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http://www.maizegdb.org

Collection of data related to crop plant and model organism Zea mays. Used to synthesize, display, and provide access to maize genomics and genetics data, prioritizing mutant and phenotype data and tools, structural and genetic map sets, and gene models and to provide support services to the community of maize researchers. Data stored at MaizeGDB was inherited from the MaizeDB and ZmDB projects. Sequence data are from GenBank. Data are searchable by phenotype, traits, Pests, Gel Pattern, and Mutant Images.

Proper citation: MaizeGDB (RRID:SCR_006600) Copy   

•   Source: SciCrunch Registry
  

https://www.phenx.org/Default.aspx?tabid=56

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on 05 01 2025. PhenX is a project to prioritize Phenotype and eXposure measures for Genome-wide Association Studies (GWAS). Leaders of the scientific community will assess and prioritize a broad range of domains relevant to genomics research and public health. The PhenX Steering Committee (SC), chaired by Dr. Jonathan Haines, provides leadership in the selection of domains and domain experts. Members of the SC include outstanding scientists from the research community and liaisons from the Institutes and Centers of the National Institutes of Health. Consensus measures for GWAS will have a direct impact on biomedical research and ultimately on public health. During the course of this project, up to 20 research domains will be examined, with up to 15 measures being recommended for use in future GWAS and other large-scale genomic research efforts. The goal is to maximize the benefits of future research by having comparable measures so that studies can be integrated. Each selected domain will be reviewed by a Working Group (WG) of scientists who are experts in the research area. A systematic review of the literature will guide the WGs selection of up to 15 high priority measures with standardized approaches for measurement. Selection criteria for the measures include factors such as validity, reproducibility, cost, feasibility, and burden to both investigators and participants. The scientific community will be asked to provide input on proposed measures. Consensus development is a key component of the project.

Proper citation: Consensus Measures for Phenotype and Exposure (RRID:SCR_006688) Copy   

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http://sourceforge.net/projects/powermap/

Software tool specifically designed for neuroimaging data that implements theoretical power calculation algorithms based on non-central random field theory. It can also calculate power for statistical analyses with FDR (false discovery rate) corrections. This GUI (graphical user interface)-based tool enables neuroimaging researchers without advanced knowledge in imaging statistics to calculate power and sample size in the form of 3D images. This tool is currently under limited release for beta testing. At this time, only users that have been directed to this site by the PowerMap developers will receive support.

Proper citation: PowerMap (RRID:SCR_006721) Copy   

•   Source: SciCrunch Registry
  

http://p53.fr

The UMD TP53 Mutation Database is a novel web site exclusively dedicated to mutant TP53. The following datasets, analytical tools and software are available. * The TP53 UMD mutation database in human cancer (2012 release). This novel release (35,000 mutations, 3,600 publications) has been highly curated using an original and novel statistical procedure (See Edlung et al. PNAS 2012). * TP53MUTLOAD (MUTant Loss Of Activity Database), a novel database dedicated to detailed analysis of the properties of each TP53 mutant, ranging from transactivation to cell growth properties, change of conformation, localization or various gains of functions. The database contains more than 110,000 different entries. * TP53 Mut assessor, a novel stand-alone software available for both Windows and Mac users. Check your favorite TP53 mutants and get an instant identity card. Very useful to analyze any newly discovered TP53 mutants, as the software checks for every possible TP53 mutation. * MUT-TP53 2.0, an accurate and powerful tool that automatically manages p53 mutations and generate tables ready for publication, decreasing the risk of typing errors. MUT-TP53 2.0 also provides specific information for each TP53 mutation, allowing the user to assess the quality of the data. Up to 500 TP53 mutations can be managed simultaneously.

Proper citation: UMD p53 Mutation Database (RRID:SCR_006720) Copy   

•   Source: SciCrunch Registry
  

http://www.endocrine.niddk.nih.gov/

Information dissemination service of the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) providing information about endocrine and metabolic diseases in easy-to-understand language: online, in booklets and fact sheets, by email, and over the phone to patients, health professionals and the public. The NEMDIS provides the following informational products and services: * Response to inquiries about endocrine and metabolic diseases, ranging from information about available patient and professional education materials to referrals to patient support organizations. Assistance is available by phone (8:30 a.m. to 5 p.m. eastern time, M-F), fax, mail, and email. * Publications about endocrine and metabolic diseases, provided free of copyright, in varying reading levels. Available online or in hard copy. NEMDIS also sends publications to health fairs and community events. * Referrals to health professionals through the National Library of Medicine''''s MEDLINEplus, which includes a consumer-friendly listing of organizations to assist in the search for physicians and other health professionals.

Proper citation: National Endocrine and Metabolic Diseases Information Service (RRID:SCR_006681) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/samscope/

A lightweight SAM/BAM file viewer that makes visually exploring next generation sequencing data intuitive and maybe even fun! Quickly and easily generate aggregate statistics from SAM/BAM files like coverage, polarity, and minor allele frequencies, then scroll and explore freely with a simple mouse based interface. Multiple windows can be synchronized for careful comparison across multiple experiments.

Proper citation: Samscope (RRID:SCR_006715) Copy   

•   Source: SciCrunch Registry
  

https://madb.nci.nih.gov/

Microarray data management and analysis system for NCI / Center for Cancer Research scientists / collaborators. Data is secured and backed up on a regular basis, and investigators can authorize levels of access privileges to their projects, allowing data privacy while still enabling data sharing with collaborators.

Proper citation: mAdb (RRID:SCR_006677) Copy   

•   Source: SciCrunch Registry
  

http://www.proteinatlas.org/

Open access resource for human proteins. Used to search for specific genes or proteins or explore different resources, each focusing on particular aspect of the genome-wide analysis of the human proteins: Tissue, Brain, Single Cell, Subcellular, Cancer, Blood, Cell line, Structure and Interaction. Swedish-based program to map all human proteins in cells, tissues, and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics, and systems biology. All the data in the knowledge resource is open access to allow scientists both in academia and industry to freely access the data for exploration of the human proteome.

Proper citation: The Human Protein Atlas (RRID:SCR_006710) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/dmeas/

A user-friendly DNA methylation analysis tool for DNA methylation pattern extraction, DNA methylation level estimation, DNA methylation entropy analysis and multi-sample comparison. It was developed in order to assess the DNA methylation variations for a given genomic locus or genome-wide methylation data.

Proper citation: DMEAS (RRID:SCR_006679) Copy   

•   Source: SciCrunch Registry
  

http://www.ncbi.nlm.nih.gov/books/NBK5330/

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.Searchable book regarding molecular imaging and contrast agents (under development, in clinical trials or commercially available for medical applications) that have in vivo data (animal or human) published in peer-reviewed scientific journals prior to June 30 of 2013. 1444 agents are currently listed and there will be no more updates. Also available is a downloadable list of FDA approved contrast agents (Latest update: January 2013) and a Molecular Imaging Probes and Contrast Agents List (MIP & CA List) created by the MICAD staff by screening the PubMed / MedLine databases and other appropriate sources of such information. Only agents used in animal or human studies yielding in vivo data were selected for inclusion in the list. The list is by no means considered complete. No one imaging modality has been given preference over the others and the omission of any agent(s) or the introduction of any errors in the list is purely unintentional. The MIP & CA List is subject to the same copyright and disclaimers as the rest of the MICAD content. The database includes, but is not limited to, agents developed for positron emission tomography (PET), single photon emission computed tomography (SPECT), magnetic resonance imaging (MRI), ultrasound (US), computed tomography (CT), optical imaging, planar radiography, and planar gamma imaging. The information on each agent is summarized in a book chapter format containing several sections such as Background, Synthesis, in vitro studies, Animal Studies (with sub-sections: rodents, other non-human primate animals, and human primates), Human Studies, and References. In addition, the references are linked to PubMed for retrieval of the publication abstract. Also, each chapter contains links to resources at the National Center for Biotechnology Information (NCBI) and other relevant databases regarding the target of the imaging probe or contrast agent.

Proper citation: Molecular Imaging and Contrast Agent Database (RRID:SCR_006712) Copy   

•   Source: SciCrunch Registry
  

http://www.bioconductor.org/packages/2.12/bioc/html/DeconRNASeq.html

An R package for deconvolution of heterogeneous tissues based on mRNA-Seq data. It modeled expression levels from heterogeneous cell populations in mRNA-Seq as the weighted average of expression from different constituting cell types and predicted cell type proportions of single expression profiles.

Proper citation: DeconRNASeq (RRID:SCR_006713) Copy   

•   Source: SciCrunch Registry
  

https://jhuccs1.us/gpcrc/

Perform clinical, epidemiological, and therapeutic research in gastroparesis and provide an infrastructure that can rapidly and efficiently design and conduct clinical trials for effective medical, surgical, or other interventions to improve treatment of patients with gastroparesis. The GpCRC studies comprise well characterized individuals with diabetic, surgical, and idiopathic gastroparesis.

Proper citation: Gastroparesis Clinical Research Consortium (RRID:SCR_006673) Copy   

•   Source: SciCrunch Registry
  

http://www.peptideresource.com/

A guide to peptide-related research and products including custom peptide suppliers, peptide synthesis reagent suppliers that provide resins, coupling reagents, and protected amino acids as well as biologically active peptides and substrates, peptide synthesizers for solution or solid phase peptide synthesis, peptide sequence analysis services, software to calculate the chemical or biochemical properties of peptides, including the prediction of antigenicity or difficult-to-synthesize sequences. There is an additional section on Proteomics Tools for the identification of proteins from peptide sequences determined by mass spectrometry. The site also contains a set of links to educational materials about peptide related research topics.

Proper citation: Peptide Resource Page: Your Complete Guide to Peptide Research and Suppliers (RRID:SCR_006676) Copy   

•   Source: SciCrunch Registry
  

http://www.upr.edu/

Main public university system in the U.S. Commonwealth of Puerto Rico and a government-owned corporation.The oldest and largest higher learning institution in the Caribbean.

Proper citation: University of Puerto Rico; Puerto Rico; USA (RRID:SCR_006707) Copy   

•   Source: SciCrunch Registry
  

http://www.bioconductor.org/packages/2.12/bioc/html/methVisual.html

Software package that allows the visualization of DNA methylation data after bisulfite sequencing.

Proper citation: methVisual (RRID:SCR_006705) Copy   

•   Source: SciCrunch Registry
  

http://www.unavco.org/

A non-profit university-governed consortium that facilitates geoscience research and education using geodesy. It rovides access to and submission of Geodetic GPS / GNSS Data, Geodetic Imaging Data, Strain and Seismic Borehole Data, and Meteorological Data. Data access web services/API provides the ability to use a command line interface to query metadata and obtain URLs to data and products. UNAVCO also provides a variety of software, including web applications, and desktop utilities for scientists, instructors, students, and others. Web-based data visualization and mapping tools provide users with the ability to view postprocessed data while web-based geodetic utilities provide ancillary information. Downloadable stand-alone software utilities include applications for configuring instruments, managing data collection, download and transfer, and performing computations on the raw data, e.g., data pre-processing or processing. The UNAVCO Facility in Boulder, Colorado is the primary operational activity of UNAVCO and exists to support university and other research investigators in their use of geophysical sensor technology for Earth sciences research. The Facility performs this task in part by archiving GNSS/GPS data and data products for current and future applications. Other data types that scientists use for Earth deformation studies are also held in the UNAVCO Archive collections. UNAVCO operates a community Archive, which provides long-term secure storage and easy retrieval of GNSS data, strain data, various derived products and related metadata. The Archive primarily stores high-precision geodetic data used for research purposes, collected under National Science Foundation and NASA sponsored projects. UNAVCO provides many learning opportunities including: Short Courses and Workshops, Educational Resources, RESESS Research Student Internships, and Technical Training.

Proper citation: UNAVCO (RRID:SCR_006706) Copy   

•   Source: SciCrunch Registry
  

http://www.niaid.nih.gov/topics/malaria/Pages/default.aspx

Nearly one million people die of malaria every year, mostly infants, young children, and pregnant women, and most of them in Africa. Finding effective ways to control and eventually eradicate the disease is a high priority of NIAID. For the latest in NIAID-supported malaria research, NIAID Strategic Plan for Malaria Research, NIAID Research Agenda for Malaria, Quick Facts, Transmission, Symptoms, Diagnosis, Treatment, Prevention, Publications, News and Events please refer to this site., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: NIAID Malaria Research Program (RRID:SCR_006743) Copy   

•   Source: SciCrunch Registry
  

https://www.oxfordbiomed.com/

An Antibody supplier

Proper citation: Oxford Biomedical Research (RRID:SCR_006864) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/hiahia/

A sequence alignment tool to align both short and long reads to a reference genome. HIA has two indexes, a hash table index and a suffix array index. The hash table is capable of the direct lookup of a q-gram and the suffix array is very fast in the lookup of a variable length q-gram. Our experiments show that the hybrid of hash table and suffix array is useful at the perspective of speed to map NGS sequencing reads to a reference genome sequence.

Proper citation: HIA (RRID:SCR_006865) Copy   

•   Source: SciCrunch Registry
  

http://sempublishing.svn.sourceforge.net/viewvc/sempublishing/SPAR/index.html

A suite of orthogonal and complementary ontology modules for creating comprehensive machine-readable RDF metadata for all aspects of semantic publishing and referencing. The ontologies can be used either individually or in conjunction. The component ontologies within SPAR: * Semantic Publishing ** FaBiO - FRBR-aligned Bibliographic Ontology ** PRO - Publishing Roles Ontology ** PSO - Publications Status Ontology ** PWO - Publishing Workflow Ontology * Referencing ** CiTO - Citation Typing Ontology ** BiRO - Bibliographic Reference Ontology ** C4O - Citation Counting and Context Characterization Ontology ** DoCO - Document Components Ontology Each is encoded in the Web ontology language OWL 2.0 DL. Together, they provide the ability to describe far more than simply bibliographic entities such as books and journal articles, by enabling RDF metadata to be created to relate these entities to reference citations, to bibliographic records, to the component parts of documents, and to various aspects of the scholarly publication process. Where appropriate, the SPAR ontologies, specifically FaBiO, the FRBR-aligned Bibliographic Ontology, and BiRO, the Bibliographic Reference Ontology, employ the FRBR (Functional Requirements for Bibliographic Records) classification model, a conceptual entity-relationship model developed by the International Federation of Library Associations and Institutions (IFLAI) as a generalized view of the bibliographic universe, intended to be independent of any cataloging code or implementation. FRBR distinguishes Works, Expressions, Manifestations and Items.

Proper citation: SPAR - Semantic Publishing and Referencing Ontologies (RRID:SCR_006746) Copy   

•   Source: SciCrunch Registry