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http://geoss.sourceforge.net/

A complete software system used to store and analyze gene expression data.

Proper citation: GEOSS (RRID:SCR_003401) Copy   

•   Source: SciCrunch Registry

http://www.stritch.luc.edu/pharmacology/

Department committed to excellence in teaching and research offering degrees leading to Ph.D., M.S., M.D./Ph.D. and M.S./M.B.A. The commitment to teaching is exemplified by the innovative courses and programs that the department has developed, as well as a departmental emphasis on fostering student-faculty interactions. The department offers Summer Undergraduate Research Opportunities and Postdoctoral positions. Research in Pharmacology encompasses the understanding, prevention and treatment of human disease, and therefore is at the forefront in creating innovative therapeutic interventions to improve the human condition. Research interests of the Departmental faculty include Neuroscience, Cardiovascular, Hematology and Oncology.

Proper citation: Loyola University Department of Molecular Pharmacology and Experimental Therapeutics (RRID:SCR_003400) Copy   

•   Source: SciCrunch Registry

https://github.com/mozack/abra

Software that is a realigner for next generation sequencing data. It uses localized assembly and global realignment to align reads more accurately, thus improving downstream analysis (detection of indels and complex variants in particular).

Proper citation: Assembly Based ReAligner (RRID:SCR_003277) Copy   

•   Source: SciCrunch Registry

http://braintrap.inf.ed.ac.uk/braintrap/

This database contains information on protein expression in the Drosophila melanogaster brain. It consists of a collection of 3D confocal datasets taken from EYFP expressing protein trap Drosophila lines from the Cambridge Protein Trap project. Currently there are 884 brain scans from 535 protein trap lines in the database. Drosophila protein trap strains were generated by the St Johnston Lab and the Russell Lab at the University of Cambridge, UK. The piggyBac insertion method was used to insert constructs containing splice acceptor and donor sites, StrepII and FLAG affinity purification tags, and an EYFP exon (Venus). Brain images were acquired by Seymour Knowles-Barley, in the Armstrong Lab at the University of Edinburgh. Whole brain mounts were imaged by confocal microscopy, with a background immunohistochemical label added to aid the identification of brain structures. Additional immunohistochemical labeling of the EYFP protein using an anti-GFP antibody was also used in most cases. The trapped protein signal (EYFP / anti-GFP), background signal (NC82 label), and the merged signal can be viewed on the website by using the corresponding channel buttons. In all images the trapped protein / EYFP signal appears green and the background / NC82 channel appears magenta. Original .lsm image files are also available for download.

Proper citation: BrainTrap: Fly Brain Protein Trap Database (RRID:SCR_003398) Copy   

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http://irc.cchmc.org/software/pedbrain.php

Brain imaging data collected from a large population of normal, healthy children that have been used to construct pediatric brain templates, which can be used within statistical parametric mapping for spatial normalization, tissue segmentation and visualization of imaging study results. The data has been processed and compiled in various ways to accommodate a wide range of possible research approaches. The templates are made available free of charge to all interested parties for research purposes only. When processing imaging data from children, it is important to take into account the fact that the pediatric brain differs significantly from the adult brain. Therefore, optimized processing requires appropriate reference data be used because adult reference data will introduce a systematic bias into the results. We have shown that, in the in the case of spatial normalization, the amount of non-linear deformation is dramatically less when a pediatric template is used (left, see also HBM 2002; 17:48-60). We could also show that tissue composition is substantially different between adults and children, and more so the younger the children are (right, see also MRM 2003; 50:749-757). We thus believe that the use of pediatric reference data might be more appropriate.

Proper citation: CCHMC Pediatric Brain Templates (RRID:SCR_003276) Copy   

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http://www.reproducibility.org/wiki/Main_Page

Software package for multidimensional data analysis and reproducible computational experiments. It aims to provide a powerful environment and a convenient technology transfer tool for researchers working with digital image and data processing in geophysics and related fields., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Madagascar (RRID:SCR_003274) Copy   

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http://www.rockland-inc.com/

A global biotechnology company manufacturing research tools, antibodies, and cGMP grade protein.

Proper citation: Rockland Immunochemicals (RRID:SCR_003278) Copy   

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http://ucsfeye.net/mlavailRDratmodels.shtml

Supplier of fully penetrant rat models of the retinitis pigmentosa type of inherited retinal degeneration, including the following models: * Mutant rhodopsin transgenic rats ** P23H mutant rhodopsin transgenic rats -Three lines with different rates of photoreceptor degeneration ** S334ter mutant rhodopsin transgenic rats -Five lines with different rates of photoreceptor degeneration * RCS (Royal College of Surgeons) rats with inherited retinal dystrophy ** RCS pink-eyed inbred strain ** RCS pigmented congenic strain with slowed rate of retinal dystrophy ** RCS congenic control strains of both pigmentation types, wild-type at the retinal dystrophy (Mertk) genetic locus The resource has been supported by the National Eye Institute (NEI) for the past 19 years to produce and distribute breeding pairs of these animal models to vision scientists. Thus, the following apply: * Request for rats requires only a 1-page letter/e-mail addressing 4 questions * No charge for the animals or tissues (except for shipping costs) * No Material Transfer Agreement (MTA) required * No collaboration requirement (in most cases) The resource usually provides multiple breeding pairs of the rats to vision scientists to generate breeding stock. It can also provide extra animals to breed for immediate experimental work, animals of specific ages (depending upon availability), animals with prior exposure to different lighting conditions, eyes taken at specific ages instead of rats for pilot studies and other experiments (fresh, frozen, dissected in specific ways, or fixed with special fixatives or by different methods), or other tissues (e.g., liver, spleen, brain, testis, etc.) prepared different ways.

Proper citation: Retinal Degeneration Rat Model Resource (RRID:SCR_003311) Copy   

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http://www.pediatricmri.nih.gov/

Data sets of clinical / behavioral and image data are available for download by qualified researchers from a seven year, multi-site, longitudinal study using magnetic resonance technologies to study brain maturation in healthy, typically-developing infants, children, and adolescents and to correlate brain development with cognitive and behavioral development. The information obtained in this study is expected to provide essential data for understanding the course of normal brain development as a basis for understanding atypical brain development associated with a variety of developmental, neurological, and neuropsychiatric disorders affecting children and adults. This study enrolled over 500 children, ranging from infancy to young adulthood. The goal was to study each participant at least three times over the course of the project at one of six Pediatric Centers across the United States. Brain MR and clinical/behavioral data have been compiled and analyzed at a Data Coordinating Center and Clinical Coordinating Center. Additionally, MR spectroscopy and DTI data are being analyzed. The study was organized around two objectives corresponding to two age ranges at the time of enrollment, each with its own protocols. * Objective 1 enrolled children ages 4 years, 6 months through 18 years (total N = 433). This sample was recruited across the six Pediatric Study Centers using community based sampling to reflect the demographics of the United States in terms of income, race, and ethnicity. The subjects were studied with both imaging and clinical/behavioral measures at two year intervals for three time points. * Objective 2 enrolled newborns, infants, toddlers, and preschoolers from birth through 4 years, 5 months, who were studied three or more times at two Pediatric Study Centers at intervals ranging from three months for the youngest subjects to one year as the children approach the Objective 1 age range. Both imaging and clinical/behavioral measures were collected at each time point. Participant recruitment used community based sampling that included hospital venues (e.g., maternity wards and nurseries, satellite physician offices, and well-child clinics), community organizations (e.g., day-care centers, schools, and churches), and siblings of children participating in other research at the Pediatric Study Centers. At timepoint 1, of those enrolled, 114 children had T1 scans that passed quality control checks. Staged data release plan: The first data release included structural MR images and clinical/behavioral data from the first assessments, Visit 1, for Objective 1. A second data release included structural MRI and clinical/behavioral data from the second visit for Objective 1. A third data release included structural MRI data for both Objective 1 and 2 and all time points, as well as preliminary spectroscopy data. A fourth data release added cortical thickness, gyrification and cortical surface data. Yet to be released are longitudinally registered anatomic MRI data and diffusion tensor data. A collaborative effort among the participating centers and NIH resulted in age-appropriate MR protocols and clinical/behavioral batteries of instruments. A summary of this protocol is available as a Protocol release document. Details of the project, such as study design, rationale, recruitment, instrument battery, MRI acquisition details, and quality controls can be found in the study protocol. Also available are the MRI procedure manual and Clinical/Behavioral procedure manuals for Objective 1 and Objective 2.

Proper citation: NIH MRI Study of Normal Brain Development (RRID:SCR_003394) Copy   

•   Source: SciCrunch Registry

http://www.hopkinsmedicine.org/pharmacology/

The Department of Pharmacology and Molecular Sciences is proud of its history. Founded in 1893 by John J. Abel, the "Father of Pharmacology" in the United States, the Johns Hopkins Pharmacology Department's advances over the years have included the first crystals of insulin, the first measurement of a drug level in a human, discovery of both the insulin and opiate receptors, and discovery of a cancer preventive principle in broccoli. Many of these and other key contributions have been made by students pursuing advanced degrees in our Department. We are also proud of our track record in student training. Many of our graduates have gone on to become academic and industrial leaders in biomedical research throughout the country and world. Not resting on our laurels, we are continuing to maintain our strong commitment to creative scholarship and education. Additionally, there is an Anti-Cancer Drug Development Training Program for predoctoral and postdoctoral students as well ad other Postdoctoral research opportunities. Each of our faculty is engaged in cutting-edge research spanning many areas including: chemical biology, immunology, virology, cancer, and neuroscience. We believe the opportunities for discovering new drug targets and developing novel therapeutics have never been brighter and will continue to be lustrous for the century ahead. The Johns Hopkins University and School of Medicine provide an excellent scientific environment, with a friendly and supportive atmosphere, filled with energetic students, faculty, fellows, and staff.

Proper citation: Johns Hopkins University Pharmacology (RRID:SCR_003391) Copy   

•   Source: SciCrunch Registry

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

An ontology designed to represent the conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms.

Proper citation: Experimental Conditions Ontology (RRID:SCR_003306) Copy   

•   Source: SciCrunch Registry

https://catalog.allegheny.edu/preview_program.php?catoid=44&poid=3489&returnto=1542

Allegheny's neuroscience major formalizes an alliance dating back 25 years between the College's well-known biology and psychology departments. The major brings faculty and students together to study the brain and the nervous system using principles from the natural and social sciences. It requires a common core of biology, chemistry, and psychology courses. Students may choose from two tracks: "cellular neurobiology" or "behavioral and cognitive neuroscience", and they have the opportunity to explore interdisciplinary topics through the Junior Seminar and the year-long Senior Research Project.

Proper citation: Allegheny College Neuroscience (RRID:SCR_003305) Copy   

•   Source: SciCrunch Registry

http://www.bioontology.org

Organization that provides biomedical researchers with online tools and a web portal enabling them to access, review, and integrate disparate ontological resources in all aspects of biomedical investigation and clinical practice. A major focus of the work involves the use of biomedical ontologies to aid in the management and analysis of data derived from complex experiments.

Proper citation: National Center for Biomedical Ontology (RRID:SCR_003304) Copy   

•   Source: SciCrunch Registry

http://sagebase.org/

Non-profit biomedical research organization developing predictors of disease and accelerating health research through creation of open systems, incentives, and standards. Formed to coordinate and link academic and commercial biomedical researchers through Commons that represents new paradigm for genomics intellectual property, researcher cooperation, and contributor evolved resources.

Proper citation: Sage Bionetworks (RRID:SCR_003384) Copy   

•   Source: SciCrunch Registry

http://neuroscience.aecom.yu.edu/index.html

University department that oversees neuroscience research and graduate education.

Proper citation: Albert Einstein College of Medicine of Yeshiva University Department of Neuroscience (RRID:SCR_003303) Copy   

•   Source: SciCrunch Registry

http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/

Software R package for weighted correlation network analysis. WGCNA is also available as point-and-click application. Unfortunately this application is not maintained anymore. It is known to have compatibility problems with R-2.8.x and newer, and the methods it implements are not all state of the art., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Weighted Gene Co-expression Network Analysis (RRID:SCR_003302) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/NormqPCR.html

Software package providing functions for the selection of optimal reference genes and the normalization of real-time quantitative PCR data.

Proper citation: NormqPCR (RRID:SCR_003388) Copy   

•   Source: SciCrunch Registry

http://signalml.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.An XML-based language designed for metadescription of formats, used for digital storage of biomedical time series. Using SignalML, information on the structure of binary data files can be simply and efficiently coded. Once written, this information can be used by any software, which - owing to this metadescription - can read data files in the original format. This eliminates the need for conversions and duplication of data. signalml.org provides the following resources for interchange of relevant information and ideas: * SignalML wiki * Newsgroup / mailing list The main current software project is Svarog - a SignalML-compliant signal viewer, annotator, analyzer and (future) recorder. Svarog is written in Java and is currently best fitted for display of EEG and MEG signals. Also open platform for implementing advanced signal processing methods in user-friendly environment, at the moment interfacs for Java code, standalone executables and Matlab code via Matlab Builder for Java.

Proper citation: signalml.org (RRID:SCR_003383) Copy   

•   Source: SciCrunch Registry

http://www.exbio.cz/

An Antibody supplier

Proper citation: EXBIO Praha (RRID:SCR_003381) Copy   

•   Source: SciCrunch Registry

http://www.gene-quantification.de/bestkeeper.html

Excel-based tool using pair-wise correlations for determination of stable housekeeping genes, differentially regulated target genes and sample integrity. It determines the best suited standards, out of ten candidates, and combines them into an index. The index can be compared with further ten target genes to decide, whether they are differentially expressed under an applied treatment. All data processing is based on crossing points.

Proper citation: BestKeeper (RRID:SCR_003380) Copy   

•   Source: SciCrunch Registry