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http://www.nitrc.org/projects/bash-rs-fcmri

THIS RESOURCE IS NO LONGER IN SERVICE, documented July 23, 2015. Of note: most functions have been integrated in 1000 Functional Connectomes Project (www.nitrc.org/projects/fcon_1000). This package is not updated, thus please visit 1000 Functional Connectomes Project site and download relevant bash scripts. BASH Scripts for a resting-state functional MRI study. The functions include seed-based correlation analysis, amplitude analysis and independent component analysis. Note: this tool is just a plug-in for FSL, AFNI and FreeSurfer. Thus, you need have them before you use BASH4RfMRI.

Proper citation: BASH4RfMRI (RRID:SCR_005970) Copy   

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http://vbrc.org/index.asp

One of eight Bioinformatics Resource Centers nationwide providing comprehensive web-based genomics resources including a relational database and web application supporting data storage, annotation, analysis, and information exchange to support scientific research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. These centers serve the scientific community and conduct basic and applied research on microorganisms selected from the NIH/NIAID Category A, B, and C priority pathogens that are regarded as possible bioterrorist threats or as emerging or re-emerging infectious diseases. The VBRC provides a variety of analytical and visualization tools to aid in the understanding of the available data, including tools for genome annotation, comparative analysis, whole genome alignments, and phylogenetic analysis. Each data release contains the complete genomic sequences for all viral pathogens and related strains that are available for species in the above-named families. In addition to sequence data, the VBRC provides a curation for each virus species, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype, with special emphasis on pathogenesis.

Proper citation: VBRC (RRID:SCR_005971) Copy   

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http://brainvis.wustl.edu/wiki/index.php/Caret:About

Software package to visualize and analyze structural and functional characteristics of cerebral and cerebellar cortex in humans, nonhuman primates, and rodents. Runs on Apple (Mac OSX), Linux, and Microsoft Windows operating systems.

Proper citation: Computerized Anatomical Reconstruction and Editing Toolkit (RRID:SCR_006260) Copy   

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https://www.rndsystems.com/

An Antibody supplier who also provides assay services and products.

Proper citation: R and D Systems (RRID:SCR_006140) Copy   

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http://hfv.lanl.gov/content/index

The Hemorrhagic Fever Viruses (HFV) sequence database collects and stores sequence data and provides a user-friendly search interface and a large number of sequence analysis tools, following the model of the highly regarded and widely used Los Alamos HIV database. The database uses an algorithm that aligns each sequence to a species-wide reference sequence. The NCBI RefSeq database is used for this; if a reference sequence is not available, a Blast search finds the best candidate. Using this method, sequences in each genus can be retrieved pre-aligned. Hemorrhagic fever viruses (HFVs) are a diverse set of over 80 viral species, found in 10 different genera comprising five different families: arena-, bunya-, flavi-, filo- and togaviridae. All these viruses are highly variable and evolve rapidly, making them elusive targets for the immune system and for vaccine and drug design. About 55,000 HFV sequences exist in the public domain today. A central website that provides annotated sequences and analysis tools will be helpful to HFV researchers worldwide.

Proper citation: HFV Database (RRID:SCR_006017) Copy   

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http://ed.ted.com/

Video library of curated educational videos, many of which represent collaborations between talented educators and animators nominated through the TED-Ed platform. This platform also allows users to take any useful educational video, not just TED''s, and easily create a customized lesson around the video. Users can distribute the lessons, publicly or privately, and track their impact on the world, a class, or an individual student. TED-Ed''s videos aim to capture and amplify the voices of the world''s greatest educators.

Proper citation: TED-Ed (RRID:SCR_006138) Copy   

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http://sourceforge.net/projects/bless-ec/

Software tool for Bloom-filter-based error correction for next-generation sequencing (NGS) reads. The algorithm produces accurate correction results with much less memory.

Proper citation: BLESS (RRID:SCR_005963) Copy   

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http://cibsr.stanford.edu/tools/

A multiplatform, highly modular image processing and visualization application which is under development by the Center for Interdisciplinary Brain Sciences Research. The goal of this project is provide a framework application for neuroimaging which facilitates the interchange of software tools developed by researchers. BrainImageJava can: * Delineate ROIs in slices along X, Y, or Z axes, with 3D feedback in the other axes. * Create and display triangular mesh surfaces from MRI volumes. * Draw Surfaces-of-Interest (SOIs) in 3D, and edit them in a planar display. * Set Talairach grid on a volume, export an AC/PC stack, and measure the values within each grid unit. This 3D image processing and analysis program for the Apple Macintosh PowerPC is based on the public domain application, NIH Image. It includes interactive procedures for 3D MRI quantification including semi-automated procedures for removing non-brain tissues from images, fuzzy segmentation of tissue compartments, global or local parcellation (based on the Talairach atlas), region-growing, etc. The last version of the software included multiplatform capability, volume visualization and advanced image analysis tools.

Proper citation: BrainImage Software (RRID:SCR_006139) Copy   

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http://fungidb.org/fungidb/

FungiDB is a database for functional and evolutionary comparison of fungal genomes. FungiDB is a functional genomic resource for pan-fungal genomes that was developed in partnership with the Eukaryotic Pathogen Bioinformatic resource center (http://EuPathDB.org). FungiDB uses the same infrastructure and user interface as EuPathDB, which allows for sophisticated and integrated searches to be performed using an intuitive graphical system. The current release of FungiDB contains genome sequence and annotation from 18 species spanning several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal "Zygomycete" lineage Mucormycotina. Additionally, FungiDB contains cell cycle microarray data, hyphal growth RNA-sequence data and yeast two hybrid interaction data. The underlying genomic sequence and annotation combined with functional data, additional data from the FungiDB standard analysis pipeline and the ability to leverage orthology provides a powerful resource for in silico experimentation.

Proper citation: FungiDB (RRID:SCR_006013) Copy   

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http://cnas.ucr.edu/guppy/

A project that observes the processes of adaptive evolution in nature, and tests evolutionary hypotheses, by studying populations of guppies on the Caribbean island of Trinidad. Darwin thought that evolution by natural selection occurred very slowly, over hundreds if not thousands of years. Evolutionary biologists now know that evolutionary changes in species can happen very quickly, over a relatively few generations. The National Science Foundation (NSF), through its Integrative Biological Research (FIBR) program, is funding a 5-year study by 13 biologists from colleges, universities, and research institutions throughout the United States and Canada, to study the relationship of adaptive evolution and environmental circumstances. The Trinidadian guppy (Poecilia reticulata) is an excellent species for these purposes because: * It matures rapidly (one generation = 3-4 months) * It inhabits different ecological environments that can be easily manipulated On Trinidad, guppies live in streams, or portions of streams, that can differ in the species of predators that the guppies have to contend with. Some streams are high-predation environments, others low-predation. Different predation environments are often right next to one another, separated by a waterfall (which neither guppies nor predators can cross). Guppies from high-predation environments experience much higher mortality rates than do guppies in low-predation environments. High mortality is associated with the following characteristics, all of which have a genetic basis: * Earlier maturity * Greater investment of resources in reproduction * More and smaller offspring. We have found that mortality rates can be manipulated by: * Transplanting guppies from high-predation localities into sites from which they and their predators had previously been excluded by natural waterfalls, thus lowering mortality rates; * Introducing predators into low-predation sites, thus increasing mortality rates. Such experiments have shown that species evolve as predicted by theory. We have also found that evolution by natural selection can be remarkably fast, on the order of four to seven orders of magnitude faster than had been inferred from the fossil record.

Proper citation: Guppy Project (RRID:SCR_006255) Copy   

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http://web.mit.edu/Edgerton/www/HighSpeed.html

The MIT Edgerton Center carries on the legacy of Doc Edgerton''s research and teaching by providing the Institute with a continuing expertise in high-speed and scientific imaging. Our facilities include a large studio space, a photographic darkroom, and a digital imaging studio equipped with an array of scanners, digital cameras, printers and plotters, and Macintosh computers. In addition, we have several technical digital cameras, including: * Redlake MASD PCI Motionscope, monochrome high-speed video at up to 8,000 images per second. * Concurrent analog data acquisition via a National Instruments A/D card. * Midas 2.0 motion analysis software from Xcitex, Inc. * NAC Model color high-speed camera (in process of donation). * Redlake MASD Ektapro 1012 high-speed video, monochrome, up to 12,000 images per second. * Redlake MASD Megaplus 1.4i scientific still camera These systems are available for use by interested MIT researchers and instructors, and by students pursuing hands-on projects. Each summer we offer a week-long course on high-speed imaging through the MIT Professional Institute. This subject (6.51s) is designed for scientists, engineers, and photographers who need to gather data on rapidly moving subjects and events for study, motion analysis, and trouble-shooting. Mornings are spent in the lecture hall learning the fundamentals for lighting, imaging technologies, and motion analysis. Afternoons are spent making high-speed images in the laboratory. For MIT students, we offer the popular Strobe Project Lab (6.163) to 24 students each term, where students learn the fundamentals of high-speed imaging and apply these techniques to final projects of their own choosing. Two subjects are offered that investigate digital imaging and image manipulation, SP.757 in Fall terms, and SP.747 in Spring terms.

Proper citation: Edgerton Center High Speed Imaging (RRID:SCR_005960) Copy   

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http://jjwanglab.org:8080/gwasdb/

Combines collections of genetic variants (GVs) from GWAS and their comprehensive functional annotations, as well as disease classifications. Used to maximize utilility of GWAS data to gain biological insights through integrative, multi-dimensional functional annotation portal. In addition to all GVs annotated in NHGRI GWAS Catalog, we manually curate GVs that are marginally significant (P value < 10-3) by looking into supplementary materials of each original publication and provide extensive functional annotations for these GVs. GVs are manually classified by diseases according to Disease Ontology Lite and HPO (Human Phenotype Ontology) for easy access. Database can also conduct gene based pathway enrichment and PPI network association analysis for those diseases with sufficient variants. SOAP services are available. You may Download GWASdb SNP. (This file contains all of the significant SNP in GWASdb. In the pvalue column, 0 means this P-value is not reported in the study but it is significant SNP. In the source column, GWAS:A represents the original data in GWAS catalog, while GWAS:B is our curation data which P-value < 10-3)

Proper citation: GWASdb (RRID:SCR_006015) Copy   

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https://www.infrafrontier.eu/emma/

Non-profit repository for the collection, archiving (via cryopreservation) and distribution of relevant mutant strains essential for basic biomedical research. Users may browse by strain, gene, phenotype, or human disease. Its primary objective is to establish and manage a unified repository for maintaining medically relevant mouse mutants and making them available to the scientific community. Therefore, EMMA archives mutant strains and distributes them to requesting researchers. EMMA also hosts courses in cryopreservation, to promote the use and dissemination of frozen embryos and spermatozoa. Dissemination of knowledge is further fostered by a dedicated resource database. Anybody who wants their mutant mouse strains cryopreserved may deposit strains with EMMA. However depositors must be aware that these strains become freely available to other researchers after being deposited.With more than 8400 mutant mouse strains and asmall but increasing number of rat mutant strains available, EMMA is the primary mouse repository in Europe and the third largest non-profit repository worldwide.

Proper citation: European Mouse Mutant Archive (RRID:SCR_006136) Copy   

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http://www.fimre.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 7, 2022. Federation of International Mouse Resources (FIMRe) is a collaborating group of Mouse Repository and Resource Centers worldwide whose collective goal is to archive and provide strains of mice as cryopreserved embryos and gametes, ES cell lines, and live breeding stock to the research community. Goals of the Federation of International Mouse Resources: * Coordinate repositories and resource centers to: ** archive valuable genetically defined mice and ES cell lines being created worldwide ** meet research demand for these genetically defined mice and ES cell lines * Establish consistent, highest quality animal health standards in all resource centers * Provide genetic verification and quality control for genetic background and mutations * Provide resource training to enhance user ability to utilize cryopreserved resources

Proper citation: Federation of International Mouse Resources (RRID:SCR_006137) Copy   

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http://202.38.126.151:8080/SDisease/

Curated database of experimentally supported data of RNA Splicing mutation and disease. The RNA Splicing mutations include cis-acting mutations that disrupt splicing and trans-acting mutations that affecting RNA-dependent functions that cause disease. Information such as EntrezGeneID, gene genomic sequence, mutation (nucleotide substitutions, deletions and insertions), mutation location within the gene, organism, detailed description of the splicing mutation and references are also given. Users are able to submit new entries to the database. This database integrating RNA splicing and disease associations would be helpful for understanding not only the RNA splicing but also its contribution to disease. In SpliceDisease database, they manually curated 2337 splicing mutation disease entries involving 303 genes and 370 diseases, which have been supported experimentally in 898 publications. The SpliceDisease database provides information including the change of the nucleotide in the sequence, the location of the mutation on the gene, the reference PubMed ID and detailed description for the relationship among gene mutations, splicing defects and diseases. They standardized the names of the diseases and genes and provided links for these genes to NCBI and UCSC genome browser for further annotation and genomic sequences. For the location of the mutation, they give direct links of the entry to the respective position/region in the genome browser.

Proper citation: SpliceDisease (RRID:SCR_006130) Copy   

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http://www.stembase.ca

A publicly accessible database containing data on Affymetrix DNA microarray experiments, and Serial Analysis of Gene Expression, mostly on human and mouse stem cell samples and their derivatives to facilitate the discovery of gene functions relevant to stem cell control and differentiation. It has grown in both size and scope into a system with analysis tools that examine either the whole database at once, or slices of data, based on tissue type, cell type or gene of interest. There is currently more than 210 stem cell samples in 60 different experiments, with more being added regularly. The samples were originated by researchers of the Stem Cell Network and processed at the Core Facility of Stemcore Laboratories under the management of Ms. Pearl Campbell in the frame of the Stem Cell Genomics Project. Periodically, new expression data is submitted to the Gene Expression Omnibus (GEO) repository at the National Center for Biotechnological Information, in order to allow researchers to compare the data deposited in StemBase to a large amount of gene expression data sets. StemBase is different from GEO in both focus and scope. StemBase is concerned exclusively with stem cell related data. we are focused in Stem Cell research. We have made a significant effort to ensure the quality and consistency of the data included. This allows us to offer more specialized analysis tools related to Stem Cell data. GEO is intended as a large scale public archive. Deposition in a public repository such as GEO is required by most important scientific journals and it is advantageous for a further diffusion of the data since GEO is more broadly used than StemBase.

Proper citation: StemBase (RRID:SCR_006252) Copy   

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http://equilibrator.weizmann.ac.il/

Web interface designed for thermodynamic analysis of biochemical systems. eQuilibrator enables free-text search for biochemical compounds and reactions and provides thermodynamic estimates for both in a variety of conditions. It can provide estimates for compounds in the KEGG database, and individual compounds and enzymes can be searched for by their common names (water, glucosamine, hexokinase). Reactions can be entered in a free-text format that eQuilibrator parses automatically. eQuilibrator also allows manipulation of the conditions of a reaction - pH, ionic strength, and reactant and product concentrations.

Proper citation: eQuilibrator (RRID:SCR_006011) Copy   

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http://www.ddcf.org/

The mission of the Doris Duke Charitable Foundation is to improve the quality of people''s lives through grants supporting the performing arts, environmental conservation, medical research and the prevention of child abuse, and through preservation of the cultural and environmental legacy of Doris Duke''s properties. Established in 1996, the foundation supports four national grant-making programs. It also supports three properties that were owned by Doris Duke in Hillsborough, New Jersey; Honolulu, Hawaii; and Newport, Rhode Island. The foundation is headquartered in New York and is governed by a board of 12 Trustees. DDCF''s activities are guided by the will of Doris Duke, who endowed the foundation with financial assets that totaled approximately $1.6 billion as of December 31, 2010. The foundation regularly evaluates and modifies its allocation of resources from the endowment to support the programs and properties and to respond to fluctuations in portfolio returns. The foundation awarded its first grants in 1997. As of December 31, 2011, the foundation has awarded grants totaling more than $1 billion. DDCF awards grants in four core program areas: * The Arts Program supports performing artists with the creation and public performance of their work. * The Environment Program supports efforts that enable communities to protect and manage wildlife habitat and create efficient built environments. * The Medical Research Program seeks to contribute to the prevention and cure of disease by supporting clinical research. * The Child Abuse Prevention Program seeks to protect children from abuse and neglect in order to promote their healthy development. In the fall of 2007, DDCF also launched the African Health Initiative, with the goal of strengthening health systems in sub-Saharan Africa. The Building Bridges Program, which seeks to increase public understanding of Islamic cultures through media and the arts, is funded through the Doris Duke Foundation for Islamic Art and is headquartered in DDCF''s offices in New York. The Properties In her will, Doris Duke requested that several operating foundations manage the properties listed below. She also expressed her wishes that the properties be opened for public visitation and used for educational programs. The operating foundations receive funding from the Doris Duke Charitable Foundation. * The Duke Farms Foundation manages a 2,700-acre property in Hillsborough, New Jersey, which is known as Duke Farms and has a mission of environmental stewardship. * The Doris Duke Foundation for Islamic Art manages Doris Duke''s home in Honolulu, Hawaii, which is known as Shangri La and serves as a center for the study of Islamic art and cultures. * The Newport Restoration Foundation preserves historic houses in Newport, Rhode Island, and operates Doris Duke''s home in Newport known as Rough Point, which is also a public museum.

Proper citation: Doris Duke Charitable Foundation (RRID:SCR_006012) Copy   

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http://freesurfer.net/fswiki/HippocampalSubfieldSegmentation

A software package for automatic segmentation of hippocampal subfields in magnetic resonance imges. Given a pair of T1-weighted and T2-weighted images (the latter acquired using a protocol tuned for hippocampus imaging), ASHS will automatically label main subfields of the hippocampus, and some extra-hippocampal structures, using multi-atlas segmentation. The main method is described in the Yushkevich et al. 2011 Neuroimage paper (http://tinyurl.com/cffrp3p). * execution requires: Advanced Normalization Tools, FSL

Proper citation: Segmentation of Hippocampus Subfields (RRID:SCR_005996) Copy   

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

Ontology specifically for Randomized Controlled Trials in order to facilitate the production of systematic reviews and metaanalysis.

Proper citation: Randomized Controlled Trials Ontology (RRID:SCR_005992) Copy   

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