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http://users.loni.ucla.edu/~shattuck/brainsuite/

Suite of image analysis tools designed to process magnetic resonance images (MRI) of the human head. BrainSuite provides an automatic sequence to extract genus-zero cortical surface mesh models from the MRI. It also provides a set of viewing tools for exploring image and surface data. The latest release includes graphical user interface and command line versions of the tools. BrainSuite was specifically designed to guide its users through the process of cortical surface extraction. NITRC has written the software to require minimal user interaction and with the goal of completing the entire process of extracting a topologically spherical cortical surface from a raw MR volume within several minutes on a modern workstation. The individual components of BrainSuite may also be used for soft tissue, skull and scalp segmentation and for surface analysis and visualization. BrainSuite was written in Microsoft Visual C using the Microsoft Foundation Classes for its graphical user interface and the OpenGL library for rendering. BrainSuite runs under the Windows 2000 and Windows XP Professional operating systems. BrainSuite features include: * Sophisticated visualization tools, such as MRI visualization in 3 orthogonal views (either separately or in 3D view), and overlayed surface visualization of cortex, skull, and scalp * Cortical surface extraction, using a multi-stage user friendly approach. * Tools including brain surface extraction, bias field correction, voxel classification, cerebellum removal, and surface generation * Topological correction of cortical surfaces, which uses a graph-based approach to remove topological defects (handles and holes) and ensure a tessellation with spherical topology * Parameterization of generated cortical surfaces, minimizing a harmonic energy functional in the p-norm * Skull and scalp surface extraction

Proper citation: BrainSuite (RRID:SCR_006623) Copy   

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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   

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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   

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http://intramural.nimh.nih.gov/

The Division of Intramural Research Programs (DIRP) at the National Institute of Mental Health (NIMH) is the internal research division of the NIMH. NIMH DIRP scientists conduct research ranging from studies into mechanisms of normal brain function, conducted at the behavioral, systems, cellular, and molecular levels, to clinical investigations into the diagnosis, treatment and prevention of mental illness. Major disease entities studied throughout the lifespan include mood disorders and anxiety, schizophrenia, obsessive-compulsive disorder, attention deficit hyperactivity disorder, and pediatric autoimmune neuropsychiatric disorders. Because of its outstanding resources, unique funding mechanisms, and location in the nation''s capital, the DIRP is viewed as a national resource, providing unique opportunities in mental health research and research training. Training is conducted in all the Institute''s clinical branches and basic neuroscience laboratories located on the 305-acre National Institutes of Health campus in Bethesda, Maryland. In addition to individualized trainee/mentor-driven postdoctoral training opportunities in the clinical and basic sciences, the DIRP offers Postbaccalaureate Research Training Awards, a Clinical Electives Program, as well as a variety of Summer Research Fellowships and an Undergraduate Internship Program. The mission of the division is to plan and conduct basic, clinical, and translational research to advance understanding of the diagnosis, causes, treatment, and prevention of mental disorders through the study of brain function and behavior; conduct state-of-the-art research that, in part, complements extramural research activities and exploits the special resources of the National Institutes of Health; and provide an environment conducive to the training and development of clinical and basic scientists. In addition the DIRP fosters standards of excellence in the ethical treatment and the provision of clinical care to research subjects; serve as a resource to the NIMH in responding to requests made by the Administration, members of Congress, and citizens'' groups for information regarding mental disorders; and analyzes and evaluates national needs and research opportunities and provides advice to the Institute Director on matters of scientific interest. Core Facilities: * Functional MRI Core * Magnetic Resonance Core * Magnetoencephalography Core * Microarray Core * Neurophysiology Imaging Facility * Non-Human Primate Core * Scientific and Statistical Computing Core * Section on Instrumentation Core * Transgenic Core * Veterinary Medicine Resources

Proper citation: NIMH Division of Intramural Research Programs (RRID:SCR_006860) Copy   

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http://sourceforge.net/projects/fitgcp/

Software providing a framework for fitting mixtures of probability distributions to genome coverage profiles.

Proper citation: fitGCP (RRID:SCR_006741) Copy   

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http://www.ncrr.nih.gov/comparative_medicine/resource_directory/primates.asp

THIS RESOURCE IS NO LONGER IN SERVICE, documented on October 16, 2013. NCRR has been absorbed into other parts of the National Institutes of Health. This organizational structure is no longer available. Provides laboratory scientists and clinical researchers with the resources and tools they need to understand, detect, treat and prevent a wide range of diseases. Animal models, such as nonhuman primates, are a critical component of biomedical research, having profound implications for public health. Scientists depend on laboratory animals and other nonhuman models for investigating biological processes, studying the causes of diseases and testing promising new therapies. Nonhuman primates, in particular, are important for translational research because of their close physiological similarities to humans. They enable discoveries that have direct application to human studies, bridging the gap between basic science and human medicine. Discoveries in animal models are helping scientists test treatments for human conditions such as drug addiction, obesity, malaria, HIV/AIDS and neurodegenerative diseases, accelerating the pace at which these research advances can be translated into treatments for patients. Through its Division of Comparative Medicine, NCRR offers a wide variety of primate resources for NIH-funded scientists across the nation. Additionally, funding opportunities are available to National Primate Research Centers. Eight National Primate Research Centers (NPRCs) located throughout the country provide animals, facilities and expertise in all aspects of nonhuman primate biology and husbandry. These facilities and resources enable collaborative research among NPRC staff scientists, investigators from the NPRC host institution and other NIH-funded researchers. Major areas of research benefiting from the primate centers include AIDS, avian flu, Alzheimer''s disease, Parkinson''s disease, diabetes, asthma and endo-metriosis. The centers????????????????? specialized resources are intended to support investigators who receive their primary research project funding from NIH, but they also may be used by investigators who are funded by other federal, state and local agencies, as well as by research foundations and the private sector. Together the primate centers have more than 28,000 nonhuman primates of 20 different species. This portal covers the following topics: * National Primate Research Centers * Monkey Research Resources * Chimpanzee Research Resources * Chimpanzee Management Program * Specific-Pathogen-Free Macaque Resources * Nonhuman Primate Research Reagents

Proper citation: National Center for Research Resources - Primate Resources (RRID:SCR_006863) Copy   

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https://itunes.apple.com/us/app/avor/id497245573?mt=8

A teaching, training and test tool app, designed for both iPhone and iPad, for the vestibulo-ocular reflex (VOR) system and its disorders, including Benign paroxysmal positional vertigo (BPPV). It demonstrates eye saccades, including those caused by canalithiasis (free-floating particles in the canals), and both functioning and dysfunctional VOR. It shows how BPPV is caused and treated. aVOR demonstrates how head movement has an automatic influence on eye direction, the impact of dysfunction of the semicircular canals, their size, shape and location in the head, and the causes of nystagmus. The application includes a Test Mode which presents the symptoms of various types of VOR dysfunction for the student to diagnose. It is designed for college-level neuropsychology students and medical professionals, and incorporates the latest research. Compatible with iPhone, iPod touch, and iPad. Requires iOS 3.2 or later Languages: English, Chinese, German, Italian, Japanese, Russian, Spanish

Proper citation: aVOR (RRID:SCR_006857) Copy   

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http://www.brainvoyager.com/products/braintutor.html

A free award-winning educational program that teaches you knowledge about the human brain through interactive exploration of rotatable 3D models. The models have been computed with BrainVoyager QX using original data from magnetic resonance imaging (MRI) scans. Besides having fun with the rotatable 3D models, the program contains information about the major lobes, gyri, sulci and Brodmann areas of the cerebral cortex. The program runs on Windows XP, Vista and Windows 7.

Proper citation: BrainVoyager Brain Tutor (RRID:SCR_006737) Copy   

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http://cancercontrol.cancer.gov/tcrb/tturc/

A transdisciplinary approach to the full spectrum of basic and applied research on tobacco use to reduce the disease burden of tobacco use, including: * Etiology of tobacco use and addiction * Impact of advertising and marketing * Prevention of tobacco use * Treatment of tobacco use and addiction * Identification of biomarkers of tobacco exposure * Identification of genes related to addiction and susceptibility to harm from tobacco Goals * Increase the number of investigators from relevant disciplines who focus on the study of tobacco use as part of transdisciplinary teams. * Generate basic research evidence to improve understanding of the etiology and natural history of tobacco use. * Produce evidence-based tobacco use interventions that can translate to the community and specific understudied or underserved populations. * Increase the number of evidence-based interventions that are novel, including the development, testing and dissemination of innovative behavioral treatments and prevention strategies based upon findings from basic research. * Train transdisciplinary investigators capable of conducting cutting-edge tobacco use research. * Increase the number of peer-reviewed publications in the areas of tobacco use, nicotine addiction, and treatment.

Proper citation: Transdisciplinary Tobacco Use Research Centers (RRID:SCR_006858) Copy   

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http://www.niehs.nih.gov/research/resources/software/biostatistics/eagleview/

An information-rich viewer for next-generation genome assembles with data integration capability. EagleView can display a dozen different types of information including base qualities, machine specific trace signals, and genome feature annotations. It provides an easy way for inspecting visually the quality of a genome assembly and validating polymorphism candidate sites (e.g., SNPs) reported by polymorphism discovery tools. It can also facilitate data interpretation and hypothesis generation. EagleView is a multi-platform application developed with C++ and is available for all three major platforms: Windows, Linux, and Mac OS.

Proper citation: EagleView (RRID:SCR_006859) Copy   

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https://github.com/uclinfectionimmunity/Decombinator

Software suite for analysis of T cell receptor repertoire data. Used for fast, efficient analysis of T cell receptor (TcR) repertoire samples, designed to be accessible to those with no previous programming experience.

Proper citation: Decombinator (RRID:SCR_006732) Copy   

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http://www.treat-nmd.eu/

TREAT-NMD is a network for the neuromuscular field that is creating the infrastructure to ensure that the most promising new therapies reach patients as quickly as possible. Since its launch in January 2007 the network''s focus has been on the development of tools that industry, clinicians and scientists need to bring novel therapeutic approaches through preclinical development and into the clinic, and on establishing best-practice care for neuromuscular patients worldwide.

Proper citation: Treat-NMD (RRID:SCR_006612) Copy   

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http://csbio-linux001.cs.unc.edu/nextgen/software/FDM/

A graph-based statistical method to detect differential transcription using RNA-seq data.

Proper citation: FDM (RRID:SCR_006733) Copy   

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http://www.millenniumcohort.org/

The Millennium Cohort Study is the largest prospective health project in military history. It is designed to evaluate the long-term health effects of military service, including deployments. The Department of Defense recognized after the 1991 Gulf War that there was a need to collect more information about the long-term health of service members. The Millennium Cohort Study was designed to address that critical need, and the study was launched by 2001. Funded by the Department of Defense, and supported by military, Department of Veterans Affairs, and civilian researchers, almost 150,000 people are already participating in this groundbreaking study. As force health protection continues to be a priority for the future of the United States military, the Millennium Cohort Study will be providing critical information towards enhancing the long-term health of future generations of military members. Participants include Panel 1 (enrolled beginning in 2001), Panel 2 (enrolled beginning in 2004), and Panel 3 (enrolled beginning in 2007). A Panel 4 will be invited to participate throughout the upcoming survey cycle, and we expect to have over 200,000 participants total upon completion of the cycle. Participants are asked to complete one questionnaire (by mail or online) every three years, through 2022.

Proper citation: Millenium cohort study (RRID:SCR_006854) Copy   

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http://www.hematology.org/

The American Society of Hematology (ASH) is the world''s largest professional society concerned with the causes and treatments of blood disorders. The mission of the Society is to further the understanding, diagnosis, treatment, and prevention of disorders affecting the blood, bone marrow, and the immunologic, hemostatic and vascular systems, by promoting research, clinical care, education, training, and advocacy in hematology.

Proper citation: American Society of Hematology (RRID:SCR_006734) Copy   

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http://www.bioconductor.org/packages/2.14/bioc/html/htSeqTools.html

Software tools for quality control, visualization and processing for High-Throughput Sequencing data. These include MDS plots (analogues to PCA), detecting inefficient immuno-precipitation or over-amplification artifacts, tools to identify and test for genomic regions with large accumulation of reads, and visualization of coverage profiles.

Proper citation: htSeqTools (RRID:SCR_006614) Copy   

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https://simonsfoundation.org/

The Simons Foundation is a private foundation based in New York City, incorporated in 1994 by Jim and Marilyn Simons. The Simons Foundation''s mission is to advance the frontiers of research in mathematics and the basic sciences. We sponsor a range of programs that aim to promote a deeper understanding of our world. The primary focus of the foundation''s Mathematics & the Physical Sciences (MPS) program is on the theoretical sciences radiating from mathematics: in particular, the fields of mathematics, theoretical computer science and theoretical physics. Although we have supported basic research in mathematics and physics for years at institutions around the globe, the mode of our support entered an important new phase in fall 2009 with the introduction of grant opportunities with open application procedures. It is intended that this will become our primary mode of operation. In 2010, the MPS program issued its first requests for grant applications. These requests offered grants to establish post-doctoral fellowships, grants to promote collaboration between researchers, grants to create professorships that combine mathematics with other fields, and a grant to endow an institute for theoretical computer science. Other projects are under way, including the Africa Mathematics Project, intended to bolster mathematics scholarship on the African continent, and an oral history project: a series of interviews with renowned mathematicians and scientists which will be made available to the public for viewing. The Simons Foundation''s initial support of life sciences work has tended to focus on research that promotes synergy between biology and mathematics. Such projects have included quantitative biology programs at Cold Spring Harbor Laboratory, the Institut des Hautes ��tudes Scientifiques, the Institute for Advanced Study, and The Rockefeller University. The Life Sciences program is expected to expand in scope over the next two to three years. To date, the Simons Foundation''s single largest initiative has been in autism research. The Simons Foundation Autism Research Initiative (SFARI) program seeks to improve the diagnosis and treatment of autism spectrum disorders by funding, catalyzing, and driving innovative research of the greatest quality and relevance. In 2007, SFARI issued its first Request for Applications, its goal being to attract the best researchers to the field. In the years since, SFARI has given grants to 150 investigators in the United States and abroad. Additionally, to facilitate the field as a whole, SFARI has created the Simons Simplex Collection of extensive genetic and phenotypic data from almost 3,000 families with a child affected by autism. Although SFARI''s immediate priority is to benefit individuals challenged by autism spectrum disorders, the program''s research is expected to yield insights into the neural mechanisms of fundamental human capabilities, complementing the mission of the Simons Foundation to advance research in the basic sciences and mathematics.

Proper citation: Simons Foundation (RRID:SCR_006735) Copy   

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http://garm-meta-assem.sourceforge.net/

A new software pipeline to merge and reconcile assemblies from different algorithms or sequencing technologies.

Proper citation: GARM (RRID:SCR_006731) Copy   

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https://www.pblassaysci.com/

An Antibody supplier

Proper citation: PBL Assay Science (RRID:SCR_006852) Copy   

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http://dgidb.genome.wustl.edu/

A database of drug-gene relationships that provides drug-gene interactions and potential druggability data given list of genes. There are about 15 data sources that are being aggregated by DGIdb, with update date and these data sources are listed on this page: http://dgidb.genome.wustl.edu/sources, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: DGIdb (RRID:SCR_006608) Copy   

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