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http://www.macfound.org/

The John D. and Catherine T. MacArthur Foundation supports creative people and effective institutions committed to building a more just, verdant, and peaceful world. In addition to selecting the MacArthur Fellows, the Foundation works to defend human rights, advance global conservation and security, make cities better places, and understand how technology is affecting children and society. MacArthur is one of the nation's largest independent foundations. Through the support it provides, the Foundation fosters the development of knowledge, nurtures individual creativity, strengthens institutions, helps improve public policy, and provides information to the public, primarily through support for public interest media. The Foundation makes grants and loans through four programs. * International Programs focus on international issues, including human rights and international justice, peace and security, conservation and sustainable development, higher education in Nigeria and Russia, migration, and population and reproductive health. MacArthur grantees work in about 60 countries; the Foundation has offices in India, Mexico, Nigeria, and Russia. * U.S. Programs address issues in the United States, including community and economic development; housing, with a focus on the preservation of affordable rental housing; juvenile justice reform; education, with an emerging interest in digital media and learning; and policy research and analysis. * Media, Culture, and Special Initiatives support public interest media, including public radio, documentary programming, and work to explore the use of digital technologies to reach and engage the public. Grants are also made to arts and cultural institutions in the Chicago area and for special initiatives. * The MacArthur Fellows Program awards five-year, unrestricted fellowships to individuals across all ages and fields who show exceptional merit and promise of continued creative work. It is limited to U.S. citizens and residents. John D. MacArthur (1897-1978) developed and owned Bankers Life and Casualty Company and other businesses, as well as considerable property in Florida and New York. His wife Catherine (1909-1981) held positions in many of these companies and served as a director of the Foundation.

Proper citation: MacArthur Foundation (RRID:SCR_000612) Copy   

•   Source: SciCrunch Registry

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

An information retrieval system that provides knowledge enriched searching facilities across the ever growing MEDLINE collection, the world's most comprehensive source of life sciences and biomedical bibliographic information. The semantic faceted search, using named entity recognition, can be accessed from your browser. By combining a selection of software services they can provide enhanced results through a process that identifies key entities within the text, such as gene names or proteins, and improves the querying method with unique identifiers by automatically including synonyms, spelling variants and even disambiguating acronyms. This combines with the traditional features found in other interfaces to provide a much needed solution to the growing problem of finding valuable information within the ever increasing volume of modern publications. The current available categories: * PROTEIN, GENE, METABOLITE, DISEASE, SYMPTOM, ORGAN, * DIAG_PROC, THERAPEUTIC_PROC, (diagnostic/therapeutic procedure, e.g. MRI, cerebral blood flow) * GENERAL_PHENOM, HUMAN_PHENOM, NATURAL_PHENOM, (Medical phenomenon or process, e.g. UV radiation ) * INDICATOR (Reagent or diagnostic aid, e.g. hydrogen peroxide, sulfhydryl reagent) * ACRONYM, AUTHOR, PUBLICATIONTYPE (e.g. Journal Article, Technical Report) Reference: C. Nobata, P. Cotter, N. Okazaki, B. Rea, Y. Sasaki, Y. Tsuruoka, J. Tsujii and S. Ananiadou. Kleio: a knowledge-enriched information retrieval system for biology. In Proc. of the 31st Annual International ACM SIGIR Conference, pp. 787--788, 2008

Proper citation: KLEIO (RRID:SCR_000698) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/finesplice/

A software pipeline based on TopHat2 combined with a splice junction detection algorithm.

Proper citation: FineSplice (RRID:SCR_000691) Copy   

•   Source: SciCrunch Registry

http://niftilib.sourceforge.net/pynifti/

PyNIfTI is no longer actively developed. At has been superseded by NiBabel -- a pure-Python package that provides everything that PyNIfTI could do, and a lot more. The PyNIfTI module is a Python interface to the NIfTI I/O libraries. Using PyNIfTI, one can easily read and write NIfTI and ANALYZE images from within Python. The NiftiImage class provides pythonic access to the full header information and for a maximum of interoperability the image data is made available via NumPy arrays.

Proper citation: PyNIfTI (RRID:SCR_000693) Copy   

•   Source: SciCrunch Registry

http://services.ibc.uni-stuttgart.de/BDPC/BISMA/

An online tool for the analysis of bisulfite sequencing DNA methylation data. The software has specificity and quality control functions that allow the user to compile a set of sequences.

Proper citation: BISMA (RRID:SCR_000688) Copy   

•   Source: SciCrunch Registry

http://dbserv2.informatik.uni-leipzig.de:8080/onex/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Web-based application that integrates versions of 16 life science ontologies including the Gene Ontology, NCI Thesaurus and selected OBO ontologies with data leading back to 2002 in a common repository to explore ontology changes. It allows to study and apply the evolution of these integrated ontologies on three different levels. It provides global ontology evolution statistics and ontology-specific evolution trends for concepts and relationships and it allows the migration of annotations in case a new ontology version was released

Proper citation: OnEx - Ontology Evolution Explorer (RRID:SCR_000602) Copy   

•   Source: SciCrunch Registry

http://www.cam.ac.uk/

Public research university in Cambridge, United Kingdom. Founded in 1209 is second oldest university in English speaking world.

Proper citation: University of Cambridge; Cambridge; United Kingdom (RRID:SCR_000996) Copy   

•   Source: SciCrunch Registry

http://www.kth.se/en

Royal Institute of Technology is a university in Stockholm, Sweden that has undergraduate, master's, and doctoral degree programs.

Proper citation: Royal Institute of Technology; Stockholm; Sweden (RRID:SCR_000992) Copy   

•   Source: SciCrunch Registry

https://dans.knaw.nl/en

Netherlands institute for permanent access to digital research resources. DANS encourages researchers to make their digital research data findable, accessible, interoperable and reusable. It does this by providing expert advice and certified services.

Proper citation: DANS (RRID:SCR_000904) Copy   

•   Source: SciCrunch Registry

http://www.aber.ac.uk/en/

A public research university located in Wales, United Kingdom. The university offers degrees at the undergraduate and postgraduate level in fields from physics and earth sciences to creative writing and international politics.

Proper citation: Aberystwyth University; Wales; United Kingdom (RRID:SCR_000949) Copy   

•   Source: SciCrunch Registry

http://www.epson.com/

Commercial vendor of visualization software, factory automation equipment and electric components.

Proper citation: Epson (RRID:SCR_000787) Copy   

•   Source: SciCrunch Registry

http://kofler.or.at/bioinformatics/SciRoKo/

Comparative genomics software that assists in whole genome microsatellite search and investigation. The command line version is called SciRoKoCo. The perl script DesignPrimer can be used to design PCR primer pairs for the SciRoKo output.

Proper citation: SciRoKo (RRID:SCR_000941) Copy   

•   Source: SciCrunch Registry

http://functionalbio.com/web/

A service that provides low cost DNA sequencing. They utilize microfluidic technology.

Proper citation: Functional Biosciences (RRID:SCR_000943) Copy   

•   Source: SciCrunch Registry

http://www.iastate.edu/

Iowa State University (ISU) is an undergraduate, graduate and research institute. ISU has 100 majors and upwards of 800 student organizations.

Proper citation: Iowa State University; Iowa; USA (RRID:SCR_000972) Copy   

•   Source: SciCrunch Registry

http://web.mit.edu/

Independent, coeducational, privately endowed university, organized into five schools: architecture and planning; engineering; humanities, arts, and social sciences; management; and science.

Proper citation: Massachusetts Institute of Technology; Massachusetts; USA; (RRID:SCR_000977) Copy   

•   Source: SciCrunch Registry

http://www.genomecanada.ca/

Genome Canada is a non-profit organization that is funded by the Government of Canada. The organization funds large-scale science and technology to fuel innovation regarding genomics in multiple sectors such as health, agriculture and agri-food, forestry, fisheries and aquaculture, environment, energy and mining. They create partnerships at the program and research project levels.

Proper citation: Genome Canada (RRID:SCR_000966) Copy   

•   Source: SciCrunch Registry

http://www.hawaii.edu/

University in Hawaii that provides undergraduate, master's, doctorate, and professional degree programs. Campuses are located in Manoa and in Hilo.

Proper citation: University of Hawaii; Hawaii; USA (RRID:SCR_000998) Copy   

•   Source: SciCrunch Registry

http://www.unimelb.edu.au/

University in Victoria, Australia that provides undergraduate and graduate degree programs.

Proper citation: University of Melbourne; Victoria; Australia (RRID:SCR_000999) Copy   

•   Source: SciCrunch Registry

http://stormo.wustl.edu/DiMO/

Software for discriminative motif optimization based on perceptron training. It takes a seed motif along with a positive and a negative database and improves the motif based on a discriminative strategy. They use the area under receiver-operating characteristic curve (AUC) as a measure of discriminating power of motifs and a strategy based on perceptron training that maximizes AUC rapidly in a discriminative manner.

Proper citation: DiMO (RRID:SCR_001168) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/exomePeak.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software package developed for the analysis of affinity-based epitranscriptome shortgun sequencing data from MeRIP-seq (maA-seq). It was built on the basis of the exomePeak MATLAB package with new functions for differential analysis of two experimental conditions to unveil the dynamics in post-transcriptional regulation of the RNA methylome. The exomePeak R-package accepts and statistically supports multiple biological replicates, internally removes PCR artifacts and multi-mapping reads, outputs exome-based binding sites (RNA methylation sites) and detects differential post-transcriptional RNA modification sites between two experimental conditions in term of percentage rather the absolute amount.

Proper citation: ExomePeak (RRID:SCR_001076) Copy   

•   Source: SciCrunch Registry