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http://www.catstests.com/Product09.htm

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. Memory impairment is one of the most common complaints after head injury, and accordingly, individuals may attempt to feign memory impairment or exaggerate symptoms of memory impairment. This free neuropsychological evaluation software contains some of the most common tests used to detect malingering of memory impairment. This software package contains a number of tests of declarative memory that assess recall of information that has a personal and temporal context. The typical example of declarative tests used for detecting malingering are the auditory verbal learning test and forced choice test. These tests are included in Symptom Validity along with other tests of declarative memory (e.g., prose recall, questionnaire tests). Unfortunately, classification of individuals is not completely accurate even with the use of multiple declarative memory tests. Thus, other tests that can complement previously used declarative memory measures by enhancing classification accuracy may be of great value to the neuropsychologist assessing the possibility of malingering. Your software contains two tests of nondeclarative memory that have been previously shown to be useful in the detection of malingered memory deficits (Davis et al., 1997a, 1997b). These tests take advantage of the general laypersons misunderstanding of the test performance of a truly memory impaired individual. That is, amnesic patients have been shown to perform normally on these nondeclarative memory tests and this is counterintuitive to the memory performance expectations of the general layperson. The nondeclarative tests included in Symptom Validity are two repetition priming tests of word stem completion and two tests of pattern categorization learning. Note: At this time this program will run only on Windows 98. We are currently working on a version that will run under the newer operating systems.

Proper citation: Colorado Assessment Tests - Symptom Validity (RRID:SCR_003520) Copy   

•   Source: SciCrunch Registry

http://www.catstests.com/Product07.htm

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. The modifiable n-Back test is free software presumed to measure executive control of the updating of information in working memory. The task requires the participant to monitor some dimension (e.g. content, position, numerosity) of a temporally present sequence of items, responding when the currently presented item matches on the relevant dimension an item that was just recently presented. The match can be with an item present either 1 back, 2 back, 3 back or n back. Considerable flexibility is provided to the experimenter in specifying various parameters of the experiment (e.g. presentation rate, n back, content, position, color). The n-Back test is presumed to measure executive control of the updating of information in working memory. (Shimamura, 2000) Watter, Geffen and Geffen (2001) based on their work with the P300 event-related-potential have suggested that the n-Back is a dual task in that latencies of the P300 did not change with increasing task difficulty, that is memory load while amplitude did reflecting in their view a reallocation of attention and processing capacity away from the matching subtask. The n-Back task is one in which the participant is presented a series of stimuli at a constant rate. The task of the participant is to determine if the currently presented stimulus is similar (along some dimension) to one they have recently (usually one, two or three positions back) seen in the stream. Match criteria can be dimensions like material, position on the screen, color or some combination. CATs n-Back allows for substantial control over the position in which the material is presented (nine different positions), the nature of the material (any character or dingbat string, and any color. The experimenter can set the speed at which the sequence is presented including both the stimulus on time and the inter-stimulus interval. Participant responses can be made either using the keyboard or the mouse. At this time no normative data is available for this test.

Proper citation: Colorado Assessment Tests: n-Back (RRID:SCR_003517) Copy   

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http://www.fugu-sg.org/

THIS RESOURCE IS NO LONGER IN SERVICE,documented on August 16, 2019. Fugu genome is among the smallest vertebrate genomes and has proved to be a valuable reference genome for identifying genes and other functional elements such as regulatory elements in the human and other vertebrate genomes, and for understanding the structure and evolution of vertebrate genomes. This site presents version 4 of the Fugu genome, released in October 2004 by the International Fugu Genome Consortium. Fugu rubripes has a very compact genome, with less than 15 consisting of dispersed repetitive sequence, which makes it ideal for gene discovery. A draft sequence of the fugu genome was determined by the International Fugu Genome Consortium in 2002 using the ''whole-genome shotgun'' sequencing strategy. Fugu is the second vertebrate genome to be sequenced, the first being the human genome. This webpage presents the annotation made on the fourth assembly by the IMCB team using the Ensembl annotation pipeline. We are continuing with the gap filling work and linking of the scaffolds to obtain super-contigs.

Proper citation: Fugu Genome Project (RRID:SCR_013014) Copy   

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http://tubic.tju.edu.cn/deg

THIS RESOURCE IS NO LONGER IN SEVICE. Documented on August 19,2019.It hosts records of currently available essential genes among a wide range of organisms. For prokaryotes, DEG contains essential genes in more than 10 bacteria, such as E. coli, B. subtilis, H. pylori, S. pneumoniae, M. genitalium and H. influenzae, whereas for eukaryotes, DEG contains those in yeast, humans, mice, worms, fruit flies, zebra fish and the plant A. thaliana. Users can Blast query sequences against DEG, and can also search for essential genes by their functions and names. Essential gene products comprise excellent targets for antibacterial drugs. Essential genes in a bacterium constitute a minimal genome, forming a set of functional modules, which play key roles in the emerging field, synthetic biology.

Proper citation: DEG - Database of Essential Genes (RRID:SCR_012929) Copy   

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http://www.phenomicdb.de/

PhenomicDB is a multi-organism phenotype-genotype database including human, mouse, fruit fly, C.elegans, and other model organisms. The inclusion of gene indices (NCBI Gene) and orthologs (same gene in different organisms) from HomoloGene allows to compare phenotypes of a given gene over many organisms simultaneously. PhenomicDB contains data from publicly available primary databases: FlyBase, Flyrnai.org, WormBase, Phenobank, CYGD, MatDB, OMIM, MGI, ZFIN, SGD, DictyBase, NCBI Gene, and HomoloGene. We brought this wealth of data into a single integrated resource by coarse-grained semantic mapping of the phenotypic data fields, by including common gene indexes (NCBI Gene), and by the use of associated orthology relationships (HomoloGene). PhenomicDB is thought as a first step towards comparative phenomics and will improve the understanding of the gene functions by combining the knowledge about phenotypes from several organisms. It is not intended to compete with the much more dedicated primary source databases but tries to compensate its partial loss of depth by linking back to the primary sources. The basic functional concept of PhenomicDB is an integrated meta-search-engine for phenotypes. Users should be aware that comparison of genotypes or even phenotypes between organisms as different as yeast and man can have serious scientific hurdles. Nevertheless finding that the phenotype of a given mouse gene is described as ��similar to psoriasis�� and at the same time that the human ortholog has been described as a gene causing skin defects can lead to novelty and interesting hypotheses. Similarly, a gene involved in cancer in mammalian organisms could show a proliferation phenotype in a lower organism such as yeast and thus, give further insights to a researcher.

Proper citation: PhenomicDB (RRID:SCR_013051) Copy   

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http://www.treefam.org

A database of phylogenetic trees of animal genes. It aims at developing a curated resource that gives reliable information about ortholog and paralog assignments, and evolutionary history of various gene families. TreeFam defines a gene family as a group of genes that evolved after the speciation of single-metazoan animals. It also tries to include outgroup genes like yeast (S. cerevisiae and S. pombe) and plant (A. thaliana) to reveal these distant members.TreeFam is also an ortholog database. Unlike other pairwise alignment based ones, TreeFam infers orthologs by means of gene trees. It fits a gene tree into the universal species tree and finds historical duplications, speciations and losses events. TreeFam uses this information to evaluate tree building, guide manual curation, and infer complex ortholog and paralog relations.The basic elements of TreeFam are gene families that can be divided into two parts: TreeFam-A and TreeFam-B families. TreeFam-B families are automatically created. They might contain errors given complex phylogenies. TreeFam-A families are manually curated from TreeFam-B ones. Family names and node names are assigned at the same time. The ultimate goal of TreeFam is to present a curated resource for all the families. phylogenetic tree, animal, vertebrate, invertebrate, gene, ortholog, paralog, evolutionary history, gene families, single-metazoan animals, outgroup genes like yeast (S. cerevisiae and S. pombe), plant (A. thaliana), historical duplications, speciations, losses, Human, Genome, comparative genomics

Proper citation: Tree families database (RRID:SCR_013401) Copy   

•   Source: SciCrunch Registry

http://americaninstituteofstress.org/interviews/

From time to time the Editor of Health and Stress interviews leaders in the field of stress management on a variety of topics for inclusion in our publications. Some interviews are listed below. For a complete list of interviews and content, you must be a member of AIS and access the Archives.

Proper citation: American Institute of Stress Interviews (RRID:SCR_005420) Copy   

•   Source: SciCrunch Registry

http://publications.nigms.nih.gov/computinglife/

An NIGMS magazine that showcases the exciting ways that scientists are using the power of computers to expand our knowledge of biology and medicine. From text messaging friends to navigating city streets with GPS technology, we''re all living the computing life. But as we''ve upgraded from snail mail and compasses, so too have scientists. Computer advances now let researchers quickly search through DNA sequences to find gene variations that could lead to disease, simulate how flu might spread through your school and design three-dimensional animations of molecules that rival any video game. By teaming computers and biology, scientists can answer new and old questions that could offer insights into the fundamental processes that keep us alive and make us sick. This booklet introduces you to just some of the ways that physicists, biologists and even artists are computing life. Each section focuses on a different research problem, offers examples of current scientific projects and acquaints you with the people conducting the work. You can follow the links for online extras and other opportunities to learn aboutand get involved inthis exciting new interdisciplinary field.

Proper citation: NIGMS Computing Life (RRID:SCR_005850) Copy   

•   Source: SciCrunch Registry

http://www.thehamner.org/technology-and-development/technology-transfer/index.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 24, 2013. BMDExpress is a Java application used to analyze dose-response data from microarray experiments. The program was designed to perform a stepwise analysis on microarray data that combines bench mark dose (BMD) calculations with gene ontology (GO) classification analysis. The combination provides dose estimates at which different cellular processes are altered at a defined increase in risk based on expression levels in the untreated controls. The fitting of the data to the statistical models (linear, 2 polynomial models, 3 polynomial, and power models) is performed using source code borrowed from the U.S. Environmental Protection Agency''''s BMDS software. The MPPD model is a computational model that can be used for estimating human and rat airway particle dosimetry. The model is applicable to risk assessment, research, and education. The MPPD model calculates the deposition and clearance of monodisperse and polydisperse aerosols in the respiratory tracts of rats and human adults and children (deposition only) for particles ranging in size from ultrafine (0.01 m) to coarse (20 m). The models are based on single-path and multiple-path methods for tracking air flow and calculating aerosol deposition in the lung. The single-path method calculates deposition in a typical path per airway generation, while the multiple-path method calculates particle deposition in all airways of the lung and provides lobar-specific and airway-specific information. Within each airway, deposition is calculated using theoretically derived efficiencies for deposition by diffusion, sedimentation, and impaction within the airway or airway bifurcation. Filtration of aerosols by the head is determined using empirical efficiency functions. The MPPD model includes calculations of particle clearance in the lung following deposition. Eight tutorials are provided so that the user can learn to interact with the software.

Proper citation: The Hamner Institute for Health Sciences: BMDExpress and The multiple-path particle dosimetry (RRID:SCR_005511) Copy   

•   Source: SciCrunch Registry

http://www.dkfz.de/en/mga/Groups/LIFEdb-Database.html

Database that integrates large-scale functional genomics assays and manual cDNA annotation with bioinformatics gene expression and protein analysis. LifeDB integrates data regarding full length cDNA clones and data on expression of encoded protein and their subcellular localization on mammalian cell line. LifeDB enables the scientific community to systematically search and select genes, proteins as well as cDNA of interest by specific database identifiers as well as gene name. It enables to visualize cDNA clone and subcellular location of proteins. It also links the results to external biological databases in order to provide a broader functional information. LifeDB also provides an annotation pipeline which facilitates an improved mapping of clones to known human reference transcripts from the RefSeq database and the Ensembl database. An advanced web interface enables the researchers to view the data in a more user friendly manner. Users can search using any one of the following search options available both in Search gene and cDNA clones and Search Sub-cellular locations of human proteins: By Keyword, By gene/transcript identifier, By plate name, By clone name, By cellular location. * The Search genes and cDNA clones results include: Gene Name, Ensemble ID, Genomic Region, Clone name, Plate name, Plate position, Classification class, Synonymous SNP''s, Non- synonymous SNP''s, Number of ambiguous positions, and Alignment with reference genes. * The Search sub-cellular locations of human proteins results include: Subcellular location, Gene Name, Ensemble ID, Clone name, True localization, Images, Start tag and End tag. Every result page has an option to download result data (excluding the microscopy images). On click of ''Download results as CSV-file'' link in the result page the user will be given a choice to open or save result data in form of a CSV (Comma Separated Values) file. Later the CSV file can be easily opened using Excel or OpenOffice.

Proper citation: LifeDB (RRID:SCR_006899) Copy   

•   Source: SciCrunch Registry

http://www.liden.cc/Visionary/

It is a dictionary for terminology used in the study of human and animal vision. It includes terms from the areas of biological and machine vision, visual psychophysics, visual neuroscience and other related fields. Sponsors: Visionary is sponsored by Educational Software for Autism.

Proper citation: Visionary: A Dictionary for the Study of Vision (RRID:SCR_008307) Copy   

•   Source: SciCrunch Registry

http://cprc.rcm.upr.edu/

Center for the study of non-human primates. Its mission is the study and use of non-human primates as models for studies of social and biological interactions and for the discovery of methods of prevention, diagnosis and treatment of diseases that afflict humans. Through the stewardship of three unique facilities—Cayo Santiago Field Station, Sabana Seca Field Station, and the Laboratory of Primate Morphology supports a diverse range of research programs that enhance understanding of primate biology and behavior, with direct applications in biomedical and translational research.

Proper citation: Caribbean Primate Research Center (RRID:SCR_008345) Copy   

•   Source: SciCrunch Registry

http://genewindow.nci.nih.gov/

Software tool for pre- and post-genetic bioinformatics and analytical work, developed and used at the Core Genotyping Facility (CGF) at the National Cancer Institute. While Genewindow is implemented for the human genome and integrated with the CGF laboratory data, it stands as a useful tool to assist investigators in the selection of variants for study in vitro, or in novel genetic association studies. The Genewindow application and source code is publicly available for use in other genomes, and can be integrated with the analysis, storage, and archiving of data generated in any laboratory setting. This can assist laboratories in the choice and tracking of information related to genetic annotations, including variations and genomic positions. Features of GeneWindow include: -Intuitive representation of genomic variation using advanced web-based graphics (SVG) -Search by HUGO gene symbol, dbSNP ID, internal CGF polymorphism ID, or chromosome coordinates -Gene-centric display (only when a gene of interest is in view) oriented 5 to 3 regardless of the reference strand and adjacent genes -Two views, a Locus Overview, which varies in size depending on the gene or genomic region being viewed and, below it, a Sequence View displaying 2000 base pairs within the overview -Navigate the genome by clicking along the gene in the Locus Overview to change the Sequence View, expand or contract the genomic interval, or shift the view in the 5 or 3 direction (relative to the current gene) -Lists of available genomic features -Search for sequence matches in the Locus Overview -Genomic features are represented by shape, color and opacity with contextual information visible when the user moves over or clicks on a feature -Administrators can insert newly-discovered polymorphisms into the Genewindow database by entering annotations directly through the GUI -Integration with a Laboratory Information Management System (LIMS) or other databases is possible

Proper citation: GeneWindow (RRID:SCR_008183) Copy   

•   Source: SciCrunch Registry

https://ostr.ccr.cancer.gov/resources/provider_details/nci-mouse-repository

The NCI Mouse Repository cryoarchives and distributes strains of genetically engineered mice that are of immediate interest to the cancer research community. These are either gene-targeted or transgenic mice that display a cancer-related phenotype, or tool strains (e.g., cre transgenics) that can be used to develop new cancer models. You do not have to be a member of the NCI Mouse Repository or a recipient of NCI funding to have your mouse model distributed through the NCI Mouse Repository. NCI Mouse Repository strains are maintained as live colonies or cryoarchived as frozen embryos, depending on demand. Up to three breeder pairs may be ordered from live colonies. Cryoarchived strains are supplied as frozen embryos or recovery of live mice by the NCI Mouse Repository may be requested.

Proper citation: NCI Mouse Repository (RRID:SCR_002264) 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://harvester.fzk.de/harvester/

Harvester is a Web-based tool that bulk-collects bioinformatic data on human proteins from various databases and prediction servers. It is a meta search engine for gene and protein information. It searches 16 major databases and prediction servers and combines the results on pregenerated HTML pages. In this way Harvester can provide comprehensive gene-protein information from different servers in a convenient and fast manner. As full text meta search engine, similar to Google trade mark, Harvester allows screening of the whole genome proteome for current protein functions and predictions in a few seconds. With Harvester it is now possible to compare and check the quality of different database entries and prediction algorithms on a single page. Sponsors: This work has been supported by the BMBF with grants 01GR0101 and 01KW0013.

Proper citation: Bioinformatic Harvester IV (beta) at Karlsruhe Institute of Technology (RRID:SCR_008017) Copy   

•   Source: SciCrunch Registry

http://cancer.case.edu/research/sharedresources/tissue/services/

A combined tissue bank and core facility which provides annotated human tissue samples for research purposes. The facility also offers high quality tissue procurement, tissue microarray, histology, immunohistochemistry, photomicroscopy, and laser capture microdissection services for both human and animal tissues to biomedical investigators conducting non-clinical research studies. The TPHC offers instruction to researchers on how to incorporate human tissue into research activities and how to work within the boundaries of patient confidentiality and other regulatory issues. The purpose of the TPHC is to provide tissue collection and processing services to intramural and extramural researchers studying cancer and other diseases. Normal, diseased, benign and malignant tissues are obtained, and matched normal adjacent tissues and tissues from different organ sites from the same donor can also be provided when available. Tissue samples are prepared according to user-specified protocols and can be fresh in a medium of choice, fixed in formalin, quick frozen in the vapor phase of liquid nitrogen or snap-frozen by plunging the sample into liquid nitrogen. Frozen tissues are held in the vapor phase of the liquid nitrogen. Tissues can also be embedded, cut and mounted on slides, and stained upon request. Tissue Microarray (TMA) services are offered for the design and construction of TMAs meeting specific project needs. Basic demographic data (age, race, gender) and histopathologic data from Surgical Pathology Reports are provided by the TPHC with the tissues.

Proper citation: Case Western Reserve Tissue Procurement and Histology Core Facility (RRID:SCR_005344) Copy   

•   Source: SciCrunch Registry

http://www.alz.washington.edu/

A clinical research, neuropathological research and collaborative research database that uses data collected from 29 NIA-funded Alzheimer's Disease Centers (ADCs). The database consists of several datasets, and searches may be done on the entire database or on individual datasets. Any researcher, whether affiliated with an ADC or not, may request a data file for analysis or aggregate data tables. Requested aggregate data tables are produced and returned as soon as the queue allows (usually within 1-3 days depending on the complexity).

Proper citation: National Alzheimer's Coordinating Center (RRID:SCR_007327) Copy   

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http://www.sanger.ac.uk/Projects/D_rerio/zmp/

Create knockout alleles in protein coding genes in the zebrafish genome, using a combination of whole exome enrichment and Illumina next generation sequencing, with the aim to cover them all. Each allele created is analyzed for morphological differences and published on the ZMP site. Transcript counting is performed on alleles with a morphological phenotype. Alleles generated are archived and can be requested from this site through the Zebrafish International Resource Center (ZIRC). You may register to receive updates on genes of interest, or browse a complete list, or search by Ensembl ID, gene name or human and mouse orthologue.

Proper citation: ZMP (RRID:SCR_006161) Copy   

•   Source: SciCrunch Registry

https://abctb.org.au/abctbNew2/default.aspx

A tissue bank which houses and supplies cancerous tissue for use by the research community. Along with tissue, the bank collects clinical history, lifestyle factors, breast pathology, treatment information, and follow up information.

Proper citation: Australia Breast Cancer Tissue Bank (RRID:SCR_000926) Copy   

•   Source: SciCrunch Registry