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http://www.dbfordummies.com/

Db for Dummies! (DBD) is a flexible, lightweight, memory-resident database. DBD manages any conceivable data structure including lists, tables, multi-rooted hierarchies, graphs and complex networks. Unlike traditional databases, DBD stores data as a network of nodes. DBD has four interfaces to manage data: * The Graphical User Interface (GUI) allows users to manage data mainly via a tree and grid. * The Natural Language Interface (NLI) allows users to mangage data via English-like expressions. * The Remote User Interface (RUI) allows users to manage data via a remote computer. * The Application Programmer Interface (API) allows programmers to manage data via a Dynamic Link Library (DLL). DBD is useful for applications where: # Data structure is complex and highly varied (non-uniform). # Data structure changes frequently. # Data structure is unknown in advance. # Minimum impact on existing code and data is desirable in adapting to new requirements. These characteristics may make DBD useful for Artificial Intelligence applications.

Proper citation: Db for Dummies! (RRID:SCR_005727) Copy   

•   Source: SciCrunch Registry
  

http://search.cpan.org/~cmungall/go-db-perl/

Software resource that extends the functionality of go-perl (on which it depends) with GO Database access functionality. go-db-perl comes bundled with various scripts and a shell command line interface that can be used as standalone tools. Installation is more involved than for go-perl; you will need a MySQL database plus the requisite DBI and DBD Perl modules. Full installation instructions are included in the download. go-db-perl is in use both to drive AmiGO and internally within Ensembl. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: go-db-perl (RRID:SCR_005721) Copy   

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http://www.bioinf.uni-freiburg.de/Software/GraphProt/

Software for modeling binding preferences of RNA-binding proteins from high-throughput experiments such as CLIP-seq and RNAcompete.

Proper citation: GraphProt (RRID:SCR_005842) Copy   

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https://medicine.yale.edu/lab/rimm/research/software/

Software tool for biomarker assessment and outcome based cut point optimization.

Proper citation: X-Tile (RRID:SCR_005602) Copy   

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http://brain-development.org/

brain-development.org hosts data and resources used in computational analysis of brain development, including MRI data sets of developing human, software tools, atlases, protocols and software. Several different atlas datasets are available including: * Adult * Pediatric * Neonatal (T2 Templates, Probability Maps) * Neonatal (High-definition, T1 and T2 Templates, Probability Maps) * Fetal (High-definition, T2 Templates, Probability Maps) * Atlas software Anatomical segmentation protocols are available, as well as an Image Registration Toolkit.

Proper citation: brain-development.org (RRID:SCR_005838) Copy   

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http://brain-development.org/ixi-dataset/

Data set of nearly 600 MR images from normal, healthy subjects, along with demographic characteristics, collected as part of the Information eXtraction from Images (IXI) project available for download. Tar files containing T1, T2, PD, MRA and DTI (15 directions) scans from these subjects are available. The data has been collected at three different hospitals in London: * Hammersmith Hospital using a Philips 3T system * Guy''s Hospital using a Philips 1.5T system * Institute of Psychiatry using a GE 1.5T system

Proper citation: IXI dataset (RRID:SCR_005839) Copy   

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http://code.google.com/p/pido/

The Primary Immunodeficiency Disease Ontology Project is developing an ontology for the phenotypic description of Primary Immunodeficiency Diseases. The ontology can be used for integrative research in both biomedical and clinical research. Primary Immunodeficiency Diseases (PIDs) are Mendelian diseases, caused by defects or deletions of genes involved in the development, regulation and maintenance of the immune system. They usually affect newborns and toddlers, but can also manifest much later in life. Information about PIDs is often widely scattered across the research literature and a number of databases. PIDO is an attempt to develop both a machine- as well as a human-comprehensible representation of these diseases, starting with a phenotypic descriptions of disease.

Proper citation: PIDO - Primary Immunodeficiency Disease Ontology (RRID:SCR_005834) Copy   

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http://www.biotec.tu-dresden.de/

The Biotechnology Center (BIOTEC) of the Technische Universit��t Dresden is a unique interdisciplinary center focusing on research and teaching in molecular bio-engineering. The BIOTEC hosts top international research groups working on genomics, proteomics, biophysics, cellular machines, molecular genetics, tissue engineering, and bioinformatics. The Biotechnology Center (BIOTEC) was founded in 2000 as a central scientific unit of the Technische Universit��t Dresden. The center is an essential part of implementing the Biotechnology-Offensive of the Free State of Saxony within the TU Dresden. The main goal in establishing and developing this center was to link the revolutionary change within molecular and cell biology to Dresden''s traditionally strong background in engineering. Dresden''s aspired innovation advantages as a location for developing state-of-the-art biotechnology are already visible in some parts. The BIOTEC plays a central role in the Molecular Bioengineering and Regenerative Medicine profile of the TU Dresden, fostering developments in the new field of Biotechnology/Biomedicine. Establishing and developing a strong and internationally competitive research center molecular bioengineering required a powerful nucleus. The BIOTEC started with five professorships and one junior research group recruited within the Biotechnology-Offensive of the Free State of Saxony. Through the interdisciplinary work of these researchers from different fields and faculties, the development of the center was catalyzed, and the main goal of building an internationally competitive research structure is now well underway. Today, the BIOTEC houses six professorships and seven junior research groups. Their work has given rise not only to novel discoveries in modern life sciences, but the translation of these finding into economically useful innovations. The BIOTEC is located within the BioInnovation Center in Dresden, which has provided an atmosphere essential for its development. In accordance with its motto Science and Economy under one roof, the BioInnovation Center offers a unique opportunity for knowledge and technology transfer between the research center and start-ups working on biotechnology and related fields of cutting-edge technology. The BIOTEC has about 230 members from over 35 countries, including Eastern and Western Europe, Asia, Australia, and the Americas. These researchers have diverse backgrounds, covering biology, medicine, physics, chemistry, computer science, and engineering. The BIOTEC offers excellent lab facilities and infrastructure, as well as close links to companies residing in the same building.

Proper citation: Biotechnology Center of the TU Dresden (RRID:SCR_005715) Copy   

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http://www.antoniahamilton.com/amat.html

AMAT is a Matlab-based, open source interface for searching fMRI coordinates together with a simple database of coordinates. The AMAT database is deliberately designed to be minimal. Effectively, the database reproduces the tables of XYZ coordinates which are common in fMRI papers. Each coordinate is associated with the anatomical label given by the authors of the original paper, a ag for Talaraich or MNI coordinates, a very brief description of the description of the functional task or contrast which activated this coordinate, and the PubMed ID of the published paper. The latter links directly to the abstract in PubMed and allows the user to retrieve the original publication. Anatomical information labeling a coordinate as a particular Brodmann area or functional region is optional, and is normally only included if the authors of the original paper included these labels. No other information is stored.

Proper citation: AMAT (RRID:SCR_005836) Copy   

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http://medschool.umaryland.edu/

Medical school of the University of Maryland, Baltimore and is affiliated with the University of Maryland Medical Center and Medical System. Located in Baltimore City, Maryland, U.S.

Proper citation: University of Maryland School of Medicine; Maryland; USA (RRID:SCR_005837) Copy   

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http://hadvwg.gmu.edu/

The Human Adenovirus Type Classification coordinates the naming of candidate new types, prior to manuscript submission for peer review. This resource contains a method of submitting candidate HAdV, criteria for a new HAdV type, and a Serotyping tool, which displays all potential types corresponding to the query serotype entered by a user. The criteria are based on discussions at the International Adenovirus Meeting (Dobog��k, Hungary; 26-30 April, 2009) and the NIH Human Adenovirus Working Group Workshop (Bethesda, MD. USA; 3 February 2011), which are summarized in a Letter to the Editor.

Proper citation: Human Adenovirus Type Classification (RRID:SCR_005753) Copy   

•   Source: SciCrunch Registry
  

http://www.crystallography.net/

Database of crystal structures of organic, inorganic, metal-organic compounds and minerals, excluding biopolymers. It currently contains ~291204 entries (July 2014) in crystallographic information file format, with nearly full coverage of the International Union of Crystallography publications, and is growing in size and quality. Deposit your data: An interface allows you to upload, validate and edit CIF files before submitting them for deposition.

Proper citation: Crystallography Open Database (COD) (RRID:SCR_005874) Copy   

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http://www.clipz.unibas.ch/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 20,2019.Database and analysis environment for experimentally determined binding sites of RNA-binding proteins. It supports the automatic functional annotation of short reads resulting primarily from crosslinking and immunoprecipitation experiments (CLIP) performed with RNA-binding proteins in order to identify the binding sites of these proteins. The functional annotation could be also applied to short reads resulting from other types of experiments such as mRNA-Seq, Digital Gene Expression, small RNA cloning, etc. The platform enables visualization and mining of individual data sets as well as analysis involving multiple experimental data sets. The platform can support collaborative projects involving multiple users and groups of users as well as public and private datasets.

Proper citation: CLIPZ (RRID:SCR_005755) Copy   

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http://www.icpsr.umich.edu/icpsrweb/NACDA/

Archive of data relevant to gerontological and aging research. Used to advance research on aging. Subjects include demographic, social, economic, and psychological characteristics of older adults, physical health and functioning of older adults, and health care needs of older adults. NACDA staff represents team of professional researchers, archivists and technicians who work together to obtain, process, distribute, and promote data relevant to aging research.

Proper citation: National Archive of Computerized Data on Aging (NACDA) (RRID:SCR_005876) Copy   

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http://www.antibodiesinc.com/index.html

An Antibody supplier

Proper citation: Antibodies Incorporated (RRID:SCR_005877) Copy   

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http://en.opasnet.org

Opasnet is a wiki-based website and workspace for helping societal decision making. The website collects, synthesizes, and distributes people''s values and scientific information. Opasnet welcomes anyone who wants to promote science-based decision-making in any field. The specialty is that the information is structured for both scientific scrutiny and for policy use at the same time. In practice, you can do original research, store data, make models, and perform policy assessments and discuss all of that work in one workspace. Originally, the developers of Opasnet came from the environmental health, i.e. a research field that studies the impacts of environment on human health. We are actively working, among other things, on climate change and air pollution, but you can also start a new assessment about a decision of your own interest, or participate in an existing assessment. Opasnet is a website that has basically two parts. One part is a wiki site (called Opasnet wiki or simply Opasnet) that has descriptive pages with text, figures, and tables; it also contains files. The other part is a database called Opasnet Base that contains quantitative estimates about anything that is described in Opasnet. The majority of information is openly available. However, both Opasnet wiki and Opasnet Base have a protected area for working with material that is non-public for some reason.

Proper citation: Opasnet (RRID:SCR_005751) Copy   

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http://www.terryfox.org/

The Terry Fox Foundation is responsible for supporting close to $20 million in discovery based research each year in Canada - all monies raised outside Canada must be distributed to (a) an institute approved by the Foundation and its advisors or (b) remitted to Canada. The Terry Fox Research Institute (TFRI) is a recipient of TFF funding for translational research. TFRI is an exciting new initiative whose goal is to translate rapidly today''s best science into better cancer treatment and diagnosis for all Canadians. The Institute will bring scientists and clinicians together across the country into a functionally integrated, geographically dispersed Institute with nodes in several provinces. Terry Fox was diagnosed with osteogenic sarcoma (bone cancer) in his right leg in 1977 and had his leg amputated 15 cm (six inches) above the knee. While in hospital, Terry was so overcome by the suffering of other cancer patients that he decided to run across Canada to raise money for cancer research. He called his journey the Marathon of Hope. Terry''s Marathon of Hope took place in 1980 with the simple objective of informing Canadians of the importance of finding a cure for cancer. With fierce determination, he ran an average of 42 kilometres (26 miles) every day for 143 days. Terry was forced to end his run on September 1, 1980 when the cancer spread to his lungs. By February 1, 1981, Terry''s dream of raising $1 for every Canadian was realized - the Terry Fox Marathon of Hope fund totaled $24.17 million. Terry died in June 1981. On May 26, 1988, The Terry Fox Run became a Trust, independent from the Canadian Cancer Society, and received tax-exempt charitable registration as a public foundation. In addition to our signature and long-standing National Terry Fox Run Day in September of each year, The Terry Fox Foundation is proud to include in its events portfolio The National School Run Day. The Foundation recognizes the duality of its mandate. Not only does it raise money for research, but it also continues to share the story of Terry Fox. The Terry Fox Foundation strives to maintain the heroic effort and integrity that Terry embodied. It is a grassroots organization that does not allow the Terry Fox name or likeness to be commercialized or conjoined with other worthy causes. To date, over $600 million has been raised worldwide for cancer research in Terry''s name.

Proper citation: Terry Fox Foundation (RRID:SCR_005873) Copy   

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http://www.sanger.ac.uk/resources/software/lookseq/

A web-based application for alignment visualization, browsing and analysis of genome sequence data.

Proper citation: LookSeq (RRID:SCR_005625) Copy   

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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   

•   Source: SciCrunch Registry