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http://www.ccp4.ac.uk/

Portal for Macromolecular X-Ray Crystallography to produce and support an integrated suite of programs that allows researchers to determine macromolecular structures by X-ray crystallography, and other biophysical techniques. Used in the education and training of scientists in experimental structural biology for determination and analysis of protein structure.

Proper citation: CCP4 (RRID:SCR_007255) Copy   

•   Source: SciCrunch Registry

http://www.cmrr.umn.edu/stimulate

An fMRI analysis software package with a GUI (Graphical User Interface) front end. Stimulate offers a comprehensive set of fMRI analysis tools integrated into a single package for convenient and flexible data processing. Users can point and click with the mouse to modify analysis or display variables. Activation maps can be calculated from the fMRI data and overlaid onto structural MRI image displays.

Proper citation: Stimulate (RRID:SCR_007375) Copy   

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http://www.bitplane.com/imaris/imaris

Imaris provides range of capabilities for working with three dimensional images. Uses flexible editing and processing functions, such as interactive surface rendering and object slicing capabilities. And output to standard TIFF, Quicktime and AVI formats. Imaris accepts virtually all image formats that are used in confocal microscopy and many of those used in wide-field image acquisition. Imaris version 10.1 for image analysis workflows using AI trainable object detection.

Proper citation: Imaris (RRID:SCR_007370) Copy   

•   Source: SciCrunch Registry

http://pbil.univ-lyon1.fr/cap3.php

This form allows you to assemble a set of contiguous sequences (contigs) with the CAP3 program. The CAP3 program has a capability to clip 5'' and 3'' low-quality regions of reads. It uses base quality values in computation of overlaps between reads, construction of multiple sequence alignments of reads, and generation of consensus sequences. The program also uses forward-reverse constraints to correct assembly errors and link contigs. Results of CAP3 on four BAC data sets are presented. The performance of CAP3 was compared with that of PHRAP on a number of BAC data sets. PHRAP often produces longer contigs than CAP3 whereas CAP3 often produces fewer errors in consensus sequences than PHRAP. It is easier to construct scaffolds with CAP3 than with PHRAP on low-pass data with forward-reverse constraints. Sponsors: This project was supported by NIH Grant R01HG01502-02 from NHGRI. Keywords: CAP3, Program, Form, Computation, DNA, Dataset, Database, Program,, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CAP3 Sequence Assembly Program (RRID:SCR_007250) Copy   

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http://mipav.cit.nih.gov

A Java-based application that enables quantitative analysis and visualization of medical images of numerous modalities such as DTI, PET, MRI, CT, or microscopy. Using MIPAV's standard user-interface and analysis tools, researchers at remote sites (via the internet) can easily share research data and analyses, thereby enhancing their ability to research, diagnose, monitor, and treat medical disorders. MIPAV can be run on any Java-enabled platform such as Windows, UNIX, or Macintosh OS X. Functionality includes segmentation, inter- and intra multi-modality registration, surface rendering, volume rendering and reading and writing a large number of biomedical file formats including: DICOM 3.0, Analyze, NIFTI, SPM, MINC, Phillips, GE, Zeiss, Biorad, jpeg, png, tiff, mrc, fits, interfile, and many more.

Proper citation: MIPAV: Medical Image Processing and Visualization (RRID:SCR_007371) Copy   

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http://www.CanDRIVE.ca

Candrive''s aim is to improve the health, safety and quality-of-life of Canada''s older drivers. Candrive''s vision is to establish a national multi-disciplinary collaborative approach to identify, analyze and examine the issues pertaining to the safe operation of vehicles by older persons. One of the goals of the Candrive research program is to find a way to extend the length of time that older drivers can drive. Candrive will examine both the effectiveness of retraining programs and the use of customized or restricted licensing for older drivers who might automatically have had their licence revoked. Unfortunately, even if such measures prove useful, there will still be a small minority of older drivers who are no longer safe to drive. By identifying this minority as early as possible, the program will help protect the reputation, public image and rights of the majority of older drivers who represent the safest and most experienced drivers on the road. Sponsors: This resource is supported by a Team Grant from the Canadian Institutes of Health Research (CIHR). Candrive also receives support from the Ottawa Hospital Research Institute. Keywords: Health, Safety, Analysis, Vehicle, Driver,

Proper citation: Candrive (RRID:SCR_007246) Copy   

•   Source: SciCrunch Registry

http://www.arvo.org/

An eye and vision research organization whose goal is to encourage and assist research, training, publication, and dissemination of knowledge in vision and ophthalmology. ARVO membership is comprised of more than 11,500 individuals. Some 42% of members reside in over 70 countries outside the U.S. The membership is multidisciplinary and consists of both clinical and basic researchers (approximately 44% MD/Ophthalmologists, 26% PhDs, and 30% Other, including optometrists, osteopaths, and veterinarians). ARVO is governed by a Board of Trustees, who are elected from candidates put forth by the 13 Scientific Sections.

Proper citation: Association for Research in Vision and Ophthalmology (RRID:SCR_007400) Copy   

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http://www.bitplane.com/go/products/filamenttracer

A software application that automatically detects neurons (dendritic trees, axons and spines), microtubules, and other filament-like structures in 2D, 3D and 4D. Imaris FilamentTracer uses strategies that involve an optimal combination of automated analysis and operator decision. The choice of the best method is an essential element in optimizing efficiency. FilamentTracer allows the choice between four complementary tracing strategies ranging from manual to automatic and utilizes a creation wizard to easily guide the user through the creations steps. It has been specifically designed to deal with the complex problem of spine analysis over time.

Proper citation: FilamentTracer (RRID:SCR_007366) Copy   

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http://www.genome.umin.jp

This portal shows you the current research projects happening with in the Cancer Genomics Project. Sponsors: This project is supported by Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agenecy. Keywords: Research, Cancer, Genomics, Genetic, Gne, Project,

Proper citation: Cancer Genomics Project (RRID:SCR_007242) Copy   

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http://em3d.stanford.edu

EM3D is a software application designed to facilitate the analysis and visualization of electron microscope (EM) tomography data by cellular and molecular biologists. Such data are collected as a tilt series, a sequence of 2D electron micrographs taken at many tilt angles with respect to the electron beam. EM3D features an integrated graphical user interface that automates most of the initial alignment and reconstruction of the tilt-series data to form a 3D volume. These functions seamlessly connect with segmentation and model-generation tools that permit the user to easily and reliably extract specific structural components from the reconstructed volume. The 3D models can then be visualized and manipulated using an extensive package of surface- and volume-rendering techniques. EM3D also provides a set of analysis tools to quantify structural information from the models, including their moments, proximity relationships, and spatial reliability. Altogether, EM3D facilitates the analysis of 3D cell structure at the full resolution of a reconstructed volume (2-3 nm)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: EM3D (RRID:SCR_007362) Copy   

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http://www.avianbrain.org/index.html

This web site contains information relevant to nomenclature of the avian brain. Its current purpose is to serve as a communication means by which scientists can become more knowledgeable about the avian brain, exchange ideas, and formulate proposals for changing the existing nomenclature. Sponsors: This resource is supported by the Duke University Medical Center. Keywords: Avian, Brain, Rearch, Research, Nomenclature, Atlas,

Proper citation: Avian Brain (RRID:SCR_007243) Copy   

•   Source: SciCrunch Registry

http://www.cirm.ca.gov/

The California Institute for Regenerative Medicine is accelerating the development of new therapies for chronic disease and injury by funding stem cell research programs throughout California. T he mission of CIRM is to support and advance stem cell research and regenerative medicine under the highest ethical and medical standards for the discovery and development of cures, therapies, diagnostics and research technologies to relieve human suffering from chronic disease and injury. CIRM was established in 2004 after Californians passed Proposition 71, the California Stem Cell Research and Cures Initiative. The statewide ballot measure, which provided 3 billion in funding for stem cell research at California universities and research institutions, called for the establishment of a new state agency to make grants and provide loans for stem cell research, research facilities and other vital research opportunities. CIRM funds stem cell research at for-profit and not-for-profit institutions throughout California. Grants are awarded as part of Requests for Applications (RFAs). Applications for these RFAs are reviewed by a panel of experts, which makes recommendations to the Governing Board. The board then votes on grants to fund for each RFA. Keywords: Regenerative, Medicine, Development, Therapy, Chronic, Disease, Ilness, Stem cell, Research, Meidcal, Discovery, Cure, Therapy, Diagnostic, Technology, Human, Grant, Funding,

Proper citation: California Institute for Regenerative Medicine (RRID:SCR_007240) Copy   

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http://www.mbio.ncsu.edu/BioEdit/bioedit.html

Software tool as biological sequence alignment editor written for Windows 95/98/NT/2000/XP/7 and sequence analysis program. Provides sequence manipulation and analysis options and links to external analysis programs to view and manipulate sequences with simple point and click operations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BioEdit (RRID:SCR_007361) Copy   

•   Source: SciCrunch Registry

http://vcell.org/

V-Cell is a remote user modeling and simulation environment utilizing Java''s Remote Method Invocation (RMI). The biologically oriented user interface allows experimentalists to create models, define cellular geometry, specify simulations and analyze the simulation results. The results are run and stored on a remote server and can be reviewed in the software and/or exported in a variety of popular formats. The design of the biological to mathematical mapping allows for separate use of biological and math components, and includes automatic mathematical simplification using pseudo-steady approximations and mass conservation relationships. This allows for direct specification of mathematical problems, performing simulations and analysis on those systems. The stand alone mathematics user interface is also a powerful tool for modeling reaction-diffusion systems. A transparent general purpose solver is used to translate the initial biological description into a set of concise mathematical problems. The solver is transparent to the average user, but is accessible to the theorist as the Math Editor component. The software is composed of three main components: 1. The modeling framework represents the physiological models of the Virtual Cell and allows for persistence and database support. 2. The mathematics framework transparently solves an important class of mathematical problems encountered in the cellular modeling. 3. The WWW accessible graphical user interface provides access to the technology mentioned above. The user interface has been developed using Java 2 Applets.

Proper citation: Virtual Cell at the National Resource for Cell Analysis and Modeling (RRID:SCR_007421) Copy   

•   Source: SciCrunch Registry

http://www.translatingtime.net

Web tool for translating neurodevelopemental time across species and predicting neurodevelopemental events. This tool was created because clinicians and researchers rely on neurodevelopment data obtained from a variety of non-human species, it is essential to be able to relate studies across the different experimental animals, and ultimately to humans, in an easily accessible format. This web site is based on a mathematical model originally described by Finlay and Darlington (Science, 268:1578-84) that predicts post conception (PC) dates using log transformations. It integrates hundreds of empirically-derived neural events to translate neurodevelopmental time across hamsters, mice, rats, rabbits, spiny mice, guinea pigs, ferrets, cats, rhesus monkeys and humans.

Proper citation: Translating Time across developing mammalian brains (RRID:SCR_007424) Copy   

•   Source: SciCrunch Registry

http://www.geisha.arizona.edu/geisha/

Online repository for chicken in situ hybridization information. This site presents whole mount in situ hybridization images and corresponding probe and genomic information for genes expressed in chicken embryos in Hamburger Hamilton stages 1-25 (0.5-5 days). The GEISHA project began in 1998 to investigate using high throughput whole mount in situ hybridization to identify novel, differentially expressed genes in chicken embryos. An initial expression screen of approximately 900 genes demonstrated feasibility of the approach, and also highlighted the need for a centralized repository of in situ hybridization expression data. Objectives: The goals of the GEISHA project are to obtain whole mount in situ hybridization expression information for all differentially expressed genes in the chicken embryo between HH stages 1-25, to integrate expression data with the chicken genome browsers, and to offer this information through a user-friendly graphical user interface. In situ hybridization images are obtained from three sources: 1. In house high throughput in situ hybridization screening: cDNAs obtained from several embryonic cDNA libraries or from EST repositories are screened for expression using high throughput in situ hybridization approaches. 2. Literature curation: Agreements with journals permit posting of published in situ hybridization images and related information on the GEISHA site. 3. Unpublished in situ hybridization information from other laboratories: laboratories generally publish only a small fraction of their in situ hybridization data. High quality images for which probe identity can be verified are welcome additions to GEISHA.

Proper citation: GEISHA - Gallus Expression in Situ Hybridization Analysis: A Chicken Embryo Gene Expression Database (RRID:SCR_007440) Copy   

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https://njms.rutgers.edu/departments/neurology/graduate_programs.php

The Graduate Program in Neuroscience is committed to educating and training outstanding young scientists in the multidisciplinary concepts and contemporary techniques at the heart of modern Neuroscience. Students selected for this program generally have had exceptional undergraduate training in the physical, biological and social sciences. It offers students an outstanding opportunity for graduate training in a rapidly growing joint program of the Graduate School of Rutgers University and the Graduate School of Biomedical Sciences of the University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, both located in Piscataway/New Brunswick, New Jersey. A major goal of the Graduate Program in Neuroscience is to prepare students-in the classroom and in active research laboratories-for careers of independent research in universities, medical schools, governmental facilities and industry.

Proper citation: University of Medicine and Dentistry of New Jersey Neuroscience Graduate Program (RRID:SCR_007515) Copy   

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http://www.dental.umaryland.edu/dentaldepts/neural_pain_sciences/nps_orc_dubner.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 25,2022. Research unit in the University of Maryland School of Dentistry specializing in neural pain. The program includes a major Program Project on Plasticity and Modulation in Models of Persistent Pain and the University of Maryland, Baltimore Research Center for Neuroendocrine Influences on Pain.

Proper citation: University of Maryland Dental School, Organized Research Center on Persistant Pain (RRID:SCR_007512) Copy   

•   Source: SciCrunch Registry

https://github.com/steinmann/peakzilla

An algorithm to identify transcription factor binding sites from ChIP-seq data.

Proper citation: Peakzilla (RRID:SCR_007471) Copy   

•   Source: SciCrunch Registry

https://www.pomona.edu/academics/departments/neuroscience-department

Provides opportunity to learn fundamentals of neuroscience, perform experimental techniques in state-of-the-art teaching laboratories, and discover how neuroscience provides insight into other liberal arts disciplines, including psychology, economics, computer science and philosophy. Areas of neuroscience include:cell and molecular neuroscience;systems-level neuroscience;nervous system disorders such as anxiety and depression;neuroscientific models of social behavior and interaction;and imaging the mind at work.Majors have the opportunity to assist faculty in research or conduct their own project through the Summer Undergraduate Research Program.

Proper citation: Pomona College Department of Neuroscience (RRID:SCR_007467) Copy   

•   Source: SciCrunch Registry