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http://www.mellon.org/

The Andrew W. Mellon Foundation currently makes grants in five core program areas: * Higher Education and Scholarship * Scholarly Communications and Information Technology * Art History, Conservation, and Museums * Performing Arts * Conservation and the Environment Within each of its core programs, the Foundation concentrates most of its grantmaking in a few areas. Institutions and programs receiving support are often leaders in fields of Foundation activity, but they may also be promising newcomers, or in a position to demonstrate new ways of overcoming obstacles to achieve program goals. Our grantmaking philosophy is to build, strengthen and sustain institutions and their core capacities, rather than be a source for narrowly defined projects. As such, we develop thoughtful, long-term collaborations with grant recipients and invest sufficient funds for an extended period to accomplish the purpose at hand and achieve meaningful results.

Proper citation: Andrew W. Mellon Foundation (RRID:SCR_005864) Copy   

•   Source: SciCrunch Registry

http://simile.mit.edu/

SIMILE, a joint project conducted by the MIT Libraries and MIT CSAIL, was focused on developing robust, open source tools that empower users to access, manage, visualize and reuse digital assets. SIMILE seeks to enhance interoperability among digital assets, schemata/vocabularies/ontologies, metadata, and services. A key challenge is that the collections which must inter-operate are often distributed across individual, community, and institutional stores. We seek to be able to provide end-user services by drawing upon the assets, schemata/vocabularies/ontologies, and metadata held in such stores. SIMILE will leverage and extend DSpace, enhancing its support for arbitrary schemata and metadata, primarily though the application of RDF and semantic web techniques. The project also aims to implement a digital asset dissemination architecture based upon web standards. The dissemination architecture will provide a mechanism to add useful views to a particular digital artifact (i.e. asset, schema, or metadata instance), and bind those views to consuming services. To guide the SIMILE effort we will focus on well-defined, real-world use cases in the libraries domain. Since parallel work is underway to deploy DSpace at a number of leading research libraries, we hope that such an approach will lead to a powerful deployment channel through which the utility and readiness of semantic web tools and techniques can be compellingly demonstrated in a visible and global community. The SIMILE Project and its members are fully committed to the open source principles of software distribution and open development and for this reason, it releases the created intellectual property (both software and reports) under a BSD-style license. The SIMILE Project Team Members gladly welcome community efforts.

Proper citation: SIMILE (RRID:SCR_005862) Copy   

•   Source: SciCrunch Registry

http://www.stanford.edu/~nigam/cgi-bin/dokuwiki/doku.php?id=clench

Cluster Enrichment (CLENCH) allows A. thaliana researchers to perform automated retrieval of GO annotations from TAIR and calculate enrichment of GO terms in gene group with respect to a reference set. Before calculating enrichment, CLENCH allows mapping of the returned annotations to arbitrary coarse levels using GO slim term lists (which can be edited by the user) and a local installation of GO. Platform: Windows compatible, Linux compatible,

Proper citation: CLENCH (RRID:SCR_005735) Copy   

•   Source: SciCrunch Registry

http://www.sbur.org/

The Society for Basic Urologic Research (SBUR) is a society of scientists whose expertise includes the study of urologic cancers (prostate, bladder, kidney, testis, penis), the biology of prostate growth, kidney and bladder function, autoimmune urologic diseases, infectious diseases, neuro-urologic diseases, male reproductive biology, infertility and erectile dysfunction. Members include molecular biologists, immunologists, epidemiologists, oncologists, biochemists and clinical urologic scientists. SBUR members serve on a wide variety of advisory panels, study sections, editorial boards and in the pharmaceutical industry. The SBUR organizes two annual meetings to share new findings at a multidisciplinary level, to promote interaction among members and other interested scientists and to highlight new areas of research and funding opportunities. The Society was organized to address the following: * To provide a forum for the presentation and discussion of basic scientific topics related to urology * To develop educational forums concerning scientific advancements related to the field of urology * To promote collaborative investigations among member scientists with an emphasis on the interchange of expertise among clinical and basic scientists * To promote the communication and interests of urologic disease investigators with national funding agencies, industry representatives and academic institutions with regards to urology related research * To serve as a resource for research information and expertise to clinical urologists through the American Urological Association

Proper citation: SBUR - Society for Basic Urologic Research (RRID:SCR_005856) Copy   

•   Source: SciCrunch Registry

http://www.auanet.org/content/homepage/homepage.cfm

The American Urological Association (AUA), founded in 1902, is the premier professional association for the advancement of urologic patient care, and works to ensure that its more than 18,000 members are current on the latest research and practices in urology. The AUA also pursues its mission of fostering the highest standards of urologic care by providing a wide range of servicesincluding publications, research, the Annual Meeting, continuing medical education (CME) and the formulation of health policy.

Proper citation: American Urological Association (RRID:SCR_005859) Copy   

•   Source: SciCrunch Registry

http://drcat.sourceforge.net/

Data resource catalog that collates metadata on bioinformatics Web-based data resources including databases, ontologies, taxonomies and catalogues. An entry includes information such as resource identifier(s), name, description and URL. ''''Query'''' lines are defined for each resource that describe what type(s) of data are available, in what format, how (by what identifier) the data can be retrieved and from where (URL). DRCAT was developed to provide more extensive data integration for EMBOSS, but it has many applications beyond EMBOSS. DRCAT entries (including ''''Query'''' lines) are annotated with terms from the EDAM ontology of common bioinformatics concepts.

Proper citation: DRCAT Resource Catalogue (RRID:SCR_005931) Copy   

•   Source: SciCrunch Registry

https://fairsharing.org/standards/

Catalogue to: 1, centralize community-developed bioscience standards, linking to policies, other portals, open access resources and lists of tools and databases implementing the standards; 2. develop and maintain a set of criteria for assessing the usability and popularity of the standards, also the interoperability and relations among them; 3. foster interoperability, addressing overlaps and duplication of efforts that hamper their wider uptake and interfere with the creation of standards-compliant systems. Research community, funding agencies, and journals participate in the development of reporting standards for the bioscience domain to ensure that shared experiments are reported with enough information to be comprehensible and (in principle) reproducible, compared or integrated. Similar trends in both the regulatory arena and commercial science. The BioSharing catalogue classifies standards into three types: * reporting requirements (minimal information checklists to report of the same core set of information) * terminological artifacts (such as controlled vocabularies and ontologies to describe the information) * exchange formats (to communicate the information) You can sort columns and browse the reporting guidelines content, or you can view all the standards, or reporting guidelines, or terminological artifacts or exchange formats only. Contribute and help build the catalogue.

Proper citation: FAIRSharing Catalogue of Standards (RRID:SCR_005926) Copy   

•   Source: SciCrunch Registry

http://www.livinghuman.org/

Distributed repository of anatomo-functional data and of simulation algorithms, fully integrated into a seamless simulation environment and directly accessible. This infrastructure will be used to create the physiome of the human musculo-skeletal system.

Proper citation: LHP LHDL (RRID:SCR_005928) Copy   

•   Source: SciCrunch Registry

http://dictybase.org/Dicty_Info/dicty_anatomy_ontology.html

An ontology to describe Dictyostelium where the structural makeup of Dictyostelium and its composing parts including the different cell types, throughout its life cycle is defined. There are two main goals for this new tool: (1) promote the consistent annotation of Dictyostelium-specific events, such as phenotypes (already in use), and in the future, of gene expression information; and (2) encourage researchers to use the same terms with the same intended meaning. To this end, all terms are defined. The complete ontology can be browsed using EBI''s ontology browser tool. (http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=DDANAT)

Proper citation: Dictyostelium Anatomy Ontology (RRID:SCR_005929) Copy   

•   Source: SciCrunch Registry

https://array.nci.nih.gov/caarray/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on Sep 18, 2018. Open-source, web and programmatically accessible microarray data management system. caArray guides the annotation and exchange of array data using a federated model of local installations whose results are shareable across the cancer Biomedical Informatics Grid (caBIG). caArray furthers translational cancer research through acquisition, dissemination and aggregation of semantically interoperable array data to support subsequent analysis by tools and services on and off the Grid. As array technology advances and matures, caArray will extend its logical library of assay management.

Proper citation: caArray (RRID:SCR_006053) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/RCD

Ontology of clinical terms Version 3 (CTV3) (Read Codes) (Q199): National Health Service National Coding and Classification Centre

Proper citation: Read Codes Clinical Terms Version 3 (RRID:SCR_006055) Copy   

•   Source: SciCrunch Registry

http://genomefoundation.org/index.php/Main_Page

The Genome Foundation (AKA Genome Research Foundation) is a fully government accredited and registered non-profit research foundation. GRF aims to provide genome philosophy, science, and technology. GRF is a nonprofit publisher, and research and advocacy organization to promote completely free publication of knowledge with minimum restriction. Our core objectives are to: * Provide ways to overcome unnecessary barriers to immediate availability, access, and use of research * Pursue a publishing strategy that optimizes the openness, quality, and integrity of the publication process * Develop innovative approaches to the assessment, organization, and reuse of ideas and data Genome Foundation Research * Personalized Medicine * Personal Genomics * AngioGenesis drug * Bioinformatics * RNA expression * Protein structure * Human Genome Rights Projects at Genome Foundation * The Human Genome Rights * Human Genome Rights Petition * Free Personal Genome Sequencing Project * Free Personal Genome Sequencing Petition * Tiger Genome Initiative: Amur Tiger and big cat genomes * Whale Genome Project

Proper citation: Genome Research Foundation (RRID:SCR_006056) Copy   

•   Source: SciCrunch Registry

http://www.scytek.com/

An Antibody supplier

Proper citation: ScyTek Laboratories (RRID:SCR_005919) Copy   

•   Source: SciCrunch Registry

http://www.vectorbase.org

Bioinformatics Resource Center for invertebrate vectors. Provides web-based resources to scientific community conducting basic and applied research on organisms considered potential agents of biowarfare or bioterrorism or causing emerging or re-emerging diseases.

Proper citation: VectorBase (RRID:SCR_005917) Copy   

•   Source: SciCrunch Registry

https://www.facebase.org/content/ocdm

To satisfy the need for standardized terminologies several ontologies, we are developing the Ontology of Craniofacial Development and Malformation. When complete, this ontology will describe several realms of anatomy and development relevant to FaceBase, including: * Human craniofacial anatomy, including developmental progressions * Craniofacial malformations * Mouse craniofacial anatomy * Mappings between mouse and human anatomy These ontologies are currently undergoing active development. As a result, these files should be considered very preliminary. They may not work correctly, and contents will almost certainly undergo significant change. Five (sub) ontologies in this zip archive correspond to the categories described above. * OCDM - Ontology of Craniofacial Development and Malformation: currently imports the CHO, CMO, and the CHMMO. * CHO - Craniofacial Human Ontoloogy: normal adult human craniofacial anatomy derived from the FMA. * CMO - Craniofacial Mouse Ontology: normal adult mouse craniofacial anatomy * CHMMO - Craniofacial Human-Mouse Mapping Ontology: mappings of classes in the * CHO to related (homologous) structures in the CMO. CFMO - Craniofacial Malformation Ontology: abnormal human anatomy, includes the CHO All ontologies are in Protege Frames format (requires Protege 3.x). Ontologies refer to other ontologies via the Protege include mechanism. The CHMMO includes the CHO and the CMO. The OCDM (which is the umbrella ontology) includes all of the rest. Future releases will include translations to the OWL language.

Proper citation: OCDM - Ontology of Craniofacial Development and Malformation (RRID:SCR_005999) Copy   

•   Source: SciCrunch Registry

http://www.umich.edu/~neurosci/

The Graduate Program at the University of Michigan was constituted in 1971, making it the longest-standing neuroscience graduate program in the United States. We are a collegial and interactive group of 75 students and 115 faculty that perform research across the breadth of the neuroscience field. Neuroscience graduate students on this campus form a cohesive group, which promotes interactions among the faculty, making the Graduate Program the nexus of the neuroscience community. Graduates receive a Ph.D. in Neuroscience, which provides tremendous flexibility in choosing one's career path. There are more than 100 alumni of our Program, and these graduates work in academic research, industrial research and development, academic medicine and biotechnology. Our program captures the excitement and interaction intrinsic to the field of neuroscience. Students can seek admission to the Neuroscience Program by three different routes direct application to the Neuroscience Program, application via the Program in Biomedical Sciences and application via the Medical Scientist Training Program.

Proper citation: University of Michigan Department of Neuroscience Graduate Program (RRID:SCR_006002) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.charite.de/voronoia/

Voronoia is a program suite to analyse and visualize the atomic packing of protein structures. It is based on the Voronoi Cell method and can be used to estimate the quality of a protein structure, e.g. by comparing the packing density of buried atoms to a reference data set or by highlighting protein regions with large packing defects. Voronoia is also targeted to detect locations of putative internal water or binding sites for ligands. Accordingly, Voronoia is beneficial for a broad range of protein structure approaches. It is applicable as a standalone version coming with a user friendly GUI or, alternatively, as a Pymol Plugin. Finally, Voronoia is also available as an easy to use webtool to process user defined PDB-files or to asses precalculated packing files from DOPP, the regularly updated Dictionary of Packing in Proteins.

Proper citation: Voronoia (RRID:SCR_006005) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/MetaQC/

Software for quality control and diagnosis for microarray meta-analysis. Quantitative quality control measures include: (1) internal homogeneity of co-expression structure among studies (internal quality control; IQC); (2) external consistency of co-expression structure correlating with pathway database (external quality control; EQC); (3) accuracy of differentially expressed gene detection (accuracy quality control; AQCg) or pathway identification (AQCp); (4) consistency of differential expression ranking in genes (consistency quality control; CQCg) or pathways (CQCp). For each quality control index, the p-values from statistical hypothesis testing are minus log transformed and PCA biplots were applied to assist visualization and decision. Results generate systematic suggestions to exclude problematic studies in microarray meta-analysis and potentially can be extended to GWAS or other types of genomic meta-analysis. The identified problematic studies can be scrutinized to identify technical and biological causes (e.g. sample size, platform, tissue collection, preprocessing etc) of their bad quality or irreproducibility for final inclusion / exclusion decision.

Proper citation: MetaQC (RRID:SCR_006000) Copy   

•   Source: SciCrunch Registry

http://www.digital-scholarship.org/sepb/sepb.html

Bibliography with over 3,800 selected English-language articles, books, and other printed and electronic sources that are useful in understanding scholarly electronic publishing efforts on the Internet. It covers a wide range of topics, such as digital copyright, digital libraries, digital preservation, digital repositories, e-books, e-journals, license agreements, metadata, and open access. It includes Scholarly Electronic Publishing Resources, a selective directory of related Web sites, and the Scholarly Electronic Publishing Weblog, a frequently updated list of new publications and other resources that may be of interest to bibliography readers. Most sources have been published from January 1, 1990 through October 30, 2011; however, a limited number of earlier key sources are also included. The bibliography includes links to freely available versions of included works. It does not include digital media works (such as MP3 files), editorials, e mail messages, letters to the editor, daily newspaper articles, presentation slides or transcripts, or weblog postings. An archive of prior versions of SEPB is available as a downloadable compressed file (.zip) that includes all versions of the bibliography. The Scholarly Electronic Publishing Bibliography 2010 is available as a paperback (466 pages, $18.95, ISBN-10: 1456453289 and ISBN-13: 9781456453282) and an open access PDF file.

Proper citation: Scholarly Electronic Publishing Bibliography (RRID:SCR_005949) Copy   

•   Source: SciCrunch Registry

http://bishopw.loni.ucla.edu/AIR5/

A tool for automated registration of 3D (and 2D) images within and across subjects and within and sometimes across imaging modalities. The AIR library can easily incorporate automated image registration into site specific programs adapted to your particular needs.

Proper citation: Automated Image Registration (RRID:SCR_005944) Copy   

•   Source: SciCrunch Registry