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http://www.biorad.com

Commercial instrument and chemical vendor. Developer and manufacturer of specialized technological products for life science research and clinical diagnostics markets.

Proper citation: Bio-Rad Laboratories (RRID:SCR_008426) Copy   

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http://noble.gs.washington.edu/proj/sdp-svm/

A statistical framework for genomic data fusion is a computational framework for integrating and drawing inferences from a collection of genome-wide measurements. Each dataset is represented via a kernel function, which defines generalized similarity relationships between pairs of entities, such as genes or proteins. The kernel representation is both flexible and efficient, and can be applied to many different types of data. Furthermore, kernel functions derived from different types of data can be combined in a straightforward fashion. Recent advances in the theory of kernel methods have provided efficient algorithms to perform such combinations in a way that minimizes a statistical loss function. These methods exploit semidefinite programming techniques to reduce the problem of finding optimizing kernel combinations to a convex optimization problem. Computational experiments performed using yeast genome-wide datasets, including amino acid sequences, hydropathy profiles, gene expression data and known protein-protein interactions, demonstrate the utility of this approach. A statistical learning algorithm trained from all of these data to recognize particular classes of proteins--membrane proteins and ribosomal proteins--performs significantly better than the same algorithm trained on any single type of data. Matlab code to center a kernel matrix and Matlab code for normalization are available.

Proper citation: A statistical framework for genomic data fusion (RRID:SCR_007219) Copy   

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http://www.pedigree-draw.com/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2024. Software application for pedigree drawing (entry from Genetic Analysis Software)

Proper citation: Pedigree-Draw (RRID:SCR_008302) Copy   

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http://www.catstests.com/Product05.htm

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. CATs Card Sort is a free, general purpose card sorting program which allows the user to design sorting tasks similar to those described by Vigotsky (1934), Weigel (1941), and Grant and Berg (1948). Card sorting tasks have been shown to be particularly sensitive to frontal lobe dysfunction, but have also shown sensitivity to motor disorders, schizophrenia, chronic alcoholism, aging, and attention deficit disorder. The CATs Card Sort package provides extensive flexibility in the development of stimulus cards, allowing the experimenter to define the relevant dimensions of cards in terms of figures, letters or words, figure/letter/word color, card color, figure/letter numerosity, and a user defined dimension. Considerable flexibility is also provided in designing lists of to be sorted cards, sort criteria, and the criteria for sort classification shift. The package also provides limited analysis capabilities as described by Grant and Berg (1948). However, as with all CATs packages raw data can be copied to the clipboard in a format acceptable for import into commonly available spreadsheets such as Excel allowing the user to design analysis routines appropriate to their needs.

Proper citation: Colorado Assessment Tests - Card Sort (RRID:SCR_007331) Copy   

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http://www.epa.qld.gov.au/

The department handles some of the most complex issues facing Queensland, including securing water for the future, managing land use, meeting the challenges of climate change, and conserving the states natural and cultural heritage. We promote sustainable living and resource use, and employ the latest science to underpin decision making. We are responsible for developing initiatives which ensure Queensland reduces its carbon footprint while also making sure the State is well-placed to meet the impacts of climate change. The Queensland Centre for Climate Change Excellence (QCCCE) provides specific climate science and research on climate change impacts and addresses issues that are specifically relevant to Queensland. A suite of ClimateSmart programs encourages householders and business to contribute to minimising the impacts of climate change by reducing their carbon emissions. This will help achieve the Queensland Governments Toward Q2 Green target: cut by one-third Queenslanders carbon footprint with reduced car and electricity use while also conserving water at home, work and in their communities. grants/funding Natural Resources Awareness Grants 2010 recipients announced The successful applicants for the Natural Resources Awareness Grants for 2010 have been announced. More than 100 000 has been allocated to 17 community projects to help promote the importance of natural resource management and reduce our carbon footprint. Koala disease research fund The Koala Disease Research Fund is offering grants to support high quality research that will guide DERM management actions to mitigate the effects of disease on wild populations of koalas. Indigenous cultural heritage grants Two cultural heritage grant programs administered by DERM offer funding formanaging and protecting Indigenous cultural heritage sites and helping registered Indigenous cultural heritage bodies fulfil their legislative role. Incentives for natural resource management Visit the Natural Resource Management Incentives database for information on grants offered by industry and federal, state, and local governments for natural resource management activities. Queensland Sustainable Energy Innovation Fund The Queensland Sustainable Energy Innovation Fund helps Queensland-based organisations to develop innovative technologies for reducing consumption of fossil fuels, water or greenhouse gas emissions. Great Artesian Basin Sustainability Initiative The Great Artesian Basin Sustainability Initiative provides financial assistance to landholders to rehabilitate bores and replace bore drains with piped systems, which help preserve water and restore artesian pressure. Other grants Visit Queensland GovernmentGrants, or call Smart Service Queensland on 13 13 04* for information on current funding and grants for all Queensland Government departments. * Local call costs apply Closed Low Carbon Diet Community Funding Program The Low Carbon Diet Community Funding Program assists with administration and delivery costs to help Queensland groups and organisations implement the diet. Applications for Round 4 close 7 December 2009. Lifestyle Waterwise Grants program The 10 million Lifestyle Waterwise Grants program was launched in December 2006 to encourage community-based not-for-profit organisations to reduce their water consumption.

Proper citation: Queensland DERM (RRID:SCR_012329) Copy   

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http://tikus.gsf.de

THIS RESOURCE IS NO LONGER IN SERVICE, documented on October 23, 2014. Consortium that generated a reference library of gene trap sequence tags (GTST) from insertional mutations generated in mouse embryonic stem (ES) cells. The gene trap database represents a repository of sequences produced in a large scale gene trap screen in mouse ES cells using various gene trapping vectors which are delivered either by electroporation or retroviral infections. A type of retroviral gene trap vector has been developed that can induce conditional mutations in most genes expressed in mouse embryonic stem (ES) cells. The vectors rely on directional site-specific recombination systems that can repair and re-induce gene trap mutations when activated in succession. After the gene traps are inserted into the mouse genome, genetic mutations can be produced at a particular time and place in somatic cells. In addition to their conditional features, the vectors create multipurpose alleles amenable to a wide range of post-insertional modifications. Here they have used these directional recombination vectors to assemble the largest library of ES cell lines with conditional mutations in single genes yet assembled, presently totaling 1,000 unique genes. The trapped ES cell lines, which can be ordered from the German Gene Trap Consortium, are freely available to the scientific community.

Proper citation: German Gene Trap Consortium (RRID:SCR_008532) Copy   

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http://wiki.c2b2.columbia.edu/califanolab/index.php/BCellInteractome.htm

A network of protein-protein, protein-DNA and modulatory interactions in human B cells. The network contains known interactions (reported in public databases) and predicted interactions by a Bayesian evidence integration framework which integrates a variety of generic and context specific experimental clues about protein-protein and protein-DNA interactions with inferences from different reverse engineering algorithms, such as GeneWays and ARACNE. Modulatory interactions are predicted by the MINDY, an algorithm for the prediction of modulators of transcriptional interactions (please refer to the publication section for more information). The BCI can be downloaded as one tab delimited file containing the complete network (BCI.txt) with each type of interaction explicitly defined.

Proper citation: B Cell Interactome (RRID:SCR_008655) Copy   

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https://www.facebase.org/fishface/home

ishFace is an atlas of zebrafish craniofacial development. How do the elements of the craniofacial skeleton arise, grow, and reshape? Answers to this question are coming from both molecular-genetic and cell-biological approaches, which rely, first of all, on precise description of the developmental events and processes that comprise skeletogenesis. Zebrafish, with a sophisticated knowledge of its genetics and genomics, with favorable attributes for phenotypic analyses of development, and with patterns of development conserved among all vertebrates, provides a powerful animal model for learning about craniofacial development. In particular, with current transgenic approaches one can examine craniofacial skeletal elements in exquisite cellular detail during an extended period of development within living, intact embryos and larvae an investigative method unsurpassed in accuracy and sensitivity. We constructed this developmental atlas of the craniofacial skeleton, FishFace, to serve as a guide for such study. We hope that the FishFace Atlas will be particularly useful in comparative and mutational analyses where there is interest in understanding the cellular basis of early skeletogenesis. The heart of the FishFace Atlas uses high magnification (generally a 40x objective) confocal image stacks showing transgenically-labelled chondrocytes or osteoblasts, along with mineralized bone matrix, which is visualized by vital staining with Alizarin red. We present these stacks in sequences that follow particular individual cartilages and bones of the first two pharyngeal arches as they develop during embryonic and larval stages. To do so, we build on the foundation set out in the gold standard reference for describing comprehensively skeletal elements in the zebrafish craniofacial complex, Cubbage and Mabee (1996), which used fixed preparations stained for cartilage and bone through adult stages. The FishFace Atlas element development section adds considerable detail to arch one and two early development, particularly at the cellular level, but also in description of element growth and shaping. Other sections of the FishFace Atlas, at lower magnification, provide anatomical context for the element development section, including an interactive tool made by optical projection tomography (OPT) for learning the anatomy of the entire larval skull. Hence, the FishFace Atlas provides the community with an interactive resource with which the user can understand not only the cellular details, but also complex 3D anatomical relationships, of developing elements in the craniofacial skeleton of the zebrafish.

Proper citation: FishFace - An atlas of zebrafish craniofacial development (RRID:SCR_008894) Copy   

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https://www.unr.edu/ncar/infrastructure

Nevada Center for Applied Research coordinates access to Shared Research Facilities extensive resource of labs with cutting edge research and development equipment available to internal University community and external clients from industry, government, research organizations and other institutions.In addition to services and instrumentation, we offer support from highly experienced staff with expertise in designing and conducting experiments and analyzing data. Many facilities can also provide training and education upon request.

Proper citation: University of Nevada Reno Labs and Facilities (RRID:SCR_011008) Copy   

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http://www.genepaint.org/R0_1.htm

A digital atlas of gene expression patterns in the mouse. Expression patterns are determined by non-radioactive in situ hybridization on serial tissue sections. An accompanying atlas based on maps of sagittal sections at embryonic day 14.5. E14.5 NMRI embryo was prepared, sectioned and imaged identically to the embryos used for in situ hybridization. Maps are accessed from the set viewer page using the appropriate button above the image directory. Both, the in situ hybridization section and the appropriate atlas section can be viewed side-by-side. Section thickness is 20 m and inter-section distance is 100 m. Tissue was stained with cresyl violet (Nissl-method). All sections were digitally scanned using a 5x objective. Structures annotated for gene expression are indicated in the maps with red pointers. Boundaries between brain regions are indicated with dashed yellow lines.

Proper citation: GenePaint Interactive Anatomy Atlas (RRID:SCR_007680) Copy   

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http://comkat.case.edu/index.php?title=Home

COMKAT is a software package for compartmental modeling oriented for biomedical image quantification. Free for academic research use, COMKAT has various functions for modeling and imaging analysis in both command-line function and GUIs. COMKAT is MATLAB software for compartmental modeling oriented to nuclear medicine applications (PET & SPECT). It supports models of a wide range complexity including multiple injection, receptor model with saturation. It supports many image formats, including DICOM images. Using either the command line interface or GUI, models are easily specified, solved or used to fit experimental data. Sensitivity equations are supported. No mathematical derivations are required on the part of the user.

Proper citation: Compartment Model Kinetic Analysis Tool (RRID:SCR_007359) Copy   

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http://www.ebire.org/hcnlab/software/cleave.html

A UNIX-style command-line program which quickly computes multifactorial ANOVAs for very large data sets with minimal memory use (without loading all of the data into memory). It has been used for fMRI analysis, e.g. CLEAVE adds the following to the standard ANOVA analyses: # Unlimited numbers of factors can be analyzed. # Factor Correlation and Unequal Variance Corrections # Treatment Magnitudes: omega^2, partial eta^2, and R^2 # A convenient Ranking of Factors based upon treatment magnitudes and significance levels. # Post-Hoc Significance Tests # Post-Hoc Power Table to gauge how many subjects will be needed to achieve significance. # Allows the use of Random Factors. # A Configuration File to make the program more tunable # A Histogram and Cell Line Diagrams: which help the user to detect outliers. # Associated MATLAB functions: port CLEAVE-style data sets in or out of MATLAB.

Proper citation: CLEAVE (RRID:SCR_007113) Copy   

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http://repeatmasker.genome.washington.edu

Welcome to the Department of Genome Sciences, which began in September 2001 by the fusion of the Departments of Genetics and Molecular Biotechnology. Our goal is to address leading edge questions in biology and medicine by developing and applying genetic, genomic and computational approaches that take advantage of genomic information now available for humans, model organisms and a host of other species. Our faculty study a broad range of topics, including the genetics of E. coli, yeast, C. elegans, Drosophila, and mouse; human and medical genetics; mathematical, statistical and computer methods for analyzing genomes, and theoretical and evolutionary genetics; and genome-wide studies by such approaches as sequencing, transcriptional and translational analysis, polymorphism detection and identification of protein interactions. Our chair, Dr. Robert Waterston, joined the department in January 2003. Our department includes both faculty with primary appointments in Genome Sciences, as well as adjuncts in other departments and Seattle institutions. Nine faculty are members of the National Academy of Sciences, including 2001 Nobel Prize winner Dr. Lee Hartwell, who conducted much of his groundbreaking work in the Department of Genetics. Five training faculty are Howard Hughes Medical Institute Investigators. Graduate research in the Department leads to a Ph.D. in Genome Sciences and students may also choose to participate in the Computational Molecular Biology or Molecular Medicine programs. Our department has around 55 - 60 graduate students at any given time and has moved into the new William H. Foege Building.

Proper citation: UW Genome Sciences (RRID:SCR_008562) Copy   

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http://www.ch.embnet.org/software/COILS_form.html

COILS is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. By comparing this score to the distribution of scores in globular and coiled-coil proteins, the program then calculates the probability that the sequence will adopt a coiled-coil conformation.

Proper citation: COILS: Prediction of Coiled Coil Regions in Proteins (RRID:SCR_008440) Copy   

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https://www.anl.gov/research-facilities

Argonne National Laboratory, located just outside of Chicago, is one of the U.S. Department of Energy''s largest national laboratories for scientific and engineering research to solve most important challenges in energy, environment and national security. Programmatic activities cover all aspects of innovation ecology including basic research, technology development and prototype development and testing. We regularly work with industry through exclusive licensing, joint research and variety of other mechanisms to transfer our inventions to marketplace.

Proper citation: Argonne National Laboratory Labs and Facilities (RRID:SCR_011062) Copy   

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http://www.uv.es/vista/vistavalencia/

The general goal is to achieve a deeper understanding of natural image statistics because from this knowledge it should be possible to explain the behavior of the visual cortex and propose new alternatives in a number of applications in image processing and computer vision in which the basic problem is the choice of an appropriate signal representation. The range of basic and applied topics in which we are currently working include: * Mathematical models of human vision * Statistical image models * Image distortion metrics * Image coding * Motion estimation * Video coding * Image restoration * Color representation

Proper citation: Visual Statistics Group (RRID:SCR_008317) Copy   

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http://www.strokedatabase.org/pages/software.html

Diffusion tensor imaging (DTI) tractography: An automated system for etiologic classification of ischemic stroke -- Causative Classification System for Ischemic Stroke DTI Task Card for Siemens systems, DTI Visualization platform independent tool kit, PWI analysis tools for bolus-tracking data

Proper citation: International Stroke Database/Software (RRID:SCR_007348) Copy   

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http://www.nitrc.org/projects/r-spit/

Group ICA (Independent Component Analysis) was used to generate spatial templates for 12 common resting-state networks in 62 typically-developing children, ages 9-15. They have made these available for those that will find them useful for masking and spatial template matching procedures. Basic demographic data on the sample is provided along with the protocol used to generate the templates.

Proper citation: resting-state pediatric imaging template (RRID:SCR_009647) Copy   

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http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009

Unbiased standard magnetic resonance imaging template brain volume for normal population. These volumes were created using data from ICBM project. 6 different templates are available: * ICBM 2009a Nonlinear Symmetric - template which includes T1w,T2w,PDw modalities, also T2 relaxometry (T2 values calculated for each subject using single dual echo PD/T2 scan), and tissue probabilities maps. Also included lobe atlas used for ANIMAL+INSECT segmentation, brain mask, eye mask and face mask. Intensity inhomogeneity was performed using N3 version 1.10.1. * ICBM 2009a Nonlinear Asymmetric template - template which includes T1w,T2w,PDw modalities, and tissue probabilities maps. Intensity inhomogeneity was performed using N3 version 1.10.1. Also included brain mask, eye mask and face mask. * ICBM 2009b Nonlinear Symmetric - template which includes only T1w,T2w and PDw modalities. * ICBM 2009b Nonlinear Asymmetric - template which includes only T1w,T2w and PDw modalities. * ICBM 2009c Nonlinear Symmetric - template which includes T1w,T2w,PDw modalities, and tissue probabilities maps. Also included lobe atlas used for ANIMAL+INSECT segmentation, brain mask, eye mask and face mask. Intensity inhomogeneity was performed using N3 version 1.11. Sampling is different from 2009a template. * ICBM 2009c Nonlinear Asymmetric template - template which includes T1w,T2w,PDw modalities, and tissue probabilities maps. Intensity inhomogeneity was performed using N3 version 1.11 Also included brain mask, eye mask and face mask.Sampling is different from 2009a template. All templates are describing the same anatomy, but sampling is different. Also, different versions of N3 algorithm produces slightly different tissue probability maps. Tools for using these atlases can be found in the Software section. Viewing the multiple atlas volumes online requires Java browser support. You may also download the templates - see licensing information.

Proper citation: ICBM 152 Nonlinear atlases version 2009 (RRID:SCR_008796) Copy   

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http://www.cdc.gov/nccdphp/dnpa/

Our vision a world where regular physical activity, good nutrition, and healthy weight are part of everyone''s life. Our mission to lead strategic public health efforts to prevent and control obesity, chronic disease, and other health conditions though regular physical activity and good nutrition. Our goals: * Increase health-related physical activity through population-based approaches. * Improve those aspects of dietary quality most related to the population burden of chronic disease and unhealthy child development. * Decrease prevalence of obesity through preventing excess weight gain and maintenance of healthy weight loss. Our Work With fiscal year (FY) 2008 funding of 38 million, CDC''s DNPAO is working to reduce obesity and obesity-related diseases. This is done through state programs, research, surveillance, training, intervention development and evaluation, leadership, policy and environmental change, communication and social marketing, and partnership development. See At A Glance 2009 for more. Supporting State Programs The Nutrition, Physical Activity and Obesity Program (NPAO) is a cooperative agreement between the Centers for Disease Control and Prevention''s Division of Nutrition, Physical Activity and Obesity (DNPAO) and 23 state health departments. The program goal is to prevent and control obesity and other chronic diseases through healthful eating and physical activity. The state program will develop strategies to leverage resources and coordinate statewide efforts with multiple partners to address all of the following DNPAO principal target areas: 1. Increase physical activity. 2. Increase the consumption of fruits and vegetables. 3. Decrease the consumption of sugar sweetened beverages. 4. Increase breastfeeding initiation, duration and exclusivity. 5. Reduce the consumption of high energy dense foods. 6. Decrease television viewing. Our Research DNPAO supports research to enhance the effectiveness of physical activity and nutrition programs. Topics of these research activities include: * the effectiveness of parent-focused strategies to reduce the time children spend watching television * the influences of the home environment on sugar-sweetened beverage consumption * the use of policy interventions to promote physical activity * the effectiveness of breastfeeding interventions in various settings. Publications: http://www.cdc.gov/nccdphp/DNPAO/aboutus/manuscripts/index.html

Proper citation: Division of Nutrition, Physical Activity and Obesity (RRID:SCR_008557) Copy   

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