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https://www.mristudio.org/

An image processing program running under Windows suitable for such tasks as tensor calculation, color mapping, fiber tracking, and 3D visualization. Most of operations can be done with only a few clicks. This tool evolved from DTI Studio. Tools in the program can be grouped in the following way: * Image Viewer * Diffusion Tensor Calculations * Fiber Tracking and Editing * 3D Visualization * Image File Management * Region of Interesting (ROI) Drawing and Statistics * Image Registration

Proper citation: MRI Studio (RRID:SCR_001398) Copy   

•   Source: SciCrunch Registry

http://bmsr.usc.edu/software/pneuma/

A set of modules that are used to simulate the autoregulation of the cardiovascular and respiratory systems under conditions of changing sleep-wake state and a variety of physiological and pharmacological interventions. It models the dynamic interactions that take place among the various component mechanisms, including those involved in the chemical control of breathing, heart rate, and blood pressure, as well as the effects of changes in the sleep-wake state and arousal from sleep. PNEUMA includes the autonomic control of the cardiovascular system, chemoreflex and state-related control of breath-to-breath ventilation, state-related and chemoreflex control of upper airway potency, as well as respiratory and circulatory mechanics. The model is capable of simulating the cardiorespiratory responses to sleep onset, arousal, continuous positive airway pressure, the administration of inhaled carbon dioxide and oxygen, Valsalva and Mueller maneuvers, and Cheyne-Stokes respiration during sleep. In PNEUMA 3.0, we have extended the existing integrative model of respiratory, cardiovascular, and sleepwake state control, to incorporate a sub-model of glucoseinsulinfatty acid regulation. The extended model is capable of simulating the metabolic control of glucoseinsulin dynamics and its interactions with the autonomic nervous system. The interactions between autonomic and metabolic control include the circadian regulation of epinephrine secretion, epinephrine regulation on dynamic fluctuations in glucose and free fatty acids in plasma, metabolic coupling among tissues and organs mediated by insulin and epinephrine, as well as the effect of insulin on peripheral vascular sympathetic activity. This extended model represents a starting point from which further in silico investigations into the interaction between the autonomic nervous system and the metabolic control system can proceed. Features in PNEUMA 3.0 * Incorporates metabolic component based on prior models of glucose-insulin regulation and free fatty acid (FFA) regulation. * Changes in sympathetic activity from the autonomic portion of PNEUMA produce changes in epinephrine output, which in turn affects the metabolic sub-model. * Inputs from the dietary intake of glucose and external interventions, such as insulin injections, have also been incorporated. * Also incorporated is autonomic feedback from the metabolic component to the rest of PNEUMA: changes in insulin level lead to changes in sympathetic tone. System Requirements: PNEUMA requires Matlab R2007b or higher with the accompanying version of Simulink to be installed on your computer.

Proper citation: PNEUMA (RRID:SCR_001391) Copy   

•   Source: SciCrunch Registry

http://slicer.org/

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.

Proper citation: 3D Slicer (RRID:SCR_005619) Copy   

•   Source: SciCrunch Registry

http://www.patternlabforproteomics.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented July 5, 2018. Gene Ontology Explorer (GOEx) combines data from protein fold changes with GO over-representation statistics to help draw conclusions in proteomic experiments. It is tightly integrated within the PatternLab for Proteomics project and, thus, lies within a complete computational environment that provides parsers and pattern recognition tools designed for spectral counting. GOEx offers three independent methods to query data: an interactive directed acyclic graph, a specialist mode where key words can be searched, and an automatic search. A recent hack included in GOEx is to load the sparse matrix index file directly into GOEx, instead of going through the report generation using the AC/T-fold methods. This makes it easy for GOEx to analyze any list of proteins as long as the list follows the index file format (described in manuscript) . Please note that if using this alternative strategy, there will be no protein fold information. Platform: Windows compatible

Proper citation: GOEx - Gene Ontology Explorer (RRID:SCR_005779) Copy   

•   Source: SciCrunch Registry

https://proteomecommons.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A public resource for sharing general proteomics information including data (Tranche repository), tools, and news. Joining or creating a group/project provides tools and standards for collaboration, project management, data annotation, permissions, permanent storage, and publication.

Proper citation: Proteome Commons (RRID:SCR_006234) Copy   

•   Source: SciCrunch Registry

http://www.genenetwork.org/

Web platform that provides access to data and tools to study complex networks of genes, molecules, and higher order gene function and phenotypes. Sequence data (SNPs) and transcriptome data sets (expression genetic or eQTL data sets). Quantitative trait locus (QTL) mapping module that is built into GN is optimized for fast on-line analysis of traits that are controlled by combinations of gene variants and environmental factors. Used to study humans, mice (BXD, AXB, LXS, etc.), rats (HXB), Drosophila, and plant species (barley and Arabidopsis). Users are welcome to enter their own private data.

Proper citation: GeneNetwork (RRID:SCR_002388) Copy   

•   Source: SciCrunch Registry

http://www.macaque.org/

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.. Documented on June 8, 2020.Macaque genomic and proteomic resources and how they are providing important new dimensions to research using macaque models of infectious disease. The research encompasses a number of viruses that pose global threats to human health, including influenza, HIV, and SARS-associated coronavirus. By combining macaque infection models with gene expression and protein abundance profiling, they are uncovering exciting new insights into the multitude of molecular and cellular events that occur in response to virus infection. A better understanding of these events may provide the basis for innovative antiviral therapies and improvements to vaccine development strategies.

Proper citation: Macaque.org (RRID:SCR_002767) Copy   

•   Source: SciCrunch Registry

http://loni.usc.edu/Software/

Portal provides list of software resources. LONI is leader in development of advanced computational algorithms and software for comprehensive and quantitative mapping of brain structure and function. Aims to encourage communication between users and LONI software engineers in order to improve effectiveness.

Proper citation: University of Southern California LONI Software (RRID:SCR_002802) Copy   

•   Source: SciCrunch Registry

http://www.loni.usc.edu/Software/FFT

Java library used for the execution of discrete Fourier transforms in 1-D, 2-D and 3-D through the implementation of Fast Fourier Transform (FFT) algorithms. * The FFT library has been written in Java for portability across different platforms, integrated into a single jar file for easy implementation. * The FFT library provides forward and backward fast Fourier transforms in 1-D, 2-D and 3-D with an easy-to-use manner. * The FFT requires the length equal to a number with an integer power of two. This library automatically examines the input data and detects the length to prevent improper execution.

Proper citation: FFT Library (RRID:SCR_002698) Copy   

•   Source: SciCrunch Registry

http://www.LONI.usc.edu/Software/ShapeViewer

Java-based geometry viewer that supports file formats used by Center for Computational Biology (CCB) researchers and provides necessary viewing functions. ShapeViewer uses ShapeTools library support to read and display LONI Ucf, VTX XML, FreeSurfer, Minc Obj (both binary and ascii), Open Dx, Gifti, and OFF format data files.

Proper citation: LONI ShapeViewer (RRID:SCR_002695) Copy   

•   Source: SciCrunch Registry

http://www.loni.usc.edu/Software/SHIVA

A Java-based visualization and analysis application that can process 2D and 3D image files and provides convenient methods for users to overlay multiple datasets. * Simultaneous visualization of multiple image volumes. * Tools for labeling and masking of structures. * Framework for the Mouse Atlas Project.

Proper citation: Synchronized Histological Image Viewing Architecture (RRID:SCR_002690) Copy   

•   Source: SciCrunch Registry

http://www.mmrrc.org/

National public repository system for mutant mice. Archives and distributes scientifically valuable spontaneous and induced mutant mouse strains and ES cell lines for use by biomedical research community. Includes breeding/distribution facilities and information coordinating center. Mice strains are cryopreserved, unless live colony must be established. Live mice are supplied from production colony, from colony recovered from cryopreservation, or via micro-injection of cell line into host blastocysts. MMRRC member facilities also develop technologies to improve handling of mutant mice, including advances in assisted reproductive techniques, cryobiology, genetic analysis, phenotyping and infectious disease diagnostics.

Proper citation: Mutant Mouse Resource and Research Center (RRID:SCR_002953) Copy   

•   Source: SciCrunch Registry

http://www.ambystoma.org/

Portal that supports Ambystoma-related research and educational efforts. It is composed of several resources: Salamander Genome Project, Ambystoma EST Database, Ambystoma Gene Collection, Ambystoma Map and Marker Collection, Ambystoma Genetic Stock Center, and Ambystoma Research Coordination Network.

Proper citation: Sal-Site (RRID:SCR_002850) Copy   

•   Source: SciCrunch Registry

http://www.ncrr.nih.gov/clinical_research_resources/resource_directory/general_clinical_research_centers/program_information/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. Through the General Clinical Research Centers (GCRC) program, NCRR funds a national network that provides settings for medical investigators to conduct safe, controlled, state-of-the-art, in-patient and out-patient studies of both children and adults. GCRCs also provide infrastructure and resources that support several career development opportunities.

Proper citation: General Clinical Research Centers Program (RRID:SCR_002847) Copy   

•   Source: SciCrunch Registry

http://www.jax.org/smsr/index.html

Resource of special strains of mice that are valuable tools for genetic analysis of complex diseases. They include panels of recombinant inbred (RI) and chromosome substitution (CS) strains.

Proper citation: Special Mouse Strains Resource (RRID:SCR_002885) Copy   

•   Source: SciCrunch Registry

http://www.ouhsc.edu/compmed/documents/DevelopmentofaSpecificPathogenFreeBaboonColony.pdf

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. Program developing a self-sustaining colony of baboons free of all known herpesviruses, four retroviruses, and SV40 for research. When the program is fully developed, they will provide healthy, behaviorally normal, SPF baboons that are free of all known herpes viruses, four retroviruses, and SV40. To accomplish this goal, the center has established in collaboration with co-investigators and consultants serological and PCR tests for each of the 11 target viruses. These baboon viruses include six herpesviruses (analogs of human HSV, VZV, CMV, HHV6, EBV, and HHV8), four retroviruses (simian foamy virus, SRV/D, SIV, and STLV), and SV40. Twenty-four infant baboons are being recruited into the SPF program in each of the first five years, for a final total of at least 66 SPF baboons. All infants will be repeatedly tested for each of the target viruses. At one month of age, larger social groups of 4-6 SPF animals are formed. Beginning at 2-3 years of age, SPF animals will be integrated into larger socially compatible groups. These groups will eventually mature into breeding harems of SPF animals. This approach provides infants with age-matched companions for socialization during their early period of development, minimizes opportunities for transmission of viruses to the infants from adult animals, and allows for the simultaneous elimination of many different viruses from SPF animals.

Proper citation: Development of a Specific-Pathogen-Free Baboon Colony (RRID:SCR_002900) Copy   

•   Source: SciCrunch Registry

http://www.jax.org/imr/index.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 08, 2012. The function of the IMR is to select, import, cryopreserve, maintain, and distribute these important strains of mice to the research community. To improve their value for research, the IMR also undertakes genetic development of stocks, such as transferring mutant genes or transgenes to defined genetic backgrounds and combining transgenes and/or targeted mutations to create new mouse models for research. The function of the IMR is to: * select biomedically important stocks of transgenic, chemically induced, and targeted mutant mice * import these stocks into the Jackson Laboratory by rederivation procedures that rid them of any pathogens they might carry * cryopreserve embryos from these stocks to protect them against accidental loss and genetic contamination * backcross the mutation onto an inbred strain, if necessary * distribute them to the scientific community More than 1000 mutant stocks have been accepted by the IMR from 1992 through December 2006. Current holdings include models for research on cancer; breast cancer; immunological and inflammatory diseases; neurological diseases; behavioral, cardiovascular and heart diseases; developmental, metabolic and other diseases; reporter (e.g., GFP) and recombinase (e.g., cre/loxP) strains. About eight strains a month are being added to the IMR holdings. Research is being conducted on improved methods for assisted reproduction and speed congenic production. Most of the targeted mutants arrive on a mixed 129xC57BL/6 genetic background, and as many of these as possible are backcrossed onto an inbred strain (usually C57BL/6J). In addition, new mouse models are being created by intercrossing carriers of specific transgenes and/or targeted mutations. Simple sequence length polymorphism DNA markers are being used to characterize and evaluate differences between inbred strains, substrains, and embryonic stem cell lines.

Proper citation: Induced Mutant Resource (RRID:SCR_008366) Copy   

•   Source: SciCrunch Registry

http://www.loni.usc.edu/Software/jViewbox

A portable software framework for medical imaging research. jViewbox consists of a set of Java classes organized under a simple but extensive API that provides the core functionality of 2D image presentation needed by most imaging applications. It follows Java's Swing model closely to make it easy for application developers to build GUIs where end users can use various tools in a tool bar to manipulate the image displays. No optional add-ons or native code is used, which makes jViewBox compatible with any standard Java 2 Runtime Environment (version 1.3 or later).

Proper citation: jViewbox (RRID:SCR_008274) Copy   

•   Source: SciCrunch Registry

http://www.ctspedia.org/do/view/CTSpedia

CTSpedia is a national effort to collect wisdom, tools, educational materials, and other items useful for clinical and translational researchers and to provide timely and useful advice to clinical and translational researchers with specific problems. The CTSpedia is a collaborative vehicle for the CTSA''s Biostatistics/Epidemiology/Research/Design (BERD) Online Resources and Education taskforce to identify and share resources across the national consortium and community researchers world-wide. With the support of the national BERD consortia, the project obtained funding and support from the National Center for Research Resources (NCRR) to expand the original scope and content of CTSpedia and foster collaboration amongst CTSAs. The main goal of CTSpedia.org is to create a definable academic home on the internet for the discipline of clinical and translational sciences across the country and the world. * While the CTSA consortium serves the onsite physical level of the institutions involved, CTSpedia.org seeks to fill the gaps where the network is lacking, and to augment that network as the central hub for the peer to peer sharing of knowledge and resources. * While the CTSA national scope comes to fruition, the international scope of the consortia is more readily facilitated with an online resource like CTSpedia. * Utilizing the collaborative nature of the wiki-style website, CTSpedia.org allows for researchers anywhere in the world to ask questions and receive answers and related information in a timely and efficient manner, overcoming the logistical issues of distance and scheduling. * The streamlined availability of an online resource and knowledge repository will aid in addressing common issues that arise in clinical research, which will filter out consultation requests for minor questions, allowing for CTSA consultants to address more prevalent consultations.

Proper citation: CTSpedia (RRID:SCR_008733) Copy   

•   Source: SciCrunch Registry

http://meme.nbcr.net/meme/cgi-bin/gomo.cgi

Gene Ontology for Motifs (GOMO) is an alignment- and threshold-free comparative genomics approach for assigning functional roles to DNA regulatory motifs from DNA sequence. The algorithm detects associations between a user-specified DNA regulatory motif (expressed as a position weight matrix; PWM) and Gene Ontology terms. The original method for predicting the roles of transcription factors (TFs starts with a PWM motif describing the DNA-binding affinity of the TF. GOMO uses the PWM to score the promoter region of each gene in the genome for its likelihood to be bound by the TF. The resulting ''''affinity'''' scores are then used to test each term in the Gene Ontology for association with high-scoring genes. The algorithm was subsequently extended to leverage conserved signals using multiple, related species in a comparative approach, which greatly improves the resulting annotations. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: GOMO - Gene Ontology for Motifs (RRID:SCR_008864) Copy   

•   Source: SciCrunch Registry