Curator Dashboard

Database of raw data from people who have shared their direct-to-customer (DTC) genetic results from 23andMe, deCODEme or FamilyTreeDNA. Logged-In users can search the database for users with specific phenotypes and mass-download all corresponding SNP-datasets. This allows you to get datasets like All genotyping files of openSNP-users that have Alzheimer and the corresponding control group. They are currently working on providing API-access. You can also use JSON to get access to openSNP-data and some other ways: If you want to automate the file-downloads for a given phenotype the RSS-feeds could help you. Inside the RSS-XML there are 2 flags you could use to automatically create correct genotype-groups: gives you the variation of this user at the phenotype you are looking at and gives you the download link. If you were genotyped by 23andMe, deCODEme or FamilyTreeDNA (contact them regarding others) you can upload the raw genotype data which you can download from your DTC test provider. The data will then be openly available for the world to see and download. They also parse these SNPs and annotate them. For annotation they include the manually curated SNPedia and find Open Access primary publications which appear in the journals of The Public Library of Science (PLoS), an Open Access publishing group. Additionally they screen Mendeley, a crowd-sourced repository of scientific publications. You can also publish some of your phenotypes so some day it might get possible to associate some SNPs with phenotypes. You can also share your knowledge about SNPs and phenotypes with other users and can socialize.

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• SciCrunch
• 14 years ago - by Anonymous

A portal for dataset discovery across a heterogeneous, distributed group of transcriptomics, genomics, proteomics and metabolomics data resources. These resources span eight repositories in three continents and six organisations, including both open and controlled access data resources.

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• SciCrunch
• 10 years ago - submitted by Yueling Li

Software R package contains data and functions that define and allow translation between different chromosome sequence naming conventions, including function that attempts to place sequence names in their natural, rather than lexicographic order.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

VHL is a library, a decentralized and dynamic information-source collection, designed to provide equitable access to scientific knowledge on health. This collection operates as an Internet network of products and services, structured to progressively meet the need for information on health on the part of authorities, administrators, researchers, professors, students, professionals, the media and the general public. It sets itself apart from other information sources available on the Internet due to its selection criteria and quality control. The Virtual Health Library is envisioned as the broad of scientific and technical knowledge based in health-entered, organized, and stored in electronic format in the countries of the Region, universally accessible on the Internet and compatible with international databases. The VHL is a common space shared by information users, producers and intermediaries. It is based on the information paradigm set by the Internet, where users may interact with networks of information sources and with other users. The most important consequence of this paradigm is the convergence of functions and activities of production, intermediation and use of information sources. It will also be possible to enrich, schedule, reformulate, and/or translate the basic information sources into new information products and services, with value added, in order to meet more efficiently the information needs of users from specific communities. BIREME has established a plan of action to implement the Virtual Health Library based on 5 lines of action: promotion and marketing; realignment of traditional products and services; production of electronic publications; development of tools for integrating and locating information; and development of other Virtual Health Library components. Sponsors: VHL is supported by the Latin-American and Caribbean Center on Health Sciences Information.

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• SciCrunch
• 17 years ago - by Anonymous

Software tool for extendable network visualization and analysis for the life sciences. It is Java-based and allows users to create, edit and map data onto existing or new networks. Experimental datasets can be visualized on network elements as graphical charts to show time series data or data of different treatments, as well as environmental conditions in the context of the underlying biological processes. Users can utilize built-in statistical algorithms to evaluate mapped data.

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• SciCrunch
• 17 years ago - by Anonymous

Software R package as interface to the graph algorithms contained in the BOOST library.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package to apply the QL, QLShrink and QLSpline methods to quasi-Poisson or quasi-negative binomial models for identifying differentially expressed genes in RNA-seq data.

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• SciCrunch
• 13 years ago - by Anonymous

Database of information of spa-typing of MRSA, or Staphylococcus aureus, that can be used to collate and harmonize data from various geographic regions.

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• SciCrunch
• 17 years ago - by Anonymous

Software R package provides multivariate tools to analyze comparative data. Analysis of comparative evolutionary data. Used for investigating phylogenetic signal in biological traits.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

User-contributed list of biological databases available on the internet. Currently there are 1,801 entries, each describing a different database. The databases are described in a semi-structured way by using templates and entries can carry various user comments and annotations. Entries can be searched, listed or browsed by category. The site uses the same MediaWiki technology that powers Wikipedia, The Mediawiki system allows users to participate on many different levels, ranging from authors and editors to curators and designers. MetaBase aims to be a flexible, user-driven (user-created) resource for the biological database community. The main focuses of MetaBase are: * As a basic requirement, MB contains a list of databases, URLs and descriptions of the most commonly used biological databases currently available on the internet. * The system should be flexible, allowing users to contribute, update and maintain the data in different ways. * In the future we aim to generate more communication between the database developer and user communities.

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• SciCrunch
• 17 years ago - by Anonymous

Animal imaging and analysis lab that provides imaging and analytical services for SBP investigators. The facility can perform in vivo non-invasive luminescence and fluorescence imaging for xenograft tumor growth and metastasis studies. Analytical equipment supports complete blood cell counts (CBC) and analysis of serum components revealing metabolic or organ stress from small samples of mouse blood.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Software R package to compute optimal cutpoints for diagnostic tests or continuous markers.Used for selecting optimal cutoffs, analysis and diagnostic test accuracy measures.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

A place where people connected to cancer can share real-life experiences -- fears, insights, stories, and advice. Adding perspectives is easy, and every contribution builds the site into a more valuable and unique community resource. Content, resources, and support on wikiCancer: * Just been diagnosed with cancer? * Living with cancer * For cancer survivors * How to support someone with cancer * Connect with other cancer patients, survivors, family and caregivers

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• SciCrunch
• 16 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on 11132025. Facility that provides database development and management and bioinformatic network building services by utilizing on-site hardware and software. Three members of the facility are available to assist researchers with advanced bioinformatics and biostatistics analysis to help put data into biological context across various disease areas to create testable hypotheses and understand biology of the process. The bulk of support includes connecting functional genomic data with pathways and networks, connecting gene/protein expression and disease state and consultations on statistical aspects of the research with the team statistician.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Software R package for aggregating ranked lists, especially lists of genes. RRA method uses a probabilistic model for aggregation that is robust to noise and also facilitates the calculation of significance probabilities for all the elements in the final ranking.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Curated public database for autism research built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The genetic information includes data from linkage and association studies, cytogenetic abnormalities, and specific mutations associated with ASD. New gene submissions are welcome. Modules: * Human Gene: thoroughly annotated list of genes that have been studied in the context of autism, with information on the genes themselves, relevant references from the literature, and the nature of the evidence. Uniquely, SFARI Gene incorporates information on both common and rare variants. * Animal Model: information about lines of genetically modified mice that represent potential models of autism. This information includes the nature of the targeting construct, the background strain and, most importantly, a thorough summary of the phenotypic features of the mice that are most relevant to autism. * Protein Interaction (PIN): compilation of all known direct protein interactions for those gene products implicated in autism. It presents both graphical and tabular views of interactomes, highlighting connections between autism candidate genes. Each protein interaction is manually verified by consultation with the primary reference. * Copy Number Variant (CNV): a parallel resource providing genetic information about all known copy number variants linked to autism. * Gene Scoring: includes a "score" for each autism candidate gene, based on an assessment of the strength of human genetic evidence.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. A database for the study of protein inter-atomic distance distribution. Currently, the distances are extracted from the protein structures determined through X-ray Crystallography, but they could also be obtained from NMR structural models. The known structures with the resolution higher than 2A and less than 70% sequence similarities are selected. Each type of distances is specified in terms of the types of the atoms it involves, the types of the residues containing the atoms, and the types of the residues in between the two end residues in sequence. An automated system is built to generate and process the data dynamically. The system consists of two levels of databases. The first one stores the sequence and structure information for a large set of high-resolution protein structures, with a similar data structure as the structural data represented in the PDB Data Bank. The second one stores the information for the distance distributions, with each record corresponding to a distribution function. The second database is built dynamically from the first one. The database can provide structural information in terms of distance distributions to structural biologists. Such information can be valuable for the study of many fundamental biological problems including protein structure prediction and determination, protein dynamics simulation, molecular design, protein structural analysis and classification, etc.

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• SciCrunch
• 17 years ago - by Anonymous

Software package as Nanopore read de-multiplexer.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Public datasets that have been transcoded into multiple formats. This library of valid file format conversions (DICOM->NIFTI, DICOM->PAR/REC, etc.) will provide a reference for tool developers seeking to support multiple sources of data.

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• SciCrunch
• 14 years ago - by Anonymous

WikiHealth is a collaborative online health and wellness community where your participation makes a difference! WikiHealth''s goal is to offer the most comprehensive, current and insightful information to help anyone and everyone achieve optimal health. Our belief is that your knowledge matters--- and you can help others by sharing what you know. WikiHealth is a collaborative writing project aiming to build an extensive and valueable repository on a variety of health and wellness topics. Our mission is to bring free, accesible and thorough information on health and wellness into the homes of every individual worldwide. The goal is for new articles on any health and wellness topic to be added regularly and for existing articles to be improved by volunteer contributors. In time, we envision WikiHealth to be the best health resource to come to for unbiased information as well as prescriptive advice on any health or wellness topic. Please join us by writing a new article or editing an existing one.

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• SciCrunch
• 16 years ago - by Anonymous