch Registry

https://tudelftroboticsinstitute.nl

Unites all Delft University of Technology research in the field of robotics. Its main challenge is to get robots and humans to work together effectively in unstructured environments, and real settings. Institute takes a leading role in the creation of the next generation robots.

Proper citation: Delft University of Technology Robotics Institute (RRID:SCR_025112) Copy   

•   Source: SciCrunch Registry

http://neuroinformatics.usc.edu/

The USC Brain Project is engaged in the effort to develop new tools and methodologies for neuroinformatics in modeling neural mechanisms of visuomotor coordination and exploring the evolution of the human language-ready brain, as well as conducting work in both neural modeling and database construction in relation to rehabilitation after stroke. Sponsors: USCBP is funded by the University of Southern California.

Proper citation: University of Southern California Brain Project (RRID:SCR_008044) Copy   

•   Source: SciCrunch Registry

http://www.nihclinicalcollection.com

A plated array of approximately 450 small molecules that have a history of use in human clinical trials. The collection was assembled by the National Institutes of Health (NIH) through the Molecular Libraries Roadmap Initiative as part of its mission to enable the use of compound screens in biomedical research. Similar collections of FDA approved drugs have proven to be rich sources of undiscovered bioactivity and therapeutic potential. The clinically tested compounds in the NCC are highly drug-like with known safety profiles. These compounds can provide excellent starting points for medicinal chemistry optimization and, for high-affinity targets, may even be appropriate for direct human use in new disease areas.

Proper citation: NIH Clinical Collection (RRID:SCR_007349) Copy   

•   Source: SciCrunch Registry

https://www.iigm.it/site/index.php?l=ENG

Private research institute in Turin, Italy. Research programs in immunogenetics, functional genomics, genomic epidemiology, tumour diagnostic and prognostic biomarker research, epigenetic modifications in disease, quantitative biology and computational neuroscience.

Proper citation: Italian Institute for Genomic Medicine; Turin; Italy (RRID:SCR_017062) Copy   

•   Source: SciCrunch Registry

http://sagebase.org/

Non-profit biomedical research organization developing predictors of disease and accelerating health research through creation of open systems, incentives, and standards. Formed to coordinate and link academic and commercial biomedical researchers through Commons that represents new paradigm for genomics intellectual property, researcher cooperation, and contributor evolved resources.

Proper citation: Sage Bionetworks (RRID:SCR_003384) Copy   

•   Source: SciCrunch Registry

http://www.simulations-plus.com/Products.aspx?pID=13

Software program for advanced predictive modeling of Absorption, Distribution, Metabolism, Elimination, and Toxicity (ADMET) properties of chemical substances in the human body. ADMET Predictor can estimate a number of vital ADMET properties (listed below) from molecular structures and build predictive models of new properties from user's data.

Proper citation: ADMET Predictor (RRID:SCR_014903) Copy   

•   Source: SciCrunch Registry

http://www.alttox.org/

A website dedicated to advancing non-animal methods of toxicity testing, both to better protect the health of humans, animals, and the environment and to reduce the numbers and suffering of animals used in current toxicology assessments. The website is designed to encourage the exchange of technical and policy information on in vitro and in silico methods for all types of toxicity tests. The AltTox Forum is a message board for the AltTox community to use for posting news, information, and perspectives as well as encouraging feedback and commentary. This online community is intended to foster progress internationally in the development, validation, and acceptance of in vitro methods, with the goal of decreasing our reliance on animal-based safety testing. The Forum is moderated by a group of internationally-recognized subject matter experts. The Way Forward invited commentaries, which are posted in the TTRC, are opinion pieces written by experts in each relevant subfield. These essays are meant to help chart the course for future developments by advancing opportunities to overcome challenges and barriers to progress. Stakeholders are invited to comment on these essays in The AltTox Forum. AltTox users are encouraged to contribute to the website and interact with other users in several ways, including: :- Participating in the online forum :- Providing invited expert commentaries :- Suggesting or submitting content, events, monthly features, data, and graphics :- Providing feedback through the Website Feedback surve To encourage objectivity, the website content is overseen by an editorial board of distinguished subject matter experts.

Proper citation: AltTox: Non-animal Methods for Toxicity Testing (RRID:SCR_007212) Copy   

•   Source: SciCrunch Registry

https://sparc.science

SPARC data repository as of 2023 is an open data repository developed as part of the NIH SPARC initiative and has been used by SPARC funded investigator groups to curate and publish high quality datasets related to the autonomic nervous system. We are thrilled that as of August 2022, SPARC is accepting datasets from investigators that are not funded through the NIH SPARC program. The NIH's Common Fund Stimulating Peripheral Activity to Relieve Conditions (SPARC) program aims to transform our understanding of these nerve-organ interactions and ultimately advance neuromodulation field toward precise treatment of diseases and conditions for which conventional therapies fall short.

Proper citation: SPARC Portal (RRID:SCR_017041) Copy   

•   Source: SciCrunch Registry

https://hnn.brown.edu/

Open source software package for circuit level interpretation of human EEG/MEG data. Software tool for interpreting cellular and network origin of human MEG/EEG data. Simulates electrical activity of neocortical cells and circuits that generate primary electrical currents underlying EEG/MEG recordings. Designed for researchers and clinicians, without computational neural modeling experience, to develop and test hypothesis on circuit origin of their data.

Proper citation: Human Neocortical Neurosolver (RRID:SCR_017437) Copy   

•   Source: SciCrunch Registry

http://brainvis.wustl.edu/wiki/index.php/Caret:Atlases

THIS RESOURCE IS NO LONGER IS SERVICE. Documented on July,29,2022. Surface-based atlases of human, macaque, rat and mouse cerebral and cerebellar cortices derived from structural MRI volumes developed in the Van Essen laboratory can be downloaded by direct links on the SumsDB database and can be viewed using freely available Caret (offline) and WebCaret (online) software. The human and macaque atlases include a large and growing compendium of experimental data pertaining to the structural and functional organization of primate cerebral cortex.

Proper citation: Surface-Based Atlases (RRID:SCR_002099) Copy   

•   Source: SciCrunch Registry

http://bioinf.scri.sari.ac.uk/cgi-bin/atnopdb/home

Database of proteins found in the nucleoli of Arabidopsis, identified through proteomic analysis. The Arabidopsis Nucleolar Protein database (AtNoPDB) provides information on the plant proteins in comparison to human and yeast proteins, and images of cellular localizations for over a third of the proteins. A proteomic analysis was carried out of nucleoli purified from Arabidopsis cell cultures and to date 217 proteins have been identified. Many proteins were known nucleolar proteins or proteins involved in ribosome biogenesis. Some proteins, such as spliceosomal and snRNP proteins, and translation factors, were unexpected. In addition, proteins of unknown function which were either plant-specific or conserved between human and plant, and proteins with differential localizations were identified.

Proper citation: Arabidopsis Nucleolar Protein Database (RRID:SCR_001793) Copy   

•   Source: SciCrunch Registry

http://neurosynth.org

Platform for large-scale, automated synthesis of functional magnetic resonance imaging (fMRI) data extracted from published articles. It''s a website wrapped around a set of open-source Python and JavaScript packages. Neurosynth lets you run crude but useful analyses of fMRI data on a very large scale. You can: * Interactively visualize the results of over 3,000 term-based meta-analyses * Select specific locations in the human brain and view associated terms * Browse through the nearly 10,000 studies in the database Their ultimate goal is to enable dynamic real-time analysis, so that you''ll be able to select foci, tables, or entire studies for analysis and run a full-blown meta-analysis without leaving your browser. You''ll also be able to do things like upload entirely new images and obtain probabilistic estimates of the cognitive states most likely to be associated with the image.

Proper citation: NeuroSynth (RRID:SCR_006798) Copy   

•   Source: SciCrunch Registry

https://www.4dnucleome.org

Research project to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development and diseases. Portal provides free access to datasets, software packages, and protocols to advance biomedical research of nuclear architecture. Aims to develop and apply approaches to map the structure and dynamics of the human and mouse genomes.

Proper citation: 4D Nucleome (RRID:SCR_016925) Copy   

•   Source: SciCrunch Registry

http://www.proteometools.org/index.php?id=home

Project for building molecular and digital tools from human proteome to facilitate biomedical research, drug discovery, personalized medicine and life science research.

Proper citation: ProteomeTools (RRID:SCR_018535) Copy   

•   Source: SciCrunch Registry

https://physiomeproject.org/

The Physiome Project is a worldwide public domain effort to provide a computational framework for understanding human and other eukaryotic physiology. It aims to develop integrative models at all levels of biological organization, from genes to the whole organism via gene regulatory networks, protein pathways, integrative cell function, and tissue and whole organ structure/function relations. Additionally, an important goal of the project is to develop applications for teaching physiology. Current projects include the development of: - ontologies to organize biological knowledge and access to databases - markup languages to encode models of biological structure and function in a standard format for sharing between different application programs and for re-use as components of more comprehensive models - databases of structure at the cell, tissue and organ levels - software to render computational models of cell function such as ion channel electrophysiology, cell signaling and metabolic pathways, transport, motility, the cell cycle, etc. in 2 & 3D graphical form - software for displaying and interacting with the organ models which will allow the user to move across all spatial scales Sponsors: This project is supported by the International Union of Physiological Sciences (IUPS), the IEEE Engineering. in Medicine and Biology (EMBS), and the International Federation for Medical and Biological Engineering (IFMBE)

Proper citation: International Union of Physiological Sciences: Physiome Project (RRID:SCR_001760) Copy   

•   Source: SciCrunch Registry

http://www.emory.edu/LIVING_LINKS/

The primary mission of the Living Links Center is to study human evolution by investigating our close genetic, anatomical, cognitive, and behavioral similarities with great apes. The Living Links Center was established for primate studies that shed light on human behavioral evolution. It is an integrated part of the Yerkes National Primate Research Center, which is the nation's oldest and largest primate center. The Living Links Center is home to two socially housed groups of chimpanzees and two socially housed groups of capuchin monkeys. The research conducted in this center is broken down into four categories: - Chimpanzees: Chimpanzee research at the Living Links Center is conducted at the Yerkes Field Station, which is home to two socially housed chimpanzee groups known as FS1 and FS2. Each mixed gender group of 12 individuals lives in a large outdoor enclosure with wooden climbing structures and play objects attached to an indoor sleeping area. FS1 and FS2 can hear, but not see each other because their enclosures are ~200m apart and separated by a small hill. Chimpanzee research is conducted on a volunteer basis with members of each group. - Elephants: This newly found presence of mirror self-recognition in elephants, previously predicted due to their well-known social complexity, is thought to relate to empathetic tendencies and the ability to distinguish oneself from others. As a result of this study, the elephant now joins a cognitive elite among animals commensurate with its well-known complex social life and high level of intelligence. Although elephants are far more distantly related to us than the great apes, they seem to have evolved similar social and cognitive capacities making complex social systems and intelligence part of this picture. These parallels between humans and elephants suggest a convergent cognitive evolution possibly related to complex sociality and cooperation. - Capuchin Monkeys: Though there are several different species of capuchin monkey, the one most widely studied in captivity by Living Links, is the brown, or tufted, capuchin (Cebus apella). - Collaborative Projects: projects with collaborators around the world. Sponsors: This center is supported by the Yerkes National Primate Research Center.

Proper citation: Living Links: Center for the Advanced Study of Ape and Human Evolution (RRID:SCR_001776) Copy   

•   Source: SciCrunch Registry

http://sccn.ucsd.edu/

Computational neuroscience center that observes and models how functional activities in multiple brain areas interact dynamically to support human cognition, creativity and social interaction. Center research involves development computational methods and software, experimental methods and equipment, collection and analysis of human cognitive experiments, and collaborations to analyze data collected by other groups in such experiments. The Center has a 72-channel EEG recording system customized for use in the fMRI environment, and a very-high density Biosemi Active Two active-electrode EEG system, rapidly configurable either as a 256-channel system for a single subject or as two 136-channel systems for recording from two subjects simultaneously. In addition, UCSD now has a 306-channel MEG plus 128-channel EEG system (Neuromag/Elektra). Projects in the Center include studies of human cognitive processes including attention and memory, role of the anterior/posterior cingulate, time perception and emotional expression. Data acquisition includes high-density EEG, concurrent EEG and fMRI recording and analysis, and face video processing. Current analysis approaches include independent component and time-frequency analysis.

Proper citation: Swartz Center for Computational Neuroscience (RRID:SCR_001933) Copy   

•   Source: SciCrunch Registry

http://hugenavigator.net/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023. Knowledge base of genetic associations and human genome epidemiology including information on population prevalence of genetic variants, gene-disease associations, gene-gene and gene- environment interactions, and evaluation of genetic tests. This tool explores HuGENet, the Human Genome Epidemiology Network, which is a global collaboration of individuals and organizations committed to the assessment of the impact of human genome variation on population health and how genetic information can be used to improve health and prevent disease. What does HuGE Navigator offer? *HuGEpedia - an encyclopedia of human genetic variation in health and disease, includes, Phenopedia and Genopedia. Phenopedia allows you to look up gene-disease association summaries by disease, and Genopedia allows you to look up gene-disease association summaries by gene. In general, HuGEpedia is a searchable database that summarizes published articles about human disease and genetic variation, including primary studies, reviews, and meta-analyses. It provides links to Pubmed abstracts, researcher contact info, trends, and more. *HuGEtools - searching and mining the literature in human genome epidemiology, includes, HuGE Literature Finder, HuGE Investigator Browser, Gene Prospector, HuGE Watch, Variant Name Mapper, and HuGE Risk Translator. *HuGE Literature Finder finds published articles in human genome epidemiology since 2001. The search query can include genes, disease, outcome, environmental factors, author, etc. Results can be filtered by these categories. It is also possible to see all articles in the database for a particular topic, such as genotype prevalence, pharmacogenomics, or clinical trial. *HuGE Investigator Browser finds investigators in a particular field of human genome epidemiology. This info is obtained using a behind-the-scenes tool that automatically parses PubMed affiliation data. *Gene Prospector is a gateway for evaluating genes in relation to disease and risk factors. This tool allows you to enter a disease or risk factor and then supplies you with a table of genes associated w/your query that are ranked based on strength of evidence from the literature. This evidence is culled from the HuGE Literature Finder and NCBI Entrez Gene - And you're given the scoring formula. The Gene Prospector results table provides access to the Genopedia entry for each gene in the list, general info including links to other resources, SNP info, and associated literature from HuGE, PubMed, GWAS, and more. It is a great place to locate a lot of info about your disease/gene of interest very quickly. *HuGE Watch tracks the evolution of published literature, HuGE investigators, genes studied, or diseases studied in human genome epidemiology. For example, if you search Trend/Pattern for Diseases Studied you'll initially get a graph and chart of the number of diseases studied per year since 1997. You can refine these results by limiting the temporal trend to a category or study type such as Gene-gene Interaction or HuGE Review. *Variant Name Mapper maps common names and rs numbers of genetic variants using information from SNP500Cancer, SNPedia, pharmGKB, ALFRED, AlzGene, PDGene, SZgene, HuGE Navigator, LSDBs, and user submissions. *HuGE Risk Translator calculates the predictive value of genetic markers for disease risk. To do so, users must enter the frequency of risk variant, the population disease risk, and the odds ratio between the gene and disease. This information is necessary in order to yield a useful predictive result. *HuGEmix - a series of HuGE related informatics utilities and projects, includes, GAPscreener, HuGE Track, Open Source. GAPscreener is a screening tool for published literature on human genetic associations; HuGE Track is a custom track built for HuGE data in the UCSC Genome Browser; and Open Source is infrastructure for managing knowledge and information from PubMed.

Proper citation: HuGE Navigator - Human Genome Epidemiology Navigator (RRID:SCR_003172) Copy   

•   Source: SciCrunch Registry

http://www.cnbc.cmu.edu/ibsc/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 07, 2013. A framework for understanding human cognition, grounded in principles specifying the character of human cognitive processes, and constrained by properties, of the underlying neural mechanisms. The Center will exploit this framework to guide formulation of explicit, testable models of normal and disordered cognition, including models of the development of cognitive functions and of their disintegration as a result of brain damage or disease. This site is intended as a public service and as a focal point for exchange of ideas among the participants in the Interdisciplinary Behavioral Science Center (IBSC). Public areas of the site provide information about the Center as a whole and about the various projects in the Center, as well as web-accessible documents and tools that we are making available as a public service. A fundamental tenet is that cognition is an emergent phenomenon, arising from the interactions of cooperating processing elements organized into specialized populations. One aim of the center will be to investigate the utility of explicit models that are formulated in terms of this approach, addressing many aspects of cognition including semantic knowledge, language processing, cognitive control, perception, learning and memory. A second aim will also investigate the principles that are embodied in the models, including principles of learning, processing and representation. Learning will be a central focus, since it plays a crucial role in cognitive development, acquisition of skills, formation of memories, and remediation of cognitive functions. A third aim of the Center will be to incorporate constraints from neuroscience. Findings from neuroscience will guide the specification of the principles and the formulation of domain-specific details of particular models, and will provide target experimental observations against which to assess the adequacy of the models. In addition, the Center will make use of neurophysiological methods in animals and functional brain imaging in humans to test predictions and generate additional data needed to constrain and inform model development. The Center will provide training funds for interdisciplinary research fellowships, to train junior scientists in the convergent use of behavioral, computational, and neuroscience methodologies. The outcome of the Centers efforts will be a fuller characterization of the nature of human cognitive processes, a clearer formulation of the underlying principles, and a more complete understanding of normal and disordered functions across many domains of cognition. This Center includes eight projects dedicated to various aspects of cognition and various general issues that arise in the effort to build explicit models that capture different aspects of cognition, and also includes an administrative core to help foster integration and provide computing resources. * Project 1: Functional and Neural Organization of Semantic Memory * Project 2: Interactive Processes in Language: Lexical Processing * Project 3: Interactive Processes in Language: Sentence Processing * Project 4: Mechanisms of Cognitive Control * Project 5: Interactive Processes in Perception: Neurophysiology of Figure-Ground Organization * Project 6: Basic Mechanisms and Cooperating Systems in Learning Memory * Project 7: Age and Experience Dependent Processes in Learning * Project 8: Theoretical Foundations * Core: Integration, Computational Resources, and Administration

Proper citation: NIMH Interdisciplinary Behavioral Science Center (RRID:SCR_008085) Copy   

•   Source: SciCrunch Registry