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on page 1 showing 20 out of 217 results

Cite this (3D Slicer, RRID:SCR_005619)

URL: http://slicer.org/

Resource Type: Resource, data visualization software, software application, data processing software, image analysis software, software resource

A free, open source software package for visualization and image analysis including registration, segmentation, and quantification of medical image data. Slicer provides a graphical user interface to a powerful set of tools so they can be used by end-user clinicians and researchers alike. 3D Slicer is natively designed to be available on multiple platforms, including Windows, Linux and Mac Os X. Slicer is based on VTK (http://public.kitware.com/vtk) and has a modular architecture for easy addition of new functionality. It uses an XML-based file format called MRML - Medical Reality Markup Language which can be used as an interchange format among medical imaging applications. Slicer is primarily written in C++ and Tcl.

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Cite this (Accelerating Medicines Partnership - Alzheimers, RRID:SCR_003742)

URL: http://www.nih.gov/science/amp/alzheimers.htm

Resource Type: Resource, organization portal, portal, consortium, data or information resource

The Alzheimer's disease arm of the Accelerating Medicines Partnership (AMP) that will identify biomarkers that can predict clinical outcomes, conduct a large scale analysis of human AD patient brain tissue samples to validate biological targets, and to increase the understanding of molecular pathways involved in the disease to identify new potential therapeutic targets. The initiative will deposit all data in a repository that will be accessible for use by the biomedical community. The five year endeavor, beginning in 2014, will result in several sets of project outcomes. For the biomarkers project, tau imaging and EEG data will be released in year two, as baseline data becomes available. Completed data from the randomized, blinded trials will be added after the end of the five year studies. This will include both imaging data and data from blood and spinal fluid biomarker studies. For the network analysis project, each project will general several network models of late onset AD (LOAD) and identify key drivers of disease pathogensis by the end of year three. Years four and five will be dedicated to validating the novel targets and refining the network models of LOAD, including screening novel compounds or drugs already in use for other conditions that may have the ability to modulate the likely targets.

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Cite this (Accelerating Medicines Partnership Autoimmune Diseases of Rheumatoid Arthritis and Lupus, RRID:SCR_003731)

URL: http://www.nih.gov/science/amp/autoimmune.htm

Resource Type: Resource, organization portal, portal, consortium, data or information resource

The autoimmune disease arm of the Accelerating Medicine Partnership (AMP), which aims to identify and validate the most promising biological targets of disease for new diagnostic and drug development, that is focused on rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE). They seek to identify shared common flaws in inflammation, particularly those that are shared with a larger number of autoimmune disorders which can cause severe disability, greatly affect quality of life, and are associated with an increased risk of death. This project aims to reveal biomarkers and biological targets for drug development, matching existing drugs to patients with specific molecular profiles who are most likely to benefit. The research plan proposes a 5 year process. Year one will include startup activities such as validation of tissue acquisition processes and analytic technologies, and the development of operating procedures. The second year will focus on identification of disease specific pathways by comparing data from patients and healthy individuals. Years 3-5 will expand the scale to include comparisons of different subsets of patients with RA or lupus to allow molecularly based patient stratification for precise treatment. The final 12 months (2019) will also include preliminary target validation. The data will be made publicly available through an internet-based information portal.

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Cite this (Accelerating Medicines Partnership - Diabetes, RRID:SCR_003743)

URL: http://www.nih.gov/science/amp/type2diabetes.htm

Resource Type: Resource, organization portal, portal, consortium, data or information resource

The arm of the Accelerating Medicine Partnership (AMP) that is focused on identifying genetic biomarkers that are correlated to Type 2 diabetes, with particularly emphasis on accelerating development of novel drugs for this disease. While therapies are available for Type 2 Diabetes (T2D), none can reverse disease progression or prevent complications of the disease. The approach of this project is to use and supplement a large amount of recently generated genetic data on T2D in diverse populations. The goal is to validate novel molecules and pathways as targets for therapeutic development. The AMP initiative will deposit all data in a repository that will be accessible for use by the biomedical community. Over the five years, researchers will build a database of DNA sequence, functional genomic and epigenomic information, and clinical data from studies on type 2 diabetes and its cardiac and renal complications. This will involve data from 100,000-150,000 individuals combined into a T2D knowledge portal accessible to academic and industry researchers to identify and validate changes in DNA that spur the onset of diabetes, alter disease severity, speed or slow down disease progression, or have a protective effect. In addition, new genomic that fills in gaps in the knowledge portal will be generated by executing specific analysis, including DNA sequencing of particular individuals.

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Cite this (Adaptive Poisson-Boltzmann Solver, RRID:SCR_008387)

URL: http://www.poissonboltzmann.org/apbs/

Resource Type: Resource, software resource

APBS is a software package for modeling biomolecular solvation through solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. APBS was designed to efficiently evaluate electrostatic properties for such simulations for a wide range of length scales to enable the investigation of molecules with tens to millions of atoms. It also provides implicit solvent models of nonpolar solvation which accurately account for both repulsive and attractive solute-solvent interactions. APBS uses FEtk (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FEtk is a portable collection of finite element modeling class libraries written in an object-oriented version of C. It is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods.

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Cite this (Add Health (National Longitudinal Study of Adolescent Health), RRID:SCR_007434)

URL: http://www.cpc.unc.edu/projects/addhealth

Resource Type: Resource, data or information resource, database

Longitudinal study of a nationally representative sample of adolescents in grades 7-12 in the United States during the 1994-95 school year. Public data on about 21,000 people first surveyed in 1994 are available on the first phases of the study, as well as study design specifications. It also includes some parent and biomarker data. The Add Health cohort has been followed into young adulthood with four in-home interviews, the most recent in 2008, when the sample was aged 24-32. Add Health combines longitudinal survey data on respondents social, economic, psychological and physical well-being with contextual data on the family, neighborhood, community, school, friendships, peer groups, and romantic relationships, providing unique opportunities to study how social environments and behaviors in adolescence are linked to health and achievement outcomes in young adulthood. The fourth wave of interviews expanded the collection of biological data in Add Health to understand the social, behavioral, and biological linkages in health trajectories as the Add Health cohort ages through adulthood. The restricted-use contract includes four hours of free consultation with appropriate staff; after that, there''s a fee for help. Researchers can also share information through a listserv devoted to the database.

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Cite this (Adult Mouse Anatomy Ontology, RRID:SCR_006568)

URL: http://www.informatics.jax.org/searches/AMA_form.shtml

Resource Type: Resource, ontology, data or information resource, controlled vocabulary

Ontology that organizes anatomical structures for the adult mouse (Theiler stage 28) spatially and functionally, using ''is a'' and ''part of'' relationships. The ontology is used to describe expression data for the adult mouse and phenotype data pertinent to anatomy in standardized ways. The browser can be used to view anatomical terms and their relationships in a hierarchical display.

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Cite this (All About Grants Podcast, RRID:SCR_005621)

URL: http://grants.nih.gov/podcasts/All_About_Grants/index.htm

Resource Type: Resource, narrative resource, podcast, training resource, data or information resource

The Office of Extramural Research (OER) presents conversations with NIH staff members. Designed for investigators, fellows, students, research administrators, and others, we provide insights on grant topics from those who live and breathe the information. In mp3 and updated monthly. Transcripts are also available. So You Wanna... Keep Up with What''''s Hot? Prepare a Successful Grant Application? Suggest a Topic? Understand How Your Grant is Reviewed? Be an NIH Investigator?

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Cite this (ASN - American Society of Nephrology, RRID:SCR_006709)

URL: http://www.asn-online.org/

Resource Type: Resource, portal, community building portal, data or information resource

Society leading the fight against kidney disease by educating health professionals, sharing new knowledge, advancing research, and advocating the highest quality care for patients. To accomplish its mission, ASN will: # Educate health professionals by increasing the value of ASN education. # Share new knowledge by improving the quality and expanding the reach of ASN''s communications, including maintaining the premier publications in kidney disease. # Promote the highest quality care by serving as the professional organization informing health policy in kidney disease. # Advance patient care and research in kidney disease by strengthening the pipeline of clinicians, researchers, and educators. To accomplish this goal, ASN will: ## Implement a strategy to increase interest in nephrology careers, which includes promoting diversity within the nephrology workforce. ## Help fund travel to ASN educational activities for physicians and researchers training in the field of kidney disease. ## Use the ASN Grants Program to support outstanding research and foster career development. # Continue to bolster the ASN infrastructure, which includes: ## Increasing diversityincluding age and experience, ethnicity, and genderat all levels of the society. ## Providing avenues for helping ASN members facilitate professional exchange. ## Expanding ASN membership. ## Increasing the ASN Council-Designated Endowment Fund (independent of operational budget) to support grants and other priorities

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Cite this (Astrocyte Reactivity RNA-Seq Browser, RRID:SCR_015033)

URL: https://astrocyte.rnaseq.sofroniewlab.neurobio.ucla.edu

Resource Type: Resource, data or information resource, database

Database containing information about RNA-sequencing and astrocyte reactivity. Searching a gene through this engine provides differential expression data for various experimental conditions.

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    Atlas3D

Cite this (Atlas3D, RRID:SCR_001808)

URL: http://www.nesys.uio.no/Atlas3D/

Resource Type: Resource, data processing software, software application, data visualization software, software resource, atlas, data or information resource

A multi-platform visualization tool which allows import and visualization of 3-D atlas structures in combination with tomographic and histological image data. The tool allows visualization and analysis of the reconstructed atlas framework, surface modeling and rotation of selected structures, user-defined slicing at any chosen angle, and import of data produced by the user for merging with the atlas framework. Tomographic image data in NIfTI (Neuroimaging Informatics Technology Initiative) file format, VRML and PNG files can be imported and visualized within the atlas framework. XYZ coordinate lists are also supported. Atlases that are available with the tool include mouse brain structures (3-D reconstructed from The Mouse Brain in Stereotaxic Coordinates by Paxinos and Franklin (2001)) and rat brain structures (3-D reconstructed from The Rat Brain in Stereotaxic Coordinates by Paxinos and Watson (2005)). Experimental data can be imported in Atlas3D and warped to atlas space, using manual linear registration, with the possibility to scale, rotate, and position the imported data. This facilitates assignment of location and comparative analysis of signal location in tomographic images.

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Cite this (BAMS Neuroanatomical Ontology, RRID:SCR_004616)

URL: http://brancusi.usc.edu/bkms/bams-ontology.html

Resource Type: Resource, ontology, data or information resource, controlled vocabulary

BAMS Neuroanatomical Ontology is a lightweght ontology designed specifically for neuroscience. It contains a complete set of concepts that describe the structure of the rat CNS and a growing set of concepts that describe different neuron populations in the rat CNS.

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    BARD

Cite this (BARD, RRID:SCR_006283)

URL: http://bard.nih.gov/

Resource Type: Resource, data or information resource, database

Database that allows scientists without specialized training to effectively utilize Molecular Libraries Program (MLP) data. It allows the research community to utilize and develop new chemical probes to explore biological functions by building a central, permanently accessible link to all aspects of chemical biology data and analyses. The project is split into two basic segments, the first segment delivering functionality for a data dictionary, as well as assay protocol and data entry tools. The second builds a data warehouse for analysis and visualization, accessible through a public RESTful API. They will initially deploy two clients that will use this API - a web-based interface and a desktop application. Advanced access to data and the platforms will also be available to support plug-in development and the repackaging of data by others. Initially the project will focus on small molecule assays. Features: * allow scientists to annotate assay data using a common, shared language * provide facile access to data, integrating existing chemical biology and computational resources * enable meaningful analysis and interpretation of discovery data by the research community * support hypothesis generation for iterative probe- and drug-discovery projects * inform the entire small molecule discovery and development process

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Cite this (Berkeley-express, RRID:SCR_015990)

URL: http://bio.math.berkeley.edu/eXpress/index.html

Resource Type: Resource, data analysis software, data processing software, software application, sequence analysis software, software resource, software toolkit

THIS RESOURCE IS NO LONGER IN SERVICE. Documented January 29, 2018.
From website: "Note that the eXpress software is also no longer being developed. We recommend you use kallisto instead." Kallisto can be found at http://pachterlab.github.io/kallisto/.

Software for streaming quantification for high-throughput DNA/RNA sequencing.
Can be used in any application where abundances of target sequences need to be estimated from short reads sequenced from them.

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Cite this (BiGG Database, RRID:SCR_005809)

URL: http://bigg.ucsd.edu/

Resource Type: Resource, data or information resource, database

A knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. BiGG integrates several published genome-scale metabolic networks into one resource with standard nomenclature which allows components to be compared across different organisms. BiGG can be used to browse model content, visualize metabolic pathway maps, and export SBML files of the models for further analysis by external software packages. Users may follow links from BiGG to several external databases to obtain additional information on genes, proteins, reactions, metabolites and citations of interest.

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Cite this (Biomedical Resource Ontology, RRID:SCR_004443)

URL: http://www.ncbcs.org/biositemaps/

Resource Type: Resource, ontology, data or information resource, controlled vocabulary

A controlled terminology of resources, which is used to improve the sensitivity and specificity of web searches. It includes ''resource_type'', ''area of research'', and ''activity''. It is under development by a number of NIH-funded researchers who have a combined interest in classification of biomedical resources. The publication site for BRO is the BioPortal.

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    BioPSE

Cite this (BioPSE, RRID:SCR_014044)

URL: http://www.sci.utah.edu/cibc-research/highlights/24-research-highlights/cibc-highlights/221-scirun-biopse.html

Resource Type: Resource, software resource, software application, simulation software

A simulation software package which hosts a collection of algorithms used to run bioelectric field simulations inside of SCIRun. The software provided in the package may be used for geometric modeling, simulation, and visualization for solving bioelectric field problems.

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Cite this (Biospecimens/Biorepositories: Rare Disease-HUB (RD-HUB), RRID:SCR_004327)

URL: https://ncats.nih.gov/grdr/rdhub

Resource Type: Resource, biomaterial supply resource, data or information resource, material resource, database

A database of biospecimens collected, stored, and distributed by biorepositories in the United States and around the globe. Its goals are: To help and assist interested parties and investigators search, locate, and identify desired biospecimens needed for their research; to facilitate collaboration and sharing of material and data among investigators across the globe; to accelerate research to facilitate the discovery of new treatments, therapeutics and eventually cures for rare diseases as well as common diseases; to identify, locate and increase the awareness of existing biorepositories across the globe; and to link the RD-HUB with the Global Rare Diseases Patient Registry and Data Repository (GRDR).

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    BioStar

Cite this (BioStar, RRID:SCR_002580)

URL: http://www.biostars.org/

Resource Type: Resource, forum, discussion, narrative resource, portal, community building portal, data or information resource

A question answer forum for scientists, focusing on methods in bioinformatics, computational genomics and biological data analysis. They welcome detailed and specific posts, written clearly and simply.

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Cite this (Bio-Synthesis, RRID:SCR_000820)

URL: http://www.biosyn.com/

Resource Type: Resource, biomaterial supply resource, material resource

A commercial supplier of custom synthetic molecules. They specialize in peptides, oligonucleotides, bioconjugation, molecular biology services, proteins and specialty chemistry.

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