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http://www.viprbrc.org/brc/home.do?decorator=vipr

Provides searchable public repository of genomic, proteomic and other research data for different strains of pathogenic viruses along with suite of tools for analyzing data. Data can be shared, aggregated, analyzed using ViPR tools, and downloaded for local analysis. ViPR is an NIAID-funded resource that support the research of viral pathogens in the NIAID Category A-C Priority Pathogen lists and those causing (re)emerging infectious diseases. It provides a dedicated gateway to SARS-CoV-2 data that integrates data from external sources (GenBank, UniProt, Immune Epitope Database, Protein Data Bank), direct submissions, analysis pipelines and expert curation, and provides a suite of bioinformatics analysis and visualization tools for virology research.

Proper citation: Virus Pathogen Resource (ViPR) (RRID:SCR_012983) Copy   

•   Source: SciCrunch Registry

http://mitobreak.portugene.com/cgi-bin/Mitobreak_home.cgi

Database with curated datasets of mitochondrial DNA (mtDNA) rearrangements. Users may submit new mtDNA rearrangements.

Proper citation: MitoBreak (RRID:SCR_012949) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ngsep/

Software whose main functionality is the variants detector, which allows to make simultaneous discovery of SNVs, small indels, and CNVs.Accurate variant calling across species and sequencing protocols.Used for analysis of DNA high throughput sequencing data.

Proper citation: NGSEP (RRID:SCR_012827) Copy   

•   Source: SciCrunch Registry

http://www.scienceexchange.com/facilities/german-cancer-research-center-dkfz

To perform research into cancer is the task of the German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ). DKFZ is the largest biomedical research institute in Germany and a member of the Helmholtz Association of National Research Centers. In over 70 divisions and research groups, our more than 2,500 employees, of which more than 1,000 are scientists, are investigating the mechanisms of cancer, are identifying cancer risk factors and are trying to find strategies to prevent people from getting cancer.They are developing novel approaches to make tumor diagnosis more precise and treatment of cancer patients more successful.

Proper citation: German Cancer Research Center Labs and Facilities (RRID:SCR_012708) Copy   

•   Source: SciCrunch Registry

https://www.nia.nih.gov/alzheimers

Portal for Alzheimer's disease that compiles, archives and disseminates information about current treatments, diagnostic tools and ongoing research for health professions, people with AD, their families and the public. The Center provides informational services and referrals for AD symptoms, diagnosis and treatment for patients; clinical trial information and literature searches for researchers; training materials and guidelines for caregivers; and Spanish language resources.

Proper citation: Alzheimer's Disease Education and Referral Center (RRID:SCR_012787) Copy   

•   Source: SciCrunch Registry

http://www.rcsb.org/#Category-welcome

Collection of structural data of biological macromolecules. Database of information about 3D structures of large biological molecules, including proteins and nucleic acids. Users can perform queries on data and analyze and visualize results.

Proper citation: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) (RRID:SCR_012820) Copy   

•   Source: SciCrunch Registry

http://www.sourceforge.net/projects/matcont

MATCONT is a graphical MATLAB package for the interactive numerical study of parameterized dynamical systems. It is developed in parallel with the command line continuation toolbox CL_MATCONT and with the command line continuation toolbox CL_MATCONTM for the interactive numerical study of parameterized maps and iterates of maps. MATCONT and CL_MATCONT allow the numerical continuation of equilibria, limit cycles and homoclinic orbits, detection of codimension 1 and 2 bifurcations, continuation of the codimension 1 bifurcations and computation of their normal forms. For equilibria normal form coefficients of codimension 2 bifurcations are also computed, as well as switching to the codimension 1 curves in codimension 2 points. CL_MATCONTM provides similar facilities for maps and iterates of maps, including normal form coefficients of codimension 2 bifurcations and continuation of homoclinic and heteroclinic connections and tangencies of such connections.

Proper citation: MATCONT and CL MATCONT: Continuation Software in Matlab (RRID:SCR_012822) Copy   

•   Source: SciCrunch Registry

http://www.scienceexchange.com/facilities/colorado-state-university

An Portal, Core facility

Proper citation: Colorado State University Labs and Facilities (RRID:SCR_012667) Copy   

•   Source: SciCrunch Registry

http://www.urmc.rochester.edu/smd/nanat/home/index.cfm

The Department of Neurobiology and Anatomy is strongly committed to its major academic missions of research and education. Teaching and leadership roles in both graduate and medical education remain enduring commitments today, as they have been since the inception of the medical campus in the 1920s. This is matched by our commitment to research on the structure and function of the nervous system.

Proper citation: University of Rochester Medical Center Neurobiology and Anatomy (RRID:SCR_012705) Copy   

•   Source: SciCrunch Registry

http://mobyle.pasteur.fr/

A portal for bioinformatics analyses, including the following: alignment assembly database display genetics hmm information nucleic phylogeny protein sequence structure

Proper citation: Mobyle@Pasteur (RRID:SCR_013089) Copy   

•   Source: SciCrunch Registry

http://www.cochrane.org/reviews/clibintro.htm

Contains data to inform healthcare decision-making from Cochrane and other systematic reviews, clinical trials, and more. Cochrane reviews bring you the combined results of the worlds best medical research studies, and are recognized as the gold standard in evidence-based health care. Consists of a regularly updated collection of evidence-based medicine databases, including The Cochrane Database of Systematic Reviews. This database includes systematic reviews of healthcare interventions that are produced and disseminated by The Cochrane Collaboration. It is published on a monthly basis and made available both on CD-ROM and the Internet. The review abstracts are available to browse and search free of charge on this website. The Cochrane Library Users'' Group (CLUG) provides a forum for discussion of usability, readability, searchability, and formatting issues related to the use of The Cochrane Library. The Cochrane Collaboration is an international not-for-profit and independent organization, dedicated to making up-to-date, accurate information about the effects of healthcare readily available worldwide. Funded by John Wiley and Sons Limited. The individual entities of The Cochrane Collaboration are funded by a large variety of governmental, institutional and private funding sources, and are bound by organisation-wide policy limiting uses of funds from corporate sponsors.

Proper citation: Cochrane Library (RRID:SCR_013000) Copy   

•   Source: SciCrunch Registry

http://rnai.dkfz.de

GenomeRNAi is a database of phenotypes from systematic RNA interference (RNAi) screens in cultured Drosophila cells. The phenotype database can be searched by keywords, RNAi identifiers or Drosophila gene sequences. Searches with homologous sequences from human or C. elegans are also possible. Integrated tools evaluate the specificity of long double-stranded RNAs (RNAi probes) by similarity searches against all predicted Drosophila transcripts. This site can also be used to identify pre-designed RNAi probes from available Drosophila RNAi libraries. Caenorhabditis elegans genome, human genome

Proper citation: GenomeRNAi (RRID:SCR_013088) Copy   

•   Source: SciCrunch Registry

http://www.dkfz.de/en/epidemiologie-krebserkrankungen/software/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software program that performs estimation of power and sample sizes required to detect genetic and environmental main, as well as gene-environment interaction (GxE) effects in indirect matched case-control studies (1:1 matching). When the hypothesis of GxE is tested, power/sample size will be estimated for the detection of GxE, as well as for the detection of genetic and environmental marginal effects. Furthermore, power estimation is implemented for the joint test of genetic marginal and GxE effects (Kraft P et al., 2007). Power and sample size estimations are based on Gauderman''s (2002) asymptotic approach for power and sample size estimations in direct studies of GxE. Hardy-Weinberg equilibrium and independence of genotypes and environmental exposures in the population are assumed. The estimates are based on genotypic codes (G=1 (G=0) for individuals who carry a (non-) risk genotype), which depend on the mode of inheritance (dominant, recessive, or multiplicative). A conditional logistic regression approach is used, which employs a likelihood-ratio test with respect to a biallelic candidate SNP, a binary environmental factor (E=1 (E=0) in (un)exposed individuals), and the interaction between these components. (entry from Genetic Analysis Software)

Proper citation: PIAGE (RRID:SCR_013124) Copy   

•   Source: SciCrunch Registry

http://www.nccn.org/

A not-for-profit alliance of 23 cancer centers devoted to patient care, research, and education, is dedicated to improving the quality, effectiveness, and efficiency of cancer care so that patients can live better lives. Through the leadership and expertise of clinical professionals at NCCN Member Institutions, NCCN develops resources that present valuable information to the numerous stakeholders in the health care delivery system. As the arbiter of cancer care, NCCN promotes the importance of continuous quality improvement and recognizes the significance of creating clinical practice guidelines appropriate for use by patients, clinicians, and other health care decision-makers.

Proper citation: NCCN (RRID:SCR_012959) Copy   

•   Source: SciCrunch Registry

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

Software tools for analyzing and visualizing Illumina''s 450k array data.

Proper citation: minfi (RRID:SCR_012830) Copy   

•   Source: SciCrunch Registry

http://www.cdc.gov/nceh/tracking

The goal of environmental public health tracking is to protect communities by providing information to federal, state, and local agencies. These agencies, in turn, will use this information to plan, apply, and evaluate public health actions to prevent and control environmentally related diseases. Environmental public health tracking is the ongoing collection, integration, analysis, and interpretation of data about the following factors: :- Environmental hazards :- Exposure to environmental hazards :- Health effects potentially related to exposure to environmental hazards CDC''s goal is to develop a tracking system that integrates data about environmental hazards and exposures with data about diseases that are possibly linked to the environment. This system will allow federal, state, and local agencies, and others to do the following: :- monitor and distribute information about environmental hazards and disease trends :- advance research on possible linkages between environmental hazards and disease :- develop, implement, and evaluate regulatory and public health actions to prevent or control environment-related diseases. Planning for an environmental public health tracking network is an important priority for CDC because of the opportunity it provides to address some of the most challenging problems facing local, state, and national public health leaders. From the outset, this activity has involved substantial collaboration between CDC and its public health and environmental partners (e.g., see the memorandum of understanding between HHS/CDC and the Environmental Protection Agency). Sponsors: This resource is supported by the Center for Disease Control and Prevention. Keywords: Environment, Public, Health, Disease, Analysis, Integration, Data, Hazard, Health, Prevention,

Proper citation: National Environmental Public Health Tracking Program (RRID:SCR_012832) Copy   

•   Source: SciCrunch Registry

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

Software R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. Used to process probe level data and for exploratory oligonucleotide array analysis.

Proper citation: affy (RRID:SCR_012835) Copy   

•   Source: SciCrunch Registry

http://www.ninds.nih.gov/research/parkinsonsweb/researchers.htm

This NINDS website is designed to facilitate research efforts on Parkinsons disease, as well as to provide researchers, patients and caregivers with related information and resources. Because the interests of the research and patient communities are overlapping yet distinct, the site contains separate web pages directed toward these two communities. For example, regarding funding for PD research, researchers will find information on relevant research funding opportunities, and people with PD can access information on currently funded NINDS and NIH projects. As part of their mission to decrease the burden of neurological disease, and building upon a strong foundation of research discovery, the NINDS is committed to the rapid translation of basic research findings into clinical practice. The NINDS supports a broad spectrum of basic, translational and clinical research on Parkinsons disease (PD), a chronic, progressive movement disorder that affects the lives of at least one million patients across the United States. The average onset of characteristic motor symptoms, which are initially subtle and impact purposeful movement, occurs in the sixth decade. People with PD also experience significant non-motor symptoms including changes in cognition and mood, sleep disturbances, and autonomic dysfunction. Currently available pharmacological and surgical treatments provide relief from some motor symptoms, but do not halt the ultimate progression of the disease. Although significant research advances have been made, including the recent identification of possible environmental and genetic risk factors, a clear cause and a definitive cure for PD have remained elusive. Through a constellation of funding mechanisms, representing over 86 million in fiscal year 2008, the NINDS promotes the advancement of research directed to the understanding, treatment and eventual cure of PD. Sponsors: This resource is supported by the National Institute of Neurological Disorders and Stroke. Keywords: Stroke, Neurological, Disorder, Research, Disease, Researcher, Clinical, Parkinson''s Disease, PD, Chronic, Treatment, Cure, Motor, Genetic, Environmental,

Proper citation: NINDS Parkinsons Disease Research Web (RRID:SCR_012834) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.ust.hk/BOOST.html

Software application (entry from Genetic Analysis Software) for a method for detecting gene-gene interactions. It allows examining all pairwise interactions in genome-wide case-control studies.

Proper citation: BOOST (RRID:SCR_013133) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/thornton-srv/databases/CSA/

The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. We defined a classification of catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalyzed by an enzyme. The CSA contains 2 types of entry: 1. Original hand-annotated entries, derived from the primary literature. References for these entries are given. 2. Homologous entries, found by PSI-BLAST alignment (using an e value cut-off of 0.00005) to one of the original entries. The equivalent residues, which align in sequence to the catalytic residues found in the original entry are documented. Access to the CSA is via PDB code, SWISS-PROT entry or E.C. number. Accessing via PDB code takes you straight to the CSA entry for that PDB, while accessing via SWISS-PROT or E.C. number gives a list of all PDB codes for structures assigned that particular SWISS-PROT identifier or E.C. number. Structures with entries in the CSA are given as hyperlinks. Each CSA entry lists the catalytic residues found in that entry, using PDB residue numbering. Each site is also marked with an evidence tag, which is either Literature reference or PSI-BLAST hit. If the entry is a PSI-BLAST hit you can follow the link to the original entry. You may download the CSA. JESS, an algorithm for constraint-based structural template matching and its application to 3D templates used by the CSA, is available for download.

Proper citation: CSA - Catalytic Site Atlas (RRID:SCR_013099) Copy   

•   Source: SciCrunch Registry