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http://www.opencalais.com/

Service and open API to tag the people, places, facts and events in your content. You hand the Web Service unstructured text (like news articles, blog postings, your term paper, etc.) and it returns semantic metadata in RDF format. Using natural language processing and machine learning techniques, the Calais Web Service examines your text and locates the entities, facts, and events. Calais then processes the entities, facts and events extracted from the text and returns them to the caller in RDF format. * Calais Tagaroo: If you are on WordPress, this plug-in automatically tags content as you type. It can also fetch images from Flickr and videos from Google Video. * Calais Marmoset: To manipulate your search results appearance in Google and Yahoo!, which is simple javacode you embed in your site pages. It will collect the metadata from your page (in the form of RDFa) and hand it over to Google Rich Snippets> and Yahoo! Search Monkey so that you can customize the way your search results appear. * Semantic Proxy: If you want to extract metadata from Web pages using URLs * Calais Collection: For the open source platform Drupal, you can find a complete Calais Collection of modules for easy integration. * OpenPublish: for building a new site from the ground up, this free Content Management System is based on Drupal. OpenPublish bakes-in OpenCalais from the ground up to semantify your site and automate the creation of ''related reading'' widgets, ''topic hubs'' and more.

Proper citation: OpenCalais (RRID:SCR_005906) Copy   

•   Source: SciCrunch Registry

https://trac.nbic.nl/passion/

A pattern growth algorithm based pileline for splice site detection in paired-end RNA-Seq data.

Proper citation: PASSion (RRID:SCR_005867) Copy   

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http://www.hvidovrehospital.dk/

Proper citation: Hvidovre Hospital; Hvidovre; Denmark (RRID:SCR_005747) Copy   

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http://europepmc.org/

Free access to biomedical literature resources including all of PubMed and PubMed Central, agricultural abstracts (from AGRICOLA), over 4 million international life science patents abstracts, National Health Service (NHS) clinical guidelines, and is supplemented with Chinese Biological Abstracts and the Citeseer database. As well as powerful search of abstracts and full text articles, it also includes: * article citations and sort order based on citation count * data citations mined from full text articles * links to and from related databases and institutional repositories * a tool to create bibliographies linked to your ORCID * named entity recognition of keywords and text-mining-based applications showcased in Europe PMC Labs * Tools for recipients of grants from one of the Europe PMC funders to deposit full-text manuscripts and link them to those specific grants. * Web services for programmatic access to all the above bibliographic information and 50,000 grants. * Search by publication date, relevance, or the number of times an article has been cited. * Links to public databases such as UniProt, Protein Data Bank (PDBe), and the European Nucleotide Archive (ENA) are provided. * Through textmining technologies, you can highlight and browse keywords such as gene names, organisms and diseases. * Search 40,000 biomedical research grants awarded to the 18,000 PIs supported by the Europe PMC funders. * Roadtest new tools based on Europe PMC content in Europe PMC labs. * In Europe PMC plus, PIs supported by the Europe PMC funders can link grants to publication information, view article citation and download statistics, and submit manuscripts.

Proper citation: Europe PubMed Central (RRID:SCR_005901) Copy   

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http://www.mgc.ac.cn/TrED/

TrED is a database of Trichophyton rubrum, a fungus. The database contains strains, cDNA libraries, pathways, and microarray data as well as a directed set of literature. Trichophyton rubrum is the most common dermatophyte species and the most frequent cause of fungal skin infections in humans worldwide. It''''s a major concern because feet and nail infections caused by this organism is extremely difficult to cure. A large set of expression data including expressed sequence tags (ESTs) and transcriptional profiles of this important fungal pathogen are now available. Careful analysis of these data can give valuable information about potential virulence factors, antigens and novel metabolic pathways. We intend to create an integrated database TrED to facilitate the study of dermatophytes, and enhance the development of effective diagnostic and treatment strategies. All publicly available ESTs and expression profiles of T. rubrum during conidial germination in time-course experiments and challenged with antifungal agents are deposited in the database. In addition, comparative genomics hybridization results of 22 dermatophytic fungi strains from three genera, Trichophyton, Microsporum and Epidermophyton, are also included. ESTs are clustered and assembled to elongate the sequence length and abate redundancy. TrED provides functional analysis based on GenBank, Pfam, and KOG databases, along with KEGG pathway and GO vocabulary. It is integrated with a suite of custom web-based tools that facilitate querying and retrieving various EST properties, visualization and comparison of transcriptional profiles, and sequence-similarity searching by BLAST. TrED is built upon a relational database, with a web interface offering analytic functions, to provide integrated access to various expression data of T. rubrum and comparative results of dermatophytes. It is devoted to be a comprehensive resource and platform to assist functional genomic studies in dermatophytes.

Proper citation: TrED (RRID:SCR_005869) Copy   

•   Source: SciCrunch Registry

http://www.pensoft.net/index.php

Publisher that specializes in academic and professional book and journal publishing, mostly in the field of biodiversity science and natural history. They are academic publishers based in Eastern Europe with more than 600 books and e-books published so far. They largely perform their activities in English, with only a minor fraction of publications being in French, German, Russian and Bulgarian. Pensoft is also involved as a publisher in several European Union Fp5, FP6 and FP7 projects where they have specialized in dissemination, communication and publishing; as well as in creating and maintaining websites and Internal Communication Platforms (ICP), designing of logos, flyers, leaflets and posters. Open-access journals include ZooKeys, BioRisk, and PhytoKeys. ZooKeys is a journal in biodiversity science and has implemented several innovations in digital publishing and dissemination including developing and implementing an XML-based submission, editorial, publication and dissemination workflow. The TRIADA platform, for publishing, disseminating and marketing of printed books, e-books and open access journals, provides a linked environment for content, authors, reviewers, editors and customers through four independent classifications (taxonomic, subject, geographical, and geological time scale) as well through tagging and semantic mark-up. TRIADA uses a one-time registration process which allows users to submit, review or edit manuscripts, to subscribe for E-mail and RSS alerts, and to purchase Pensoft''s products. Web services: Metadata and journal content can be harvested.

Proper citation: Pensoft (RRID:SCR_005903) Copy   

•   Source: SciCrunch Registry

http://www-math.u-strasbg.fr/genpred/spip.php?article3

R software package to study, predict and simulate the diffusion of a signal through a temporal gene network. It predicts changes in gene expressions after a biological perturbation in the network and provides graphical outputs that allow monitoring the spread of a signal through the network., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Cascade (RRID:SCR_005861) Copy   

•   Source: SciCrunch Registry

http://www.zmmsoft.com

ZMM is a molecular modeling program for theoretical studies of systems of any complexity: small molecules, peptides, proteins, nucleic acids, and ligand-receptor complexes. ZMM searches optimal structures in the space of generalized coordinates: torsion angles, bond angles, bond lengths, positions free molecules and ions, and orientation of free molecules. Any generalized coordinate may be kept fixed. Molecules and fragments that are not expected to undergo significant conformational changes may be treated as rigid bodies. Popular molecular modeling programs usually work in the space of Cartesian coordinates of atoms. During energy minimization of a big system, many Cartesian coordinates-variables move collectively. For example, rotation of a benzene ring around the C-Ph bond in the Cartesian-coordinates space involves collective motion of 33 variables. In the generalized-coordinates space, this rotation involves variation of just one torsion angle. In ZMM, any fragment of a molecular system may be treated as either rigid or flexible. The generalized-coordinates method saves large computational resources if only a small part of a system is considered flexible. Examples are ligand-protein and protein-protein interactions. The savings occur because the sampling space is reduced and because molecular interactions within rigid fragments are not computed. * ZMM runs on Windows 95, 98, 2000, XP, UNIX, and Linux * ZMM can be used via the command-line interface * ZMM can also be used at Windows via a graphical user interface

Proper citation: ZMM (RRID:SCR_005741) Copy   

•   Source: SciCrunch Registry

http://www.sociopatterns.org/

SocioPatterns is an interdisciplinary research collaboration that adopts data-driven methodology with the aim of uncovering fundamental patterns in social dynamics and coordinated human activity. To achieve its scientific goals, the SocioPatterns collaboration also contributes to the development of new technologies for collecting relevant data. In particular, the collaboration supports the development of the SocioPatterns sensing platform, which uses wireless wearable sensors to gather longitudinal data on human mobility and face-to-face proximity in real-world environments. The SocioPatterns team also works on developing tools and techniques to represent, analyze and visualize the collected data. We increasingly use digital media and computational devices in our daily activities, and leave behind a sizable amount of digital traces while doing so. The proliferation of mobile devices, and the incorporation of various sensing technologies in these devices, will further add to this growing trail of data. The possibility to mine and analyze these data, and the scale at which this can be done on contemporary computer systems, affords a novel, data-driven approach in the investigation of various aspects of human behavior. The following collection of datasets obtained through the SocioPatterns sensing platform are available: * Infectious SocioPatterns dynamic contact networks * Hypertext 2009 dynamic contact network * Primary school cumulative networks * Infectious SocioPatterns

Proper citation: SocioPatterns (RRID:SCR_005739) Copy   

•   Source: SciCrunch Registry

http://www.psb.ugent.be/cbd/papers/BiNGO/Home.html

The Biological Networks Gene Ontology tool (BiNGO) is an open-source Java tool to determine which Gene Ontology (GO) terms are significantly overrepresented in a set of genes. BiNGO can be used either on a list of genes, pasted as text, or interactively on subgraphs of biological networks visualized in Cytoscape. BiNGO maps the predominant functional themes of the tested gene set on the GO hierarchy, and takes advantage of Cytoscape''''s versatile visualization environment to produce an intuitive and customizable visual representation of the results. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: BiNGO: A Biological Networks Gene Ontology tool (RRID:SCR_005736) Copy   

•   Source: SciCrunch Registry

http://www.moe.gov.sg/

Ministry of the Government of Singapore that directs the formulation and implementation of policies related to Education in Singapore.

Proper citation: Ministry of Education - Singapore (RRID:SCR_011252) Copy   

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http://www.ema.europa.eu/

An agency responsible for the evaluation and supervision of medicines developed by pharmaceutical companies for use in the European Union. Its main responsibility is the protection and promotion of public and animal health through the evaluation and supervision of medicines for human and veterinary use. The Agency also plays a role in stimulating innovation and research in the pharmaceutical sector. The Agency gives scientific advice and other assistance to companies for the development of new medicines. It publishes guidelines on quality-, safety- and efficacy-testing requirements. A dedicated SME Office provides special assistance to small and medium-sized enterprises.

Proper citation: European Medicines Agency (RRID:SCR_011215) Copy   

•   Source: SciCrunch Registry

http://dg.dk/en/

Established by the Danish Parliament, this independent foundation, aims at strengthening Danish basic research (frontier research) within the natural sciences, the technical sciences, the health sciences, the social sciences, and the humanities. The Foundation''s primary strategy is to set up and fund Centres of Excellence and has committed itself to support the Danish research environments. The funding goes to university research groups in Denmark active in basic science. A total of 77 Centers of Excellence have been established, and a new generation of centers will be up and running by 1 January 2012. Normally these centers receive funding for ten years. It is important to mention the Niels Bohr Visiting Professorship programme in this context. This initiative is designed to further the internationalization of the Danish research establishments by attracting foreign top-level researchers to Denmark for longer periods of time. There is a new call for proposals in 2011 and the Foundation is going to fund six to eight new professorships.

Proper citation: Danish National Research Foundation (RRID:SCR_011183) Copy   

•   Source: SciCrunch Registry

http://www.ufrgs.br/english/home

Brazilian federal university based in Porto Alegre, Rio Grande do Sul. UFRGS is among the largest and highest-rated universities in Brazil, having one of the largest number of scientific publications.

Proper citation: Federal University of Rio Grande do Sul; Rio Grande do Sul; Brazil (RRID:SCR_011222) Copy   

•   Source: SciCrunch Registry

http://www.florey.edu.au/

One of the world''s top 10 brain research centres. Their scientists comprise the largest neuroscience research team in Australia.

Proper citation: Florey Institute of Neuroscience and Mental Health; Victoria; Australia (RRID:SCR_011224) Copy   

•   Source: SciCrunch Registry

http://www.fic.nih.gov/

The Fogarty International Center is dedicated to advancing the mission of the National Institutes of Health by supporting and facilitating global health research conducted by U.S. and international investigators, building partnerships between health research institutions in the U.S. and abroad, and training the next generation of scientists to address global health needs. Fogarty International Center''s programs provide funding to perform research and to train researcher in a variety of global health topics. Through these extensive programs, Fogarty and its partners throughout the National Institutes of Health (NIH) are working to build sustainable research capacity in low- and middle-income countries. Current Programs Research and Research Training Programs * Biodiversity (ICBG) * Bioethics * Brain Disorders * Chronic Diseases: Chronic, Non-communicable Diseases and Disorders Across the Lifespan (NCD-Lifespan); Millennium Promise Awards: Non-communicable Chronic Diseases Research Training (NCoD); Clinical, Operational and Health Services (ICOHRTA) * Ecology and Evolution of Infectious Diseases (EEID) * Environmental and Occupational Health (ITREOH) * Framework * Framework Innovations * Framework Signature Innovations * Global Environmental and Occupational Health (GEOHealth) * Global Infectious Diseases (GID) * HIV: Fogarty HIV Research Training; AIDS International Training and Research (AITRP); Clinical, Operational and Health Services AIDS/TB (IICOHRTA-AIDS/TB) * Informatics (ITGH) * Medical Education Partnership Initiative (MEPI) * New Foreign Investigators (GRIP) * Research Collaboration (FIRCA) * Tobacco * Trauma and Injury * Womens and Girls Health Administrative Grant Supplements Career Development Opportunities for Individuals * Fellows and Scholars Programs: Global Health Fellows and Scholars; Scholars and Fellows (FICRS-F) * Fulbright-Fogarty Fellowships in Public Health * Independent Scientist in Global Health (ISGHA) * Japanese Researcher Fellowships (JSPS) * Junior Research Scientists (IRSDA) Other Programs * American Reinvestment and Recovery Act (ARRA) * Genetics * Population * Stigma

Proper citation: Fogarty International Center (RRID:SCR_011229) Copy   

•   Source: SciCrunch Registry

http://www.ecu.edu/

East Carolina University continues to supply the nation with some of its best educators, and now it has been joined by programs of high distinction in health care and the fine and performing arts. The university is no longer a small school but an engine of economic development and a hotbed of discovery. Today, East Carolina is a constituent institution of the University of North Carolina and offers 104 bachelor''s degree programs, 74 master''s degree programs, 4 specialist degree programs, 1 first-professional MD program, and 17 doctoral programs in our professional colleges and schools, Thomas Harriot College of Arts and Sciences, and the Brody School of Medicine. With a mission of teaching, research, and service, East Carolina University is a dynamic institution connecting people and ideas, finding solutions to problems, and seeking the challenges of the future.

Proper citation: East Carolina University; Carolina; USA (RRID:SCR_011199) Copy   

•   Source: SciCrunch Registry

http://www.augusta.edu/

Augusta State University and Georgia Health Sciences University have consolidated to become Augusta University.

Proper citation: Augusta University; Georgia; USA (RRID:SCR_011233) Copy   

•   Source: SciCrunch Registry

http://www.gsu.edu/

Public research university in downtown Atlanta, Georgia, United States. Founded in 1913. One of the University System of Georgia's four research universities.

Proper citation: Georgia State University; Georgia; USA (RRID:SCR_011234) Copy   

•   Source: SciCrunch Registry

http://www.univ-lyon1.fr/

Public university in Villeurbanne, France.

Proper citation: Claude Bernard University Lyon 1; Lyon; France (RRID:SCR_011158) Copy   

•   Source: SciCrunch Registry