Curator Dashboard

Software application for modelling extended haplotypes in genetic association studies, similar to the FASTPHASE program. (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

An expanding multi-omics resource that enables rapid browsing of gene and protein expression information from publicly available studies on humans and model organisms. MOPED also serves the greater research community by enabling users to visualize their own expression data, compare it with existing studies, and share it with others via private accounts. MOPED uniquely provides gene and protein level expression data, meta-analysis capabilities and quantitative data from standardized analysis utilizing SPIRE (Systematic Protein Investigative Research Environment). Data can be queried for specific genes and proteins; browsed based on organism, tissue, localization and condition; and sorted by false discovery rate and expression. MOPED links to various gene, protein, and pathway databases, including GeneCards, Entrez, UniProt, KEGG and Reactome. The current version of MOPED (MOPED 2.5) The current version of MOPED (MOPED 2.5, 2014) contains approximately 5 million total records including ~260 experiments and ~390 conditions.

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• SciCrunch
• 15 years ago - by Anonymous

MMMDB, Mouse Multiple tissue Metabolome DataBase, is a freely available metabolomic database containing a collection of metabolites measured from multiple tissues from single mice. The datases are collected using a single instrument and not integrated from literatures, which is useful for capturing the holistic overview of large metabolomic pathway. Currently data from cerabra, cerebella, thymus, spleen, lung, liver, kidney, heart, pancreas, testis, and plasma are provided. Non-targeted analyses were performed by capillary electropherograms time-of-flight mass spectrometry (CE-TOFMS) and, therefore, both identified metabolites and unknown (without matched standard) peaks were uploaded to this database. Not only quantified concentration but also processed raw data such as electropherogram, mass spectrometry, and annotation (such as isotope and fragment) are provided.

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• SciCrunch
• 15 years ago - by Anonymous

2D mouse brain atlas of high quality coronal Nissl- and myelin-stained sections with labels, 3D images of hippocampal formation and limited other brain structures. The data for this digital atlas are based on the Atlas of the Mouse Brain and Spinal Cord, authored by Richard L. Sidman, Jay. B. Angevine and Elizabeth Taber Pierce, published as a hard cover book by Harvard University Press in 1971 and currently out of print. C57BL/6J strain adult specimens were used in creating the atlas.

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• SciCrunch
• 17 years ago - by Anonymous

The Foundation for Polish Science (FNP), formed in 1991, is an independent, self-financing, non-profit, non-governmental organization, with a mission of supporting science in Poland. It is the largest source of science funding in Poland outside the state budget. The main objectives of FNP are: * to support excellent scientists and research teams, * to facilitate technology transfer, * to support various investment initiatives serving science in Poland. The Foundation realizes these objectives by: * awarding individual prizes and scholarships to scientists, * awarding grants for the modernization of scientific facilities and the protection of scientific collections, * grants for the transfer of scientific achievements to industry, * otherwise supporting important undertakings in the service of science (e.g. through conferences and publishing programs). The Foundation also plays an increasingly active role in supporting international scientific cooperation, taking actions to facilitate the exchange of scientific ideas, and increasing the scientific independence of the younger generation of scientists.

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• SciCrunch
• 15 years ago - by Anonymous

Comprehensive lists of plant and animal species, with a rarity rank and legal status for each. It has has over 635,000 geo-located records of species occurrences and over 40,000 records of extremely rare to uncommon species in the Atlantic region, including New Brunswick, Nova Scotia, Prince Edward Island, Newfoundland, and Labrador. The Atlantic CDC also maintains biological and other types of data in a variety of linked databases. The CDC welcomes inquiries from those who would like to contribute data about plant or animal species at risk or rare communities in Atlantic Canada. Its mission is to assemble and provide objective and understandable data and expertise about species and ecological communities of conservation concern, including those at risk, and undertake field biological inventories to support decision-making, research, and education in Atlantic Canada. The Atlantic CDC develops species location data, known as element occurrence records. Occurrence precision (accuracy) ranges from quite precise (within meters) to less precise (within counties) but most commonly it is within 1 5 km. Element occurrence (EO) refers to one or more locations considered important to the continued existence of a species or ecological community. For species, over 30 types of data: taxonomy, biology, etc. are typically examined when identifying EOs. An EO is generally the habitat occupied by a local population. However, occurrence varies among species and some species have more than one type of occurrence (e.g., breeding and winter occurrences). Breeding colonies, breeding ponds, denning sites, and hibernacula are general examples of different types of animal EOs. For an ecological community, an EO may be the area containing a patch of that community type.

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• SciCrunch
• 14 years ago - by Anonymous

mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data. quantitative real-time PCR-based gene expression profiles are stored in a universal and expandable database scheme and wrapped by an intuitive user-friendly interface. A new way of accessing gene expression data in mirEX includes a simple mouse operated querying system and dynamic graphs for data mining analyses. In contrast to other publicly available databases, the mirEX interface allows a simultaneous comparison of expression levels between various microRNA genes in diverse organs and developmental stages. Currently, mirEX integrates information about the expression profile of 190 Arabidopsis thaliana pri-miRNAs in seven different developmental stages: seeds, seedlings and various organs of mature plants. Additionally, by providing RNA structural models, publicly available deep sequencing results, experimental procedure details and careful selection of auxiliary data in the form of web links, mirEX can function as a one-stop solution for Arabidopsis microRNA information. This database aims to be useful to anyone investigating the role of microRNAs in shaping plant development, organ formation and response to different biotic and abiotic stresses. To start exploring the database just press the "Browse Atlas" button or search for a particular microRNA record by typing at least two numbers from its ID in the window.

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• SciCrunch
• 15 years ago - by Anonymous

NeuroGems is a collection of neuroinformatics software modules for data and modelling in neuroscience. The emphasis is on tools for collaboration, visualisation and use of open XML standards. The project was an escience pilot project funded by the UK MRC and BBSRC and based at the Universities of Edinburgh, Newcastle and UCL running from 2002 - 2005. Software Applications available: Textensor, Axiope, NeuroML, neuroConstruct, NClamp, RatBrain, 3D Atlas, Catacomb, Protsim1, Protsim2, Neosim1, Neosim2, Growth, Marching, Voxel, Patterns.

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• SciCrunch
• 17 years ago - by Anonymous

This is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins. The nearly completed sets of MIPs have been identified from the completed genome sequence of organisms available at NCBI. The structural models of MIP proteins were created by defined protocol. The database aims to provide key information of MIPs in particular based on sequence as well as structures. This will further help to decipher the function of uncharacterized MIPs. For each MIP entry, this database contains information about the source, gene structure, sequence features, substitutions in the conserved NPA motifs, structural model, the residues forming the selectivity filter and channel radius profile. For selected set of MIPs, it is possible to derive structure-based sequence alignment and evolutionary relationship. Sequences and structures of selected MIPs can be downloaded from MIPModDB database.

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• SciCrunch
• 15 years ago - by Anonymous

Software based on evolutionary conservation of expression profiles, implemented in R, for identification of poor quality arrays in dataset composed of arrays from many independent experiments.

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• SciCrunch
• 13 years ago - by Anonymous

The Genome Foundation (AKA Genome Research Foundation) is a fully government accredited and registered non-profit research foundation. GRF aims to provide genome philosophy, science, and technology. GRF is a nonprofit publisher, and research and advocacy organization to promote completely free publication of knowledge with minimum restriction. Our core objectives are to: * Provide ways to overcome unnecessary barriers to immediate availability, access, and use of research * Pursue a publishing strategy that optimizes the openness, quality, and integrity of the publication process * Develop innovative approaches to the assessment, organization, and reuse of ideas and data Genome Foundation Research * Personalized Medicine * Personal Genomics * AngioGenesis drug * Bioinformatics * RNA expression * Protein structure * Human Genome Rights Projects at Genome Foundation * The Human Genome Rights * Human Genome Rights Petition * Free Personal Genome Sequencing Project * Free Personal Genome Sequencing Petition * Tiger Genome Initiative: Amur Tiger and big cat genomes * Whale Genome Project

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• SciCrunch
• 15 years ago - by Anonymous

Ontology of clinical terms Version 3 (CTV3) (Read Codes) (Q199): National Health Service National Coding and Classification Centre

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• SciCrunch
• 13 years ago - by Anonymous

InterEvol database is designed for the analysis of co-evolution events at the interface of known structures of hetero- and homo-oligomers. The database can be search and analyzed through 3 interconnected levels of analysis: * From a Keyword or the PDB entry of a complex, you can browse: ** structural homologs for every chain in other complexes ** structural interologs for every interface ** retrieve pre-computed sequence alignments in diverse species * From 1 or 2 sequences of interacting partners: ** build 2 multiple sequence alignments with the same species ordered in each ** query the InterEvol database with alignments using profile-profile comparison method * Visualize structure vs sequence alignment at the complex interface ** A dedicated Pymol plugin is provided ** Alignment views in Pymol are interactively restricted to the residues selected at the interface

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• SciCrunch
• 15 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on Sep 18, 2018. Open-source, web and programmatically accessible microarray data management system. caArray guides the annotation and exchange of array data using a federated model of local installations whose results are shareable across the cancer Biomedical Informatics Grid (caBIG). caArray furthers translational cancer research through acquisition, dissemination and aggregation of semantically interoperable array data to support subsequent analysis by tools and services on and off the Grid. As array technology advances and matures, caArray will extend its logical library of assay management.

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• SciCrunch
• 15 years ago - by Anonymous

A campus of the University of Massachusetts system, located in Pioneer Valley of Western Massachusetts.

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• SciCrunch
• 16 years ago - submitted by Andrea Stagg

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.

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• SciCrunch
• 15 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Indel Flanking Region Database is an online resource for indels and the flanking regions of proteins in SCOP superfamilies, including amino acid sequences, lengths, locations, secondary structure constitutions, hydrophilicity / hydrophobicity, domain information, 3D structures and so on. It aims at providing a comprehensive dataset for analyzing the qualities of amino acid insertion/deletions(indels), substitutions and the relationship between them. The indels were obtained through the pairwise alignment of homologous structures in SCOP superfamilies. The IndelFR database contains 2,925,017 indels with flanking regions extracted from 373,402 structural alignment pairs of 12,573 non-redundant domains from 1053 superfamilies. IndelFR has already been used for molecular evolution studies and may help to promote future functional studies of indels and their flanking regions.

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• SciCrunch
• 15 years ago - by Anonymous

An on-line assessment tool for cognitive strengths and weaknesses compared to the normal standards as found in the Brain Resource database. Available to clinicians and employers. The assessment takes approximately 30 minutes and the completed report is then provided within minutes to the individual''s clinician, providing detailed analysis of cognitive strengths and weaknesses., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 14 years ago - by Anonymous

IGDB.NSCLC database is aiming to facilitate and prioritize identified lung cancer genes and microRNAs for pathological and mechanistic studies of lung tumorigenesis and for developing new strategies for clinical interventions. We integrated and curated various lung cancer genomic datasets to present # lung cancer genes with somatic mutations, experimental supports and statistic significance in association with clinicopathological features; # genomic alterations with copy number alterations (CNA) detected by high density SNP arrays, gain or loss regions detected by arrayed comparative genome hybridization (aCGH), and loss of heterozygosity (LOH) detected by microsatellite markers; # aberrant expression of genes and microRNAs detected by various microarrays. IGDB.NSCLC database provides user friendly interfaces and searching functions to display multiple layers of evidence for detecting lung cancer target genes and microRNAs, especially emphasizing on concordant alterations: # genes with altered expression located in the CNA regions; # microRNAs with altered expression located in the CNA regions; # somatic mutation genes located in the CNA regions; and # genes associated with clinicopathological features located in the CNA regions. These concordant altered genes and miRNAs should be prioritized for further basic and clinical studies.

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• SciCrunch
• 15 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 3rd,2023. Secondary prevention of ischemic heart disease in primary care, a randomized controlled intervention study. The study aims to elucidate if an early, active, group-oriented intervention at the primary care level can decrease the probability of developing a new cardiovascular event within three years, when compared to primary care according to standard protocols. The study also aims at analyzing how the intervention affects parameters as physical activity, eating habits, quality of life, blood pressure, waist measure, and smoking habits. Furthermore, changes in biochemical markers related to glucose- and lipid metabolism, stress related hormone production and sub clinic inflammatory activity as well as the presence of DNA polymorphism in the IL-6- and adiponutrin (ADPN) genes, will be investigated. Types of samples * EDTA whole blood * DNA Number of sample donors: 102 (sample collection completed)

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• SciCrunch
• 15 years ago - by Anonymous