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http://www.tdt.com/

Commercial organization that provides products for basic and applied research in the neurophysiology, hearing, and speech sciences as well as for general data acquisition applications. It offers a complete line of modular DSP-based data acquisition and stimulus generation systems, ranging in complexity from a simple audio stimulator to a complete multichannel sensory and behavioral neurophysiology system for awake, behaving subjects.

Proper citation: Tucker-Davis Technologies (RRID:SCR_006495) Copy   

•   Source: SciCrunch Registry

http://www.nbic.nl/about-nbic/affiliated-organisations/cwa/introduction/

CWA is an open collaborative community that is actively addressing the challenges associated with the production of unprecedented volumes of academic and professional data. This international effort seeks to organize the massive amounts of information flooding the biological sciences and other scientific disciplines. Challenges include storage, interoperability and analysis of such massive and disparate data sets. CWA''s agreed approach is a ''Semantic Web'' strategy, meaning that disparate data on the internet are now structurally connected to each other. As the amount of scholarly communication increases, it is increasingly difficult for specific core scientific statements to be found, connected and curated. Additionally, the redundancy of these statements in multiple fora makes it difficult to determine attribution, quality, and provenance. To tackle these challenges, the Concept Web Alliance has promoted the notion of nanopublications (core scientific statements with associated context) in a manner allowing for meaningful Web-wide interconnectivity. The notion of a ''nanopublication'' is basically a general scientific assertion, written using semantic-web standard formats with additional meta-data concerning provenance.

Proper citation: Concept Web Alliance (RRID:SCR_006490) Copy   

•   Source: SciCrunch Registry

http://www.rarechromo.org/html/home.asp

Unique is a source of information and support to families and individuals affected by any rare chromosome disorder and to the professionals who work with them. Unique is a UK-based charity but welcomes members worldwide. Unique''''s Karyotype Database allows users to search the Registered Chromosome Disorders by chromosome, arm and disorder. You may have been given a diagnosis or indication of a chromosome disorder by a geneticist or other medical professional and they may have used a medical term which is unfamiliar to you. So to help you decide if Unique is the appropriate organization for you, we thought it would be useful to describe the different categories of rare chromosome disorder. Rare chromosome disorders can be grouped as structural disorders, numerical disorders and other miscellaneous disorders. Unique: * acts as an international family support group * produces a newsletter three times each year * works to promote awareness of rare chromosome disorders * arranges for families to assist in research into rare chromosome disorders * links families whose children have similar clinical and/or practical problems * works to ensure that the public at large are aware of rare chromosome disorders * works to raise funds to support the group activities and produce literature to make others more aware of our children''''s conditions * assists relevant research projects and the centralisation of information, at all times observing the need for total confidentiality * sets up local groups throughout the UK for families affected by any rare chromosome disorders and to give support and encouragement to each other * develops and maintains a comprehensive computerised database detailing the life-time effects of specific chromosome disorders on affected members * aims to hold an annual conference where families and relevant specialists can meet and be informed of the latest medical, technical and practical developments * liaises and works in co-operation, with other similar support groups and professionals world-wide for the benefit of families and individuals affected by rare chromosome disorders * ensures that hospitals, doctors, health authorities, genetic clinics and other professionals are aware of the group so that we may have early contact with families where required Membership of Unique is free but the group receives no government funding and is heavily reliant on donations and fundraising to continue its work. Please help us in whatever way you can.

Proper citation: Unique (RRID:SCR_006492) Copy   

•   Source: SciCrunch Registry

http://www.medschool.lsuhsc.edu/neuroscience/

Research center that takes multidisciplinary approach to neuroscience education and research. Research programs on molecular and cellular bases of neural diseases are the center of the innovative educational programs. Primary mission is to foster and conduct science that advances understanding of brain function and diseases that affect nervous system.

Proper citation: Louisiana State University School of Medicine Neurosciences Center (RRID:SCR_006446) Copy   

•   Source: SciCrunch Registry

http://www.informatics.jax.org/mgihome/GO/project.shtml

This resource is part of the Gene Ontology Consortium which seeks to provide controlled vocabularies for the description of the molecular function, biological process, and cellular component of gene products. These terms are to be used as attributes of gene products by collaborating databases, facilitating uniform queries across them. GO team members at MGI participate in ontology development, outreach, and functional curation of mouse gene products. The GO vocabularies have a hierarchical structure that permits a range of detail from high-level, broadly descriptive terms to very low level, highly specific terms. This broad range is useful both in annotating genes and in searching for gene information using these terms as search criteria. GO terms are defined, allowing all databases to use the terms consistently and properly. GO annotations in the databases additionally include the publication reference which allowed the association to be made and an evidence statement citing how the association was determined.

Proper citation: Mouse Genome Informatics: The Gene Ontology Project (RRID:SCR_006447) Copy   

•   Source: SciCrunch Registry

http://www.animalgenome.org/

We at NRSP-8 bioinformatics coordination program strive to serve the animal genomics research community to better use computer tools and methods, to best utilize available resources, and in working with researchers in the community, to effectively share, combine, manage, manipulate, and analyze information from genomics/genetics studies. This site is designed as an information center to serve the national animal genome research projects of cattle, chicken, pigs, sheep, horse, and aquaculture species. This is home to databases and web sites (being) built for structural, functional and application oriented studies of the animal genomics, to serve the purpose of research, education and related activities in the scientific, industrial and educational communities in the states and world wide. The challenges in bioinformatics support/research for animal genomics may involve * Effective data collection, organization and management * Rapid development of most needed bioinformatics tools and resources * Efficient use of these tools for innovative data analysis Projects: * Animal Trait Ontology (ATO) Project * Virtual Comparative Genomics * The Past, the Current, and the Potentials * Collaborative and Hosted Works

Proper citation: NAGRP Bioinformatics Coordination Program (RRID:SCR_006564) Copy   

•   Source: SciCrunch Registry

http://www.LOVD.nl/

Freely available tool for Gene-centered collection and display of DNA variations. It also provides patient-centered data storage and storage of Next Generation Sequencing (NGS) data, even of variants outside of genes. Please note that LOVD provides a system for storage of information on genes and allelic variants. To obtain information about any genes or variants, do not download the LOVD package. This information should be obtained from the respective databases, http://www.lovd.nl/2.0/index_list.php In total: 2,507,027 variants (2,208,937 unique) in 170,935 individuals in 62619 genes in 88 LOVD installations. (Aug. 2013) LOVD 3.0 shared installation, http://databases.lovd.nl/shared/genes To maintain a high quality of the data stored, LOVD connects with various resources, like HGNC, NCBI, EBI and Mutalyzer. You can download LOVD in ZIP and GZIPped TARball formats.

Proper citation: Leiden Open Variation Database (RRID:SCR_006566) Copy   

•   Source: SciCrunch Registry

http://www.prize4life.org/

Prize4Life is a 501(c)(3) nonprofit organization dedicated to accelerating the discovery of treatments and cures for ALS (amyotrophic lateral sclerosis, also known as Lou Gehrig''s disease). Our mission is to accelerate the discovery of a treatment and a cure for ALS by using powerful incentives to attract new people and new ideas and to leverage existing efforts and expertise in the ALS field. Our Values: * Patients first. Avichai Kremer, one of the Harvard Business School students who founded Prize4Life, was diagnosed with ALS in 2004. We therefore know the disease firsthand and have a sense of urgency to find a treatment. We value patients and their viewpoints. Patients, please tell us what you think. * Global awareness. We plan to push ALS to the forefront of fatal disease issues. We need your help in order to do this. Get involved. * New people and new ideas. We believe important breakthroughs in ALS may reside in the minds and laboratories of people who are not currently researching the disease. Our platform is a bridge for reaching these people. Enter the competition. * Results. Research is traditionally funded upfront, before an idea is even tested. Our prize model ensures that only clear research results, vetted by a team of scientific advisors, are rewarded. grants; funding resource;.

Proper citation: Prize4Life (RRID:SCR_006558) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/

Consortium that puts sequences into a chromosome context and provides the best possible reference assembly for human, mouse, and zebrafish via FTP. Tools to facilitate the curation of genome assemblies based on the sequence overlaps of long, high quality sequences.

Proper citation: Genome Reference Consortium (RRID:SCR_006553) Copy   

•   Source: SciCrunch Registry

http://www.asm.org/

The American Society for Microbiology is the oldest and largest single life science membership organization in the world. Membership has grown from 59 scientists in 1899 to more than 39,000 members today, with more than one third located outside the United States. The members represent 26 disciplines of microbiological specialization plus a division for microbiology educators. Eligibility for Full Membership is open to any person who is interested in microbiology and holds at least a bachelor''s degree or equivalent experience in microbiology or related field. Many members hold advanced degrees, including a large number at the master''s, PhD, ScD, DrPH and MD level. A regularly matriculated student of microbiology or a related field is eligible to become a student member. There are also separate membership categories for postdoctoral fellows and for transitional scientists in the early years of a career. Microbiologists study microbes--bacteria, viruses, rickettsiae, mycoplasma, fungi, algae and protozoa--some of which cause diseases, but many of which contribute to the balance of nature or are otherwise beneficial. Microbiological research includes infectious diseases, recombinant DNA technology, alternative methods of energy production and waste recycling, new sources of food, new drug development, and the etiology of sexually transmitted diseases, among other areas. Microbiology is also concerned with environmental problems and industrial processes. Microbiology boasts some of the most illustrious names in the annals of science--Pasteur, Koch, Fleming, Leeuwenhoek, Lister, Jenner and Salk--and some of the greatest achievements for mankind. Within the 20th century, a third of all Nobel Prizes in Physiology or Medicine have been bestowed upon microbiologists. The mission of the American Society for Microbiology is to advance the microbiological sciences as a vehicle for understanding life processes and to apply and communicate this knowledge for the improvement of health and environmental and economic well being worldwide. To achieve these goals, ASM will: * Support programs of education, training and public information; * Publish journals and books; convene meetings, workshops and colloquia; * Promote the contributions and promise of the microbiological sciences; * Recognize achievement and distinction among its practitioners; * Set standards of ethical and professional behavior.

Proper citation: American Society for Microbiology (RRID:SCR_006551) Copy   

•   Source: SciCrunch Registry

http://www.geenivaramu.ee/en/tools/gwama

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for meta analysis of whole genome association data.

Proper citation: GWAMA (RRID:SCR_006624) Copy   

•   Source: SciCrunch Registry

http://gmd.mpimp-golm.mpg.de/

It facilitates the search for and dissemination of mass spectra from biologically active metabolites quantified using Gas chromatography (GC) coupled to mass spectrometry (MS). Use the Search Page to search for a compound of your interest, using the name, mass, formula, InChI etc. as query input. Additionally, a Library Search service enables the search of user submitted mass spectra within the GMD. In parallel to the library search, a prediction of chemical sub-groups is performed. This approach has reached beta level and a publication is currently under review. Using several sub-group specific Decision Trees (DTs), mass spectra are classified with respect to the presence of the chemical moieties within the linked (unknown) compound. Prediction of functional groups (ms analysis) facilitates the search of metabolites within the GMD by means of user submitted GC-MS spectra consisting of retention index (n-alkanes, if vailable) and mass intensities ratios. In addition, a functional group prediction will help to characterize those metabolites without available reference mass spectra included in the GMD so far. Instead, the unknown metabolite is characterized by predicted presence or absence of functional groups. For power users this functionality presented here is exposed as soap based web services. Functional group prediction of compounds by means of GC-EI-MS spectra using Microsoft analysis service decision trees All currently available trained decision trees and sub-structure predictions provided by the GMD interface. Table describes the functional group, optional use of an RI system, record date of the trained decision tree, number of MSTs with proportion of MSTs linked to metabolites with the functional group present for each tree. Average and standard deviation of the 50-fold CV error, namely the ratio false over correctly sorted MSTs in the trained DT, are listed. The GMD website offers a range of mass spectral reference libraries to academic users which can be downloaded free of charge in various electronic formats. The libraries are constituted by base peak normalized consensus spectra of single analytes and contain masses in the range 70 to 600 amu, while the ubiquitous mass fragments typically generated from compounds carrying a trimethylsilyl-moiety, namely the fragments at m/z 73, 74, 75, 147, 148, and 149, were excluded.

Proper citation: GMD (RRID:SCR_006625) Copy   

•   Source: SciCrunch Registry

http://edamontology.org/

An ontology of bioinformatics operations (tool, application, or workflow functions), types of data including identifiers, topics (application domains), and data formats. The applications of EDAM are within organizing tools and data, finding suitable tools in catalogues, and integrating them into complex applications or workflows. Semantic annotations with EDAM are applicable to diverse entities such as for example Web services, databases, programmatic libraries, standalone tools and toolkits, interactive applications, data schemas, data sets, or publications within bioinformatics. Annotation with EDAM may also contribute to data provenance, and EDAM terms and synonyms can be used in text mining. EDAM - and in particular the EDAM Data sub-ontology - serves also as a markup vocabulary for bioinformatics data on the Semantic Web.

Proper citation: EDAM Ontology (RRID:SCR_006620) Copy   

•   Source: SciCrunch Registry

http://www.jisc.ac.uk/whatwedo/programmes/mrd/clip/webtracks.aspx

This project will develop an approach and mechanism to address the construction and propagation of linked data in the context of research and academic endeavour. The proposed work will build experiments in previous projects (Claddier, StoreLink) to develop a peer-to-peer protocol to underpin the construction of a web of linked data. This set of semantically annotated links between data resources forms a graph of citation and provenance and the project will build value added services to exploit these features. The project will address the following specific objectives: * To specify and implement the Intercom Protocol so that it can communicate a range of types of semantic links between resources via a secure communication mechanism. * To develop a practical working scenario involving data repositories, publication repositories, open science notebooks and publishers. * To develop aggregation techniques supporting added value services in search and impact analysis. * To evaluate of the approach with the identified stakeholders groups.

Proper citation: Webtracks (RRID:SCR_006615) Copy   

•   Source: SciCrunch Registry

https://www.tbindsc.org/

The Traumatic Brain Injury Model Systems National Data and Statistical Center (TBINDSC) located at Craig Hospital in Englewood, Colorado, is a central resource for researchers and data collectors within the Traumatic Brain Injury Model Systems (TBIMS) program. The primary purpose of the TBINDSC is to advance medical rehabilitation by increasing the rigor and efficiency of scientific efforts to longitudinally assess the experience of individuals with traumatic brain injury (TBI). The TBINDSC provides technical assistance, training, and methodological consultation to 16 TBIMS centers as they collect and analyze longitudinal data from people with TBI in their communities, and as they conduct research toward evidence-based TBI rehabilitation interventions. The project design includes * The first prospective, longitudinal multi-center study ever conducted which examines the course of recovery and outcomes following the delivery of a coordinated system of acute neurotrauma and inpatient rehabilitation. * Includes large scale follow-up to 20 years post-injury. Available from this site are links to the TBIMS Presentation and TBIMS Update, which has information about the individual model systems and descriptions of the injury and followup data that are being collected. 2007-2012 Project Priorities * Improved long-term outcomes of individuals with TBI by conducting 1-2 site-specific research projects to test innovative approaches that contribute to rehabilitation interventions and evaluating TBI outcomes in accordance with the focus areas identified in NIDRR''s Long-Range Plan. * Improved outcomes for individuals with TBI by participating in at least one collaborative research module project, which may range from pilot research to more extensive studies. * Continued assessment of long-term outcomes of TBI by enrolling at least 35 subjects per year into the longitudinal portion of the TBIMS database. * In carrying out research activities, each Center may select from the following research domains: Health and Function, Employment, Participation and Community Living, and Technology for Access and Function. In addition, each Center must: * Provide a multidisciplinary system of rehabilitation care specifically designed to meet the needs of individuals with TBI. The system must encompass a continuum of care, including emergency medical services, acute care services, acute medical rehabilitation services, and post-acute services; and * Coordinate with the NIDRR funded Model Systems Knowledge Translation Center to provide scientific results and information for dissemination to clinical and consumer audiences.

Proper citation: Traumatic Brain Injury Model Systems National Data and Statistical Center (RRID:SCR_006736) Copy   

•   Source: SciCrunch Registry

http://www.thegpm.org/

The Global Proteome Machine Organization was set up so that scientists involved in proteomics using tandem mass spectrometry could use that data to analyze proteomes. The projects supported by the GPMO have been selected to improve the quality of analysis, make the results portable and to provide a common platform for testing and validating proteomics results. The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns. This database has been integrated into GPM server pages, allowing users to quickly compare their experimental results with the best results that have been previously observed by other scientists.

Proper citation: Global Proteome Machine Database (GPM DB) (RRID:SCR_006617) Copy   

•   Source: SciCrunch Registry

http://www.nactem.ac.uk/

The first publicly-funded text mining center in the world that provides text mining services in response to the requirements of the UK academic community. You can find pointers to sources of information about text mining such as links to: * text mining services provided by NaCTeM * software tools, both those developed by the NaCTeM team and by other text mining groups * seminars, general events, conferences and workshops * tutorials and demonstrations * text mining publications NaCTeM is operated by the University of Manchester with close collaboration with the University of Tokyo.

Proper citation: National Centre for Text Mining (RRID:SCR_006738) Copy   

•   Source: SciCrunch Registry

http://www.usrds.org/

Annual report, standard analysis files and an online query system from the national data registry on the end-stage renal disease (ESRD) population in the U.S., including treatments and outcomes. The Annual Data Report is divided into two parts. The Atlas section displays data using graphs and charts. Specific chapters address trends in ESRD patient populations, quality of ESRD care, kidney transplantation outcomes, costs of ESRD care, Healthy People 2010 objectives, chronic kidney disease, pediatric ESRD, and cardiovascular disease special studies. The Reference Tables are devoted entirely to the ESRD population. The RenDER (Renal Data Extraction and Referencing) online data query system allows users to build data tables and maps for the ESRD population. National, state, and county level data are available. USRDS staff collaborates with members of Centers for Medicare & Medicaid Services (CMS), the United Network for Organ Sharing (UNOS), and the ESRD networks, sharing datasets and actively working to improve the accuracy of ESRD patient information.

Proper citation: United States Renal Data System (RRID:SCR_006699) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/casper.html

Software to infer alternative splicing from paired-end RNA-seq data. The model is based on counting paths across exons, rather than pairwise exon connections, and estimates the fragment size and start distributions non-parametrically, which improves estimation precision.

Proper citation: casper (RRID:SCR_006613) Copy   

•   Source: SciCrunch Registry

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

A set of online services created in support of MIRIAM, a set of guidelines for the annotation and curation of computational models. The core of MIRIAM Resources is a catalogue of data types (namespaces corresponding to controlled vocabularies or databases), their URIs and the corresponding physical URLs or resources. Access to this data is made available via exports (XML) and Web Services (SOAP). MIRIAM Resources are developed and maintained under the BioModels.net initiative, and are free for use by all. MIRIAM Resources are composed of four components: a database, some Web Services, a Java library and this web application. * Database: The core of the system is a MySQL database. It allows us to store the data types (which can be controlled vocabularies or databases), their URIs and the corresponding physical URLs, and other details such as documentation and resource identifier patterns. Each entry contains a diverse set of details about the data type: official name and synonyms, root URI, pattern of identifiers, documentation, etc. Moreover, each data type can be associated with several resources (or physical locations). * Web Services: Programmatic access to the data is available via Web Services (based on Apache Axis and SOAP messages). In addition, REST-based services are currently being developed. This API allows one to not only resolve model annotations, but also to generate appropriate URIs, based upon the provision of a resource name and accession number. A list of available web services, and a WSDL are provided. A browser-based online demonstration of the Web Services is also available to try. * Java Library: A Java library is provided to access the Web Services. The documentation explains where to download it, its dependencies, and how to use it. * Web Application: A Web application, using an Apache Tomcat server, offers access to the whole data set via a Web browser. It is possible to browse by data type names as well as browse by tags. A search engine is also provided.

Proper citation: MIRIAM Resources (RRID:SCR_006697) Copy   

•   Source: SciCrunch Registry