Tools   Select Another Resource Report Type

https://ida.loni.usc.edu/login.jsp

Archive used for archiving, searching, sharing, tracking and disseminating neuroimaging and related clinical data. IDA is utilized for dozens of neuroimaging research projects across North America and Europe and accommodates MRI, PET, MRA, DTI and other imaging modalities.

Proper citation: LONI Image and Data Archive (RRID:SCR_007283) Copy   

•   Source: SciCrunch Registry

http://mipgsun.mipg.upenn.edu/~Vnews/

Data-, machine-, and application- independent software system for the visualization and analysis of multidimensional images. This transportable, very inexpensive software system, has capabilities for visualizing, manipulating, and analyzing multidimensional, multimodality image information. It is designed to run on Unix machines under X-windows. It uses a data protocol that is a multidimensional generalization of the ACR-NEMA standards. We have tested it extensively on SGI and Sun workstations and PCs. Other recipients of 3DVIEWNIX have installed it on a variety of platforms including IBM RS6000s, HP700s, and Stardent, all from a single source code version. UNIQUE FEATURES OF 3DVIEWNIX * Transportable - based on UNIX, X-window, and C * Based on multidimensional generalization of ACR-NEMA standards of data representation * Application-independent * Image dimensionality independent * Can handle rigid, non-rigid, static, and dynamic objects and object assemblies * Can handle object information from multiple modalities and longitudinal acquisitions * Multitudes of visualization, manipulation, and analysis methods incorporated * Open software system distributed with source code

Proper citation: 3DViewnix (RRID:SCR_007351) Copy   

•   Source: SciCrunch Registry

http://www.visionnetwork.nei.nih.gov/

The National Eye Institute (NEI) created the VISION Public Information Network for the purpose of communicating with public information officers at NEI grantee institutions. The Network''s primary mission is to work with the NEI in disseminating research results to the national and local media. The Network also works to inform the public of the mission of the National Institutes of Health (NIH) to improve the health of America through medical research. The NEI is part of the NIH, U.S. Department of Health and Human Services (DHHS). General information portal for eye and vision related resources for the public. Sponsors: This resource is supported by the National Eye Institute.

Proper citation: Vision Public Information Network (RRID:SCR_007340) Copy   

•   Source: SciCrunch Registry

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

Xvoxtrace enables volume segmentation of tomographic data using manual tracing. This program allows the researcher to outline features on individual planes of the volume while being guided by simultaneous views of the tracing displayed on a volume rendering or tilt-series. Traced contours can be viewed using XDend or used to generate surfaces for viewing in Synu. Basic Requirements:OpenGL, X windows, and Linux platforms : :

Proper citation: Xvoxtrace (RRID:SCR_007377) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.gene-regulation.com/pub/programs.html

In an effort to strongly support the collaborative nature of scientific research, BIOBASE offers access to their tools. Programs that are available through this portal are: * AliBaba 2.1: AliBaba2 is a program for predicting binding sites of transcription factor binding sites in an unknown DNA sequence. Therefore it uses the binding sites collected in TRANSFAC. AliBaba2 is currently the most specific tool for predicting sites. * Boxshade 3.3.1: Pretty Printing and Shading of Multiple-Alignment files. * ClustalW 1.8: ClustalW Multiple Sequence Alignment Program. * Dialign2.0: Multiple Sequence Alignment Program. * F-Match 1.0: F-MATCH is a program for identifying statistically overrepresented Transcription Factor Binding Sites (TFBS) in a set of sequences compared against a control set, assuming a binomial distribution of TFBS frequency. The program reads MATCH output files for the query and control sets. F-Match uses a library of mononucleotide weight matrices from TRANSFAC 6.0 * Match 1.0 Public: Match is designed for searching potential binding sites for transcription factors (TF binding sites) nucleotide sequences. MatchTM uses a library of mononucleotide weight matrices from TRANSFAC 6.0 * molwSearch 1.0: Search for transcription factors with a certain molecular weight. * P-Match 1.0: P-Match is a new tool for identifying transcription factor binding sites (TF binding sites) in DNA sequences. It combines pattern matching and weight matrix approaches thus providing higher accuracy of recognition than each of the methods alone. P-Match uses a library of mononucleotide weight matrices from TRANSFAC 6.0 along with the site alignments associated with these matrices. * Patch 1.0: Search for potential transcription factor binding sites in your own sequences with the pattern search program using TRANSFAC 6.0 public sites. * m2transfac 1.0: m2transfac is a PWM-PWM alignment interface for the TRANSFAC(R) database. For given user motifs, m2transfac reports all non-overlapping pairwise alignments to a TRANSFAC(R) matrix which satisfy a specified threshold. * MatrixCatch 2.7: The MatrixCatch tool is designed for searching potential composite elements (CEs) for transcription factors (TFs) in any DNA sequence, which may be of interest. MatrixCatch uses a library of CE matrix models, which were compiled on a basis of experimentally identified CEs collected in TRANSCOMPEL database and mononucleotide weight matrices for single TF-binding sites collected in TRANSFAC 6.0 public database. * Composite Module Analyst (CMA) 1.0: CMA reads output of Match program and applies a genetic algorithm in order to define promoter models based on the composition of transcription factor binding sites and their pairs. * PolyA Scan 0.000707: Scanning a Sequence for potential Polyadenylation Sites. * ReadSeq 2.0: ReadSeq reads and writes nucleic/protein sequences in various formats. * SignalScan: Analysis of DNA Sequences for known Eukaryotic Signals * SbBlast 1.0: Search Tool for Sequence Search in the S/MARt Binder Database. SbBlast makes use of the BLAST Sequence Similarity Search Tool - Version 2.0.13 (May-26-2000). * SnpFind 0.3: SNPFIND is a tool for searches in the Database of Single Nucleotide Polymorphisms. The search algorithm used for the database search is the BLAST algorithm. * TfBlast 0.1: Search Tool for Sequence Search in the TRANSFAC Factor Table. SbBlast makes use of the BLAST Sequence Similarity Search Tool - Version 2.0.13 (May-26-2000).

Proper citation: Gene Regulation Programs (RRID:SCR_007787) Copy   

•   Source: SciCrunch Registry

http://cagt.bu.edu/page/PRECISE_about

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Database of interactions between amino acid residues of enzyme and its ligands. Provides summary of interactions between amino acid residues of enzyme and its various ligands including substrate and transition state analogues, cofactors, inhibitors, and products., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PRECISE (RRID:SCR_007874) Copy   

•   Source: SciCrunch Registry

http://www.repairgenes.org/index.shtml

The aim of the repairGenes site is to be a source of information about DNA repair genes and a useful resource for research on DNA repair. At the moment, the site contains information about a number of DNA repair genes from a set of selected species. The information is organized by organism and by biological process term as defined by the Gene Ontology (GO) project. The coverage of DNA repair genes is not complete, but hopefully it satisfies to demonstrate the concept and generate ideas for future versions of the system. At present, the raw data about DNA repair genes is extracted from the SWISS-PROT database, and categorized using the GO system. SWISS-PROT entries are being annotated by the Gene Ontology Annotation project at EBI. GOA is an ongoing project which will become more complete with time. As more data is released, this will be fed into repairGenes to keep it up-to-date. In future versions, the user will be able to search freely among organisms and categories of repair genes, enabling easy comparisons between species. For a taste of this, please have a look at the overview of repair genes from five major organisms. The amount of information in the system will be increased and the quality will be improved in the future. So will the features of the system.

Proper citation: repairGenes (RRID:SCR_008240) Copy   

•   Source: SciCrunch Registry

http://www.reciprocalnet.org/

Database of crystallographic information. Its membership includes crystallographic service facilities (that analyze crystals submitted by research chemists) located at major universities. These labs analyze anywhere from a few dozen to several hundred molecular structures each year and post the data online for the public to access. A distributed database engine takes care of shuttling this data across the Internet so that every structure can be located by the search engine. There may be a delay of a year or more between the time a structure is first analyzed and the time it finally becomes available for the public to see. This is due to intellectual property issues - the intervening time allows the chemists who first discovered the structure to publish it in a trade journal.

Proper citation: Reciprocal Net (RRID:SCR_008238) Copy   

•   Source: SciCrunch Registry

http://cor.physiol.ox.ac.uk/

Cellular Open Resource is a Microsoft Windows environment for cellular modeling that is built around CellML (except for reactions and metadata which are not supported). It offers, through CellML, an ''out of the box'' access to a large database of single cell models. COR was among the early adopters of this standard, eventually forming the first publicly available CellML-based modeling and collaboration environment. From the onset, COR was designed to provide an environment that could not only be used by experienced modelers, but also by experimentalists, teachers and students. It therefore tries to combine a user-friendly interface with a computationally efficient numerical engine. In this paper, we introduce the philosophy behind COR, explain its user interface and current functionality, including the editing and running of CellML files, highlight lessons learned from user feedback and problems experienced during the development of COR and conclude by exploring future development potential. Sponsors: This study has been supported by a grant from the UK Biotechnology and Biological Sciences Research Council (BB/E024955/1). Keyword: Cell, Model, Cellular, Modeling, Open resource, Microsoft, Environment, Database, Experimentalist, Teacher, Student, Modeler, Computationally, Development,

Proper citation: Cellular Open Resource (RRID:SCR_008022) Copy   

•   Source: SciCrunch Registry

http://genome.wustl.edu/projects/detail/human-gut-microbiome/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2022. Human Gut Microbiome Initiative (HGMI) seeks to provide simply annotated, deep draft genome sequences for 100 cultured representatives of the phylogenetic diversity documented by 16S rRNA surveys of the human gut microbiota. Humans are supra-organisms, composed of 10 times more microbial cells than human cells. Therefore, it seems appropriate to consider ourselves as a composite of many species - human, bacterial, and archaeal - and our genome as an amalgamation of human genes and the genes in ''our'' microbial genomes (''microbiome''). In the same sense, our metabolome can be considered to be a synthesis of co-evolved human and microbial traits. The total number of genes present in the human microbiome likely exceeds the number of our H. sapiens genes by orders of magnitude. Thus, without an understanding of our microbiota and microbiome, it not possible to obtain a complete picture of our genetic diversity and of our normal physiology. Our intestine is home to our largest collections of microbes: bacterial densities in the colon (up to 1 trillion cells/ml of luminal contents) are the highest recorded for any known ecosystem. The vast majority of phylogenetic types in the distal gut microbiota belong to just two divisions (phyla) of the domain Bacteria - the Bacteroidetes and the Firmicutes. Members of eight other divisions have also been identified using culture-independent 16S rRNA gene-based surveys. Metagenomic studies of complex microbial communities residing in our various body habitats are limited by the availability of suitable reference genomes for confident assignment of short sequence reads generated by highly parallel DNA sequencers, and by knowledge of the professions (niches) of community members. Therefore, HGMI, which represents a collaboration between Washington University''s Genome Center and its Center for Genome Sciences, seeks to provide simply annotated, deep draft genome sequences for 100 cultured representatives of the phylogenetic diversity documented by 16S rRNA surveys of the human gut microbiota.

Proper citation: Human Gut Microbiome Initiative (RRID:SCR_008137) Copy   

•   Source: SciCrunch Registry

http://www.bioinf.uni-freiburg.de/Software

This resource takes you to the Server and Web-Applications of the University of Freiburg Bioinformatics Group. Sponsors: This resource is supported by University of Freiburg. Keywords: Server, Web application, Bioinformatics, Software,

Proper citation: University of Freiburg Bioinformatics Group: Servers and Web-Applications (RRID:SCR_008256) Copy   

•   Source: SciCrunch Registry

http://www.cmbn.no/ottersen/

A laboratory that investigates the molecular mechanisms involved in the development of acute and chronic neurodegenerative disease, with a focus on the role of glutamate excitotoxicity. It aims at unraveling the molecular basis for cell death and edema development in stroke, and explores the pathophysiology of Alzheimer's disease and temporal lobe epilepsy. The main objective of the LMN is to advance understanding of the role of glutamate, as a transmitter substance in the normal brain and as a mediator of excitotoxicity in pathological conditions such as stroke. To this end the LMN employs several vital and nonvital imaging techniques. Model systems includes organotypic slice cultures and transgenic animals. An important focus of the LMN is to explore the role of DNA damage and repair in the pathogenesis of neurodegenerative disease. LMN is also engaged in research on molecular mechanism underlying brain edema, epilepsy, and Alzheimer's disease.

Proper citation: Laboratory of Molecular Neuroscience, University of Oslo (RRID:SCR_008097) Copy   

•   Source: SciCrunch Registry

http://www.virology.net/garryfavweb.html

All the Virology on the WWW is a site for virology information on the Internet. They have collected all the virology related web sites that might be of interest to virologists, and others interested in learning more about viruses. Additionally, they have created an index to virus pictures on the web, The Big Picture Book of Viruses, which also functions as a resource for viral taxonomy. A collection of some of the best Online Virology and Microbiology Course Notes available can also be found here. If users are interested in even more information, The Virology Bookshop, an on-line microbiology and virology bookstore with a significant discount for our users. It is their goal that this site will provide both the professional virologist and the general public with access to information about viruses. Over the past several years, these pages have grown to encompass something of interest for everyone. The lists of virology related sites are divided into multiple pages, all of which are accessible from this page and from the more descriptive Complete Table of Contents. There are also links to Virology Dictionaries if users are confused by some of this site''s more technical content. These sites are listed without bias and with much organization Categories: Metadatabases and Directories

Proper citation: All the Virology on the WWW (RRID:SCR_008159) Copy   

•   Source: SciCrunch Registry

http://www.gene-regulation.com/pub/databases.html

In an effort to strongly support the collaborative nature of scientific research, BIOBASE offers academic and non-profit organizations free access to reduced functionality versions of their products. TRANSFAC Professional provides gene regulation analysis solutions, offering the most comprehensive collection of eukaryotic gene regulation data. The professional paid subscription gives customers access to up-to-date data and tools not available in the free version. The public databases currently available for academic and non-profit organizations are: * TRANSFAC: contains data on transcription factors, their experimentally-proven binding sites, and regulated genes. Its broad compilation of binding sites allows the derivation of positional weight matrices. * TRANSPATH: provides data about molecules participating in signal transduction pathways and the reactions they are involved in, resulting in a complex network of interconnected signaling components.TRANSPATH focuses on signaling cascades that change the activities of transcription factors and thus alter the gene expression profile of a given cell. * PathoDB: is a database on pathologically relevant mutated forms of transcription factors and their binding sites. It comprises numerous cases of defective transcription factors or mutated transcription factor binding sites, which are known to cause pathological defects. * S/MARt DB: presents data on scaffold or matrix attached regions (S/MARs) of eukaryotic genomes, as well as about the proteins that bind to them. S/MARs organize the chromatin in the form of functionally independent loop domains gained increasing support. Scaffold or Matrix Attached Regions (S/MARs) are genomic DNA sequences through which the chromatin is tightly attached to the proteinaceous scaffold of the nucleus. * TRANSCompel: is a database on composite regulatory elements affecting gene transcription in eukaryotes. Composite regulatory elements consist of two closely situated binding sites for distinct transcription factors, and provide cross-coupling of different signaling pathways. * PathoSign Public: is a database which collects information about defective cell signaling molecules causing human diseases. While constituting a useful data repository in itself, PathoSign is also aimed at being a foundational part of a platform for modeling human disease processes.

Proper citation: Gene Regulation Databases (RRID:SCR_008033) Copy   

•   Source: SciCrunch Registry

http://ncv.unl.edu/Angelettilab/HPV/Database.html

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 August 23, 2016. The Human Papillomaviruses Database collects, curates, analyzes, and publishes genetic sequences of papillomaviruses and related cellular proteins. It includes molecular biologists, sequence analysts, computer technicians, post-docs and graduate research assistants. This Web site has two main branches. The first contains our four annual data books of papillomavirus information, called Human Papillomaviruses: A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences. and the second contains papillomavirus genetic sequence data. There is also a New Items location where we store the latest changes to the database or any other current news of interest. Besides the compendium, we also provide genetic sequence information for papilloma viruses and related cellular proteins. Each year they publish a compendium of papillomavirus information called Human Papillomaviruses: A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences. which can now be downloaded from this Web site.

Proper citation: HPV Sequence Database (RRID:SCR_008154) Copy   

•   Source: SciCrunch Registry

http://www.animalgenome.org/pigs/nagrp.html

Database and resources on the pig genome.

Proper citation: U.S. Pig Genome Project (RRID:SCR_008151) 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