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http://www.i-mouse.org/

Over recent years, the European Commission has supported an increasing number of functional genomics projects focusing on the use of the laboratory mouse as a model of human disease. (see http://www.prime-eu.org/euromouseiiprojects.htm for a fuller listing of current and recent projects). CASIMIR (Coordination and Sustainability of International Mouse Informatics Resources: http://www.casimir.org.uk) is aimed at recommending standards to allow data sharing and integration between the different projects. CASIMIR spans a number of areas: data representation (in particular the use of shared ontologies), non-semantic, technical issues concerning database compatibility and interoperability, data acquisition, curation and ownership, integration of biological collections and material resources into the data network, and user interactions. As part of the CASIMIR initiative i-mouse.org was created as a common portal to CASIMIR and other resources we hope will be helpful for investigators using the mouse as a model system for humans or systems biologists and geneticists using the mouse as an experimental system. ontology; metadata;

Proper citation: Informatics resources for mouse functional genomics (RRID:SCR_007374) Copy   

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http://dblab.duhs.duke.edu/modules/dblabs_topcat/index.php

TOPPCAT stands for T-One weighted Perfusion imaging Parameter CAlculation Toolkit. TOPPCAT creates quantitative maps of Ktrans (volume transfer constant between blood plasma and the extravascular extracellular space) and fPV (fractional plasma volume) from dynamic T1-weighted perfusion images. At the current time, analysis using the method of Patlak plots (most appropriate for first pass dynamic contrast-enhanced MR imaging) is supported. As a preliminary step for the parameter calculation, TOPPCAT also creates maps of T1 and S0 (equilibrium magnetization) from multi-flip angle T1-weighted SPGR (or FLASH) sequences.Daniel P. Barboriak, James R. MacFall, Anthony O. Padua,Gerald E. York, Benjamin L. Viglianti, and Mark W. Dewhirst. Standardized software for calculation of Ktrans and vp from dynamic T1-weighted MR images. Presented at the International Society for Magnetic Resonance in Medicine Workshop on MR in Drug Development: From Discovery to Clinical Therapeutic Trials, McLean VA, April 2004.

Proper citation: T-One weighted Perfusion imaging Parameter CAlculation Toolkit (RRID:SCR_007376) Copy   

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http://www.ebi.ac.uk/Tools/emboss/cpgplot/indexhtml

This portal allows for the detection of regions of genomic sequences that are rich in the CpG pattern is important because such regions are resistant to methylation and tend to be associated with genes which are frequently switched on. Regions rich in the CpG pattern are known as CpG islands. The function of the program cpgplot is to plot CpG rich areas, and cpgreport to report all CpG rich regions. The nuclear genomes of vertebrates are mosaics of isochores, very long stretches of DNA that are homogeneous in base composition and are compositionally correlated with the coding sequences that they embed. Isochores can be partitioned in a small number of families that cover a range of GC levels. Program isochore plots GC content over a sequence. Sponsors: This resource is supported by European Bioinformatics Institute. Keywords: Software, Plotting, Pattern, CpG, Gene, Function, Isochore, DNA, Genome, Homogeneous, Coding, Sequence, Family, Sequencing,

Proper citation: EMBOSS CpGPlot/CpGReport/Isochore (RRID:SCR_007254) Copy   

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https://bams1.org/

Knowledge management system designed to handle neurobiological information at different levels of organization of vertebrate nervous system. Database and repository for information about neural circuitry, storing and analyzing data concerned with nomenclature, taxonomy, axonal connections, and neuronal cell types. Handles data and metadata collated from original literature, or inserted by scientists that is associated to four levels of organization of vertebrate nervous system. Data about expressed molecules, neuron types and classes, brain regions, and networks of brain regions.

Proper citation: Brain Architecture Management System (RRID:SCR_007251) Copy   

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http://www.neurolens.org/NeuroLens/

An integrated environment for the analysis and visualization of functional neuroimages. It is intended to provide extremely fast and flexible image processing, via an intuitive user interface that encourages experimentation with analysis parameters and detailed inspection of both raw image data and processing results. All processing operations in NeuroLens are built around a Plugin architecture, making it easy to extend its functionality. NeuroLens runs on Apple computers based on the G4, G5, or Intel chipsets and running MacOSX 10.4 (Tiger) or later. It is available free for academic and non-profit research use. * Operating System: MacOS * Programming Language: Objective C * Supported Data Format: AFNI BRIK, ANALYZE, COR, DICOM, MGH/MGZ, MINC, Other Format

Proper citation: NeuroLens (RRID:SCR_007372) Copy   

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http://casp.sourceforge.net

CASP is a tool to image analysis in comet assay. CASP has been developed to work with either color, or gray-scale images of fluorescence-stained comets saved in TIF format. In its present version CASP does not control a video or CCD camera. Comets stained with silver (dark cells on white background) must be converted into negative images in order to be analysed correctly. An unlimited number of images can be marked, CASP will load them successively into a image view window (see screenshot). Only comets oriented from left (head) to right (tail) can be analysed correctly. The user can adjust various thresholds of sensitivity and save the adjustments for future use. A measurement frame is drawn on the screen and its size adjusted. The adjustments are frozen to prevent accidental modification. The frame is moved onto a cell and measurement is activated. An intensity profile shows up on a profile window together with selected result values (right window on figure 1) and the result can be saved. In addition to such parameter as head radius, tail length etc, the program calculates the tail moment (TM) and the Olive tail moment (OTM). If several cells are present on the same picture, the user can proceed with the measurement of another cell on the same picture or can load a new picture. The saved results can be visualized during the working session in a spreadsheet in view results window. When measurements are terminated, the results can be exported into a text file and imported into a commercial spreadsheet calculation program. CASP is optimized for a 600x800 resolution. Sponsors: This work has been supported by the University of Wroclaw. Keywords: Comet, Assay, Software, Laboratory, Camera, Negative, Cell, Analysis, Image,

Proper citation: CASPLab: Comet Assay Software Project Laboratory (RRID:SCR_007249) Copy   

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http://cardiogenomica.altervista.org/CARDIOGENOMICS/CardioGenomics%20Homepage.htm

The primary goal of the CardioGenomics PGA is to begin to link genes to structure, function, dysfunction and structural abnormalities of the cardiovascular system caused by clinically relevant genetic and environmental stimuli. The principal biological theme to be pursued is how the transcriptional network of the cardiovascular system responds to genetic and environmental stresses to maintain normal function and structure, and how this network is altered in disease. This PGA will generate a high quality, comprehensive data set for the functional genomics of structural and functional adaptation of the cardiovascular system by integrating expression data from animal models and human tissue samples, mutation screening of candidate genes in patients, and DNA polymorphisms in a well characterized general population. Such a data set will serve as a benchmark for future basic, clinical, and pharmacogenomic studies. Training and education are also a key focus of the CardioGenomics PGA. In addition to ongoing journal clubs and seminars, the PGA will be sponsoring symposia at major conferences, and developing workshops related to the areas of focus of this PGA. Information regarding upcoming events can be found in the Events section of this site, and information about training and education opportunities sponsored by CardioGenomics can be found on the Teaching and Education page. The CardioGenomics project came to a close in 2005. This server, cardiogenomics.med.harvard.edu, remains online in order to continue to distribute data that was generated by investigators under the auspices of the CardioGenomics Program for Genomic Applications (PGA). :Sponsors: This resource is supported by The National Heart, Lung and Blood Institute (NHLBI) of the NIH., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CardioGenomics (RRID:SCR_007248) Copy   

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http://www.mediacy.com/imageproplus

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18,2023. Software package to capture, process, measure, analyze and share images and data.

Proper citation: Image Pro Plus (RRID:SCR_007369) Copy   

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http://ncmir.ucsd.edu/downloads/fido.shtm

An interactive, graphic, fiducial marking software for placing, editing and tracking fiducial marks on images in a tomography tilt series. You can also use this tool to view the tilt series as well as crop it.

Proper citation: XFido (RRID:SCR_007365) Copy   

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http://jaxmice.jax.org/list/ra1642.html

Produce new neurological mouse models that could serve as experimental models for the exploration of basic neurobiological mechanisms and diseases. The impetus for the program resulted from the recognition that: * The value of genomic data would remain limited unless more information about the functionality of its individual components became available. * The task of linking genes to specific behavior would best be accomplished by employing a combination of different approaches. In an effort to complement already existing programs, the Neuroscience Mutagenesis Facility decided to use: a random, genome-wide approach to mutagenesis, i.e.N-ethyl-N-nitrosourea (ENU) as the mutagen; a three-generation back-cross breeding scheme to focus on the detection of recessive mutations; behavioral screens selective for the detection of phenotypes deemed useful for the program goals. The resulting mutant mouse lines have been available to the scientific community for the last five years and over 700 NMF mice have been sent to interested investigators for research; these mutant mouse lines will remain available as frozen embryos (which can be re-derived on request) and can be ordered through the JAX customer service at 1-800-422-6423 (or 207-288-5845). The results of the work of the Neuroscience Mutagenesis Facility and that of two other neurogenesis centers, i.e. The Neurogenomics Project at Northwestern University, and the Neuromutagenesis Project of the Tennessee Mouse Genome Consortium, can also be seen at Neuromice.org, a common web site of these three research centers; in addition, information about all mutants produced by these groups has been recorded in MGI.

Proper citation: JAX Neuroscience Mutagenesis Facility (RRID:SCR_007437) Copy   

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http://zmf.umm.uni-heidelberg.de/apps/zmf/argonaute/single.php

A database is a of mammalian miRNAs and their known or predicted regulatory targets. It provides information on origin of miRNAs, tissue specificity of their expressions and their known or proposed functions, their potential target genes as well as data on miRNA families based on their co-expression and proteins known to be involved in miRNA processing. This database also contains three other navigation tools that can be used to find information relating to miRNA: 1.) Gene Annotations is an information retrieval system for miRNA target genes. It provides comprehensive information from sequence databases and allows to simultaneously search PubMed with all synonyms of a given gene. 2.) miRNA Motif Finder - Argonaute predicts miRNA motifs binding to the gene sequence of the user. The miRNA mature sequences are taken from Agronaute 2 database. miRNA Motif Finder - Custom predicts miRNA motifs binding to the gene sequence, both the gene sequence and miRNA mature sequences provided by the user. 3.) miRNA Statistics provides statistics for the mature miRNA sequences from Argonaute 2 as well as for the miRNA sequences uploaded by the user. It provides statitics on the individual nucleotide as well as pattern of nucleotides apperaing in the sequence.

Proper citation: ARGONAUTE 2 - A database on mammalian microRNAs and their function in gene and pathway regulation (RRID:SCR_007553) Copy   

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http://www.ikaros-project.org/

Ikaros is an open infrastructure for system level modeling of the brain including databases of experimental data, computational models and functional brain data. The system makes heavy use of the emerging standards for Internet based information and makes all information accessible through an open web-based interface. In addition, Ikaros can be used as a control architecture for robots which in the extension will lead to the development of a brain inspired robot architecture. The main components of the Ikaros systems are: a platform independent simulation kernel; a set of computational brain models; a set of I/O modules for interfacing with data files and peripheral such as robots or video cameras; tools for building systems of interconnected models; a plug-in architecture that allows new models to be easily added to the system; and a database with data from learning experiments that can be used for validation of the computational models.

Proper citation: Ikaros Project (RRID:SCR_007391) Copy   

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http://www.thebiogrid.org/

Curated protein-protein and genetic interaction repository of raw protein and genetic interactions from major model organism species, with data compiled through comprehensive curation efforts.

Proper citation: Biological General Repository for Interaction Datasets (BioGRID) (RRID:SCR_007393) Copy   

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http://ngs.ym.edu.tw/ym500/index.php

An Integrative small RNA Sequencing database for miRNA research and provides an integrative web interface for miRNA quantification, isomiR identification, arm switching discovery, and, most of all, novel miRNA predictions.

Proper citation: YM500 (RRID:SCR_007429) Copy   

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http://ekhidna.biocenter.helsinki.fi/sqgraph/pairsdb

This is a web interface for ADDA, an automatic algorithm for domain decomposition and clustering of all protein domain families. We use alignments derived from an all-on-all sequence comparison to define domains within protein sequences based on a global maximum likelihood model. ADDA is downloadable. There are three ways in which you can retrieve a protein sequence and its domains from ADDA. Sequences can be located using sequence identifiers and/or accession numbers, using a identical fragment lookup, or by running BLAST against all sequences in ADDA. ADDA is a protein sequence clustering algorithm. It takes a set of sequences and returns domain families. ADDA has two steps corresponding to the two aspects of the protein sequence clustering domain. First, ADDA splits protein sequences into domains. The idea behind ADDA is in principle the application of Occam''s razor; the goal is to describe the diversity of protein sequences with a minimal set of protein domains. The algorithm behind ADDA approximates this minimal set. In practice ADDA works by looking at where BLAST alignments are located on the sequence and splits the sequences, so that as few as possible alignments are cut by domain boundaries and that as many alignments as possible stretch over complete domains. Secondly, ADDA takes all the domains and then arranges them in a minimum spanning tree, where the similarity between two domains is determined by their relative overlap given a BLAST alignment. Each link in the tree is then checked by a pairwise profile-profile comparison and links below a threshold are removed. The remaining connected components are then taken to represent protein domain families.

Proper citation: ADDA - Automatic Domain Decomposition Algorithm (RRID:SCR_007546) Copy   

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https://www.mc.vanderbilt.edu/victr/dcc/projects/acc/index.php/Main_Page

A national consortium formed to develop, disseminate, and apply approaches to research that combine DNA biorepositories with electronic medical record (EMR) systems for large-scale, high-throughput genetic research. The consortium is composed of seven member sites exploring the ability and feasibility of using EMR systems to investigate gene-disease relationships. Themes of bioinformatics, genomic medicine, privacy and community engagement are of particular relevance to eMERGE. The consortium uses data from the EMR clinical systems that represent actual health care events and focuses on ethical issues such as privacy, confidentiality, and interactions with the broader community.

Proper citation: eMERGE Network: electronic Medical Records and Genomics (RRID:SCR_007428) Copy   

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http://www.aneurist.org/

Project focused on cerebral aneurysms and provides integrated decision support system to assess risk of aneurysm rupture in patients and to optimize their treatments. IT infrastructure has been developeded for management and processing of vast amount of heterogeneous data acquired during diagnosis.

Proper citation: aneurIST (RRID:SCR_007427) Copy   

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http://sbml.org

A computer-readable format for representing models of biochemical reaction networks in software. It''s applicable to models of metabolism, cell-signaling, and many others. This website is the portal for the global SBML development effort; you can find information about all aspects of SBML.

Proper citation: SBML (RRID:SCR_007422) Copy   

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http://www.pharmacy.wsu.edu/prospectivestudents/graduateprograms.html

The research-oriented program in pharmacology and toxicology prepares students for careers in independent research and teaching in pharmacology, toxicology and related areas.The research interests of the faculty are very broad and active areas of research include cancer biology, pharmacogenomics, pharmacokinetics, immuno-pharmacology and -toxicology and neuroscience. The diversity in faculty research interests provides students with a solid foundation in many areas of molecular and cellular pharmacology and toxicology and gives them a wide variety of research programs from which a dissertation proposal may be selected.
The curriculum provides exposure of students to virtually all areas of current research in molecular and cellular biochemistry, immunology, molecular biology, pharmacology and toxicology and formal course requirements are flexible to tailor programs to individual needs.Our graduates have been successfully placed in careers in universities and colleges, the pharmaceutical and biotech industries, and in federal and state agencies. The program awards Ph.D. and M.S. degrees.

Proper citation: Washington State University Pullman WA. Pharmacology and Toxicology (RRID:SCR_007543) Copy   

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https://www.schulich.uwo.ca/physpharm/

Research-based medical science department of physiology and pharmacology in the Schulich School of Medicine and Dentistry at the University of Western Ontario that focus on biological processes from the cellular-molecular level to the integrative-systemic level, and on the effects of drugs and environmental agents on these processes. Their areas of research excellence include the physiology and pharmacology of the cardiovascular, neural, reproductive, endocrine and musculoskeletal systems. Several faculty work in the area of developmental biology related to these organ systems. Faculty members in this Department are leaders in nationally-funded collaborative research programs studying skeletal / bone development and biology, heart and vascular biology, cell communication and gap junctions, neural control of vision and movement, and osteoarthritis and pain. Funding from several large infrastructure grants from both national and provincial governments has facilitated the development of state-of-the-art research laboratories and core facilities.

Proper citation: University of Western Ontario London Ontario Canada Physiology and Pharmacology (RRID:SCR_007541) Copy   

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