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http://www.chr7.org

Database containing the DNA sequence and annotation of the entire human chromosome 7, encompassing nearly 158 million nucleotides of DNA and 1917 gene structures, are presented; the most up to date collation of sequence, gene, and other annotations from all databases (eg. Celera published, NCBI, Ensembl, RIKEN, UCSC) as well as unpublished data. To generate a higher order description, additional structural features such as imprinted genes, fragile sites, and segmental duplications were integrated at the level of the DNA sequence with medical genetic data, including 440 chromosome rearrangement breakpoints associated with disease. The objective of this project is to generate a comprehensive description of human chromosome 7 to facilitate biological discovery, disease gene research and medical genetic applications. There are over 360 disease-associated genes or loci on chromosome 7. A major challenge ahead will be to represent chromosome alterations, variants, and polymorphisms and their related phenotypes (or lack thereof), in an accessible way. In addition to being a primary data source, this site serves as a weighing station for testing community ideas and information to produce highly curated data to be submitted to other databases such as NCBI, Ensembl, and UCSC. Therefore, any useful data submitted will be curated and shown in this database. All Chromosome 7 genomic clones (cosmids, BACs, YACs) listed in GBrowser and in other data tables are freely distributed.

Proper citation: Chromosome 7 Annotation Project (RRID:SCR_007134) Copy   

•   Source: SciCrunch Registry

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://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   

•   Source: SciCrunch Registry

http://ideas.repec.org/c/boc/bocode/s360702.html

COLELMS calculates LMS values, smoothed LMS, and growth reference centiles based in smoothed LMS values. df value is set to when calculating smoothed LMS values. You are responsible for setting an appropriate df for your data. This is version 0.2 of the software. Sponsors: This resource is supported by Boston College. Keywords: Software, LMS, Calculation, Growth, Data, Stata, Module,

Proper citation: COLELMS: Stata module to calculate Coles LMS values for growth data (RRID:SCR_007244) 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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.nmpdr.org/FIG/wiki/view.cgi

The National Microbial Pathogen Data Resource provides curated annotations in an environment for comparative analysis of genomes and biological subsystems, with an emphasis on the food-borne pathogens Campylobacter, Listeria, Staphylococcus, Streptococcus, and Vibrio; as well as the STD pathogens Chlamydiaceae, Haemophilus, Mycoplasma, Neisseria, Treponema, and Ureaplasma. This edition of the NMPDR includes 47 archaeal, 725 bacterial, and 29 eukaryal genomes with 3,257,100 genetic features, of which 1,338,895 are in FIGfams curated using 616 active subsystems. ''''''Notice to NMPDR Users'''''' - The NMPDR BRC contract ended in December 2009. At that time we ceased maintenance of the NMPDR web resource and data. Bacterial data from NMPDR has been transferred to PATRIC (http://www.patricbrc.org), a new consolidated BRC for all NIAID category A-C priority pathogenic bacteria. NMPDR was a collaboration among researchers from the Computation Institute of the University of Chicago, the Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the National Center for Supercomputing Applications (NCSA) at the University of Illinois.

Proper citation: NMPDR (RRID:SCR_007821) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.hpid.org

Database that provides human protein interaction information and integrated interaction and also finds proteins from databases that can potentially react with proteins submitted by users. The human protein interaction information was pre-computed by a statistical method from existing structural and experimental data, while the integrated human protein interactions are derived from BIND, DIP and HPRD. A score composed of three parts is assigned to the predicted interaction data, and those interactions with high scores were found reliable. HPID allows the user to use the protein IDs in EMBL, Ensembl, MIM, RefSeq, HPRD and NCBI to search protein interactions of interest. A set of web-based software tools has also been developed so that users can visualize and analyze protein interaction networks.

Proper citation: HPID - Human Protein Interaction database (RRID:SCR_007724) Copy   

•   Source: SciCrunch Registry

http://t1dbase.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 26,2019. In October 2016, T1DBase has merged with its sister site ImmunoBase (https://immunobase.org). Documented on March 2020, ImmunoBase ownership has been transferred to Open Targets (https://www.opentargets.org). Results for all studies can be explored using Open Targets Genetics (https://genetics.opentargets.org). Database focused on genetics and genomics of type 1 diabetes susceptibility providing a curated and integrated set of datasets and tools, across multiple species, to support and promote research in this area. The current data scope includes annotated genomic sequences for suspected T1D susceptibility regions; genetic data; microarray data; and global datasets, generally from the literature, that are useful for genetics and systems biology studies. The site also includes software tools for analyzing the data.

Proper citation: T1DBase (RRID:SCR_007959) Copy   

•   Source: SciCrunch Registry

http://www.louisville.edu/medschool/pharmacology/

The Department of Pharmacology & Toxicology in the School of Medicine at the University of Louisville focuses upon the interaction of drugs and other chemicals with biological systems ranging from individual molecules, to cells, to tissues, to organ systems or individuals. The two disciplines are a continuum incorporating the therapeutic to toxic effect of every drug and chemical. Our departmental programs incorporate pharmacology and/or toxicology, and graduates are well trained to accept employment in either or both disciplines. Our research and curriculum incorporate molecular biology, genetics, neuroscience, biochemistry, physiology and other biomedical sciences, providing maximum flexibility for our graduates.

Proper citation: University of Louisville, Department of Pharmacology (RRID:SCR_007510) Copy   

•   Source: SciCrunch Registry

https://rwjms.rutgers.edu/departments/pharmacology/message-from-the-chair

Department of Pharmacology is committed to fulfilling its roles in education, research and service, both locally and on a broader scale. Our faculty contributes to the education of medical, graduate and undergraduate students in the classroom and in the laboratory; carries out research at the forefront of biomedical science while training the next generation of research scientists; and serves the medical school, university, national and international scientific communities.

Proper citation: Rutgers University Robert Wood Johnson Medical School Department of Pharmacology (RRID:SCR_007470) Copy   

•   Source: SciCrunch Registry

http://vega.sanger.ac.uk/

Central repository for high quality frequently updated manual annotation of vertebrate finished genome sequence. Human, mouse and zebrafish are in the process of being completely annotated, whereas for other species the annotation is only of specific genomic regions of particular biological interest. The majority of the annotation is from the HAVANA group at the Welcome Trust Sanger Institute. Users can BLAST, search for specific text, export, and download data. Genomes and details of the projects for each species are available through the homepages for human mouse and zebrafish. The website is built upon code from the EnsEMBL (http://www.ensembl.org) project. Some Ensembl features are not available in Vega. From the users point of view perhaps the most significant of these is MartView. However due to their inclusion in Ensembl, Vega human and mouse data can be queried using Ensembl MartView. Vega contains annotation of the human MHC region in eight haplotypes, and the LRC region in three haplotypes. Vega also contains annotation on the Insulin Dependent Diabetes (IDD) regions on non-reference assemblies for mouse.

Proper citation: VEGA (RRID:SCR_007907) Copy   

•   Source: SciCrunch Registry

http://variation.osu.edu/rtcgd/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Database of high throughput insertional mutagenesis screening projects of retroviral and transposon insertional mutagenesis in mouse tumors. Information in the RTCGD is obtained from sequence comparison by using public databases UCSC genome mm9 browser. Data based on previous genome assembly mm8 is also available at RTCGD mm8. MCGP has developed three web search tools including Easy Search to query proviral integration sites using mouse gene symbol of gene name; Model Search to obtain RIS information based on tumor models and/or tumor types; Interaction Search to find gene-to-gene interaction. It displays the list of genes which reside in the same tumor to your gene of interest.

Proper citation: Retroviral Tagged Cancer Gene Database (RRID:SCR_007908) Copy   

•   Source: SciCrunch Registry

http://www.mcmp.purdue.edu/

The Department of Medicinal Chemistry and Molecular Pharmacology is one of the three departments comprising the School of Pharmacy and Pharmaceutical Sciences. There are currently over 80 graduate students enrolled in the Department, the vast majority of whom are engaged in studies leading to the Ph.D. degree. The presence of approximately 30 postdoctoral associates and other research staff professionals further enriches the intellectual atmosphere. Graduate students in the Department have the opportunity to interact with researchers in a wide variety of fields, including many who are associated with other departments at Purdue. Various research groups actively collaborate with groups from departments such as biochemistry, biological sciences, chemical engineering, chemistry, foods and nutrition, horticulture, and physics. In addition, approximately half of our faculty belong to the Purdue Cancer Center, the Neuroscience Program, the Graduate Program in Virology and/or the Purdue University Biochemistry and Molecular Biology Program (BMB), leading to extensive, formalized interactions campus-wide. Graduate students attend research seminars across campus, -affording the opportunity to observe firsthand many of the world's foremost researchers.

Proper citation: Purdue University School of Pharmacy and Pharmaceutical Sciences Department of Medicinal Chemistry and Molecular Pharmacology (RRID:SCR_007468) Copy   

•   Source: SciCrunch Registry

http://fmf.igh.cnrs.fr/ISSAID/infevers

Registry for Familial Mediterranean Fever (FMF) and hereditary inflammatory disorders mutations. As of 2014, it includes twenty genes including: MEFV, MVK, TNFRSF1A, NLRP3, NOD2, PSTPIP1, LPIN2 and NLRP7, and contains over 1338 sequence variants. Confidential data, simple and complex alleles are accepted. For each gene, a menu offers: 1) a tabular list of the variants that can be sorted by several parameters; 2) a gene graph providing a schematic representation of the variants along the gene; 3) statistical analysis of the data according to the phenotype, alteration type, and location of the mutation in the gene; 4) the cDNA and gDNA sequences of each gene, showing the nucleotide changes along the sequence, with a color-based code highlighting the gene domains, the first ATG, and the termination codon; and 5) a download menu making all tables and figures available for the users, which, except for the gene graphs, are all automatically generated and updated upon submission of the variants. The entire database was curated to comply with the HUGO Gene Nomenclature Committee (HGNC) and HGVS nomenclature guidelines, and wherever necessary, an informative note was provided.

Proper citation: INFEVERS (RRID:SCR_007738) Copy   

•   Source: SciCrunch Registry

http://www.pharmacy.utah.edu/pharmtox/

The Department of Pharmacology and Toxicology at the University of Utah is located in Salt Lake City at the foot of the beautiful Wasatch Range of the Rocky Mountains. Our Department focuses on research, graduate and professional training, and service. The faculty of this department place a high priority on the teaching and research training of graduate students for the Ph.D. degree. Our program features close working relationships between individual students and their faculty mentor, rich and diverse research opportunities, and individualized programs of study based on the needs of the students. Doctoral graduates of our program gain employment in research and teaching positions at colleges and universities, engage in research and development in the biotechnology and pharmaceutical industries, and have additional opportunities in research institutes, government agencies, environmental protection organizations, and many other arenas. Our Summer Undergraduate Research Fellowship (SURF) Program provides enriching research experiences for undergraduate students anticipating research careers in the biological sciences.

Proper citation: University of Utah Salt Lake City Utah. Pharmacology & Toxicology (RRID:SCR_007537) Copy   

•   Source: SciCrunch Registry