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A tool to examine relationships between genes in different disease associated loci. Given several genomic regions or SNPs associated with a particular phenotype or disease, GRAIL looks for similarities in the published scientific text among the associated genes. As input, users can upload either (1) SNPs that have emerged from a genome-wide association study or (2) genomic regions that have emerged from a linkage scan or are associated common or rare copy number variants. SNPs should be listed according to their rs#''s and must be listed in HapMap. Genomic Regions are specified by a user-defined identifier, the chromosome that it is located on, and the start and end base-pair positions for the region. Grail can take two sets of inputs - Query regions and Seed regions. Seed regions are definitely associated SNPs or genomic regions, and Query regions are those regions that the user is attempting to evaluate agains them. In many applications the two sets are identical. Based on textual relationships between genes, GRAIL assigns a p-value to each region suggesting its degree of functional connectivity, and picks the best candidate gene. GRAIL is developed by Soumya Raychaudhuri in the labs of David Altshuler and Mark Daly at the Center for Human Genetic Research of Massachusetts General Hospital and Harvard Medical School, and the Broad Institute. GRAIL is described in manuscript, currently in preparation.

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• SciCrunch
• 17 years ago - by Anonymous

Software tool for detecting epistatic interactions in genome-wide association studies (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

GOstat is a tool that allows you to find statistically overrepresented Gene Ontologies within a group of genes. The Gene-Ontology database (GO: http://www.geneontology.org) provides a useful tool to annotate and analyze the function of large numbers of genes. Modern experimental techniques, as e.g. DNA microarrays, often result in long lists of genes. To learn about the biology in this kind of data it is desirable to find functional annotation or Gene-Ontology groups which are highly represented in the data. This program (GOstat) should help in the analysis of such lists and will provide statistics about the GO terms contained in the data and sort the GO annotations giving the most representative GO terms first. Run GOstat: * Go to search form - Computes GO statistics of a list of genes selected from a microarray. * GOstat Display - You can store results from a previously run and view them here, either by uploading them as a file or putting them on a selected URL. * Upload Custom GO Annotations - This allows you to upload your own GO annotation database and use it with GOstat. Variants of GOstat: * Rank GOstat - Takes input from all genes on microarray instead of using a fixed cutoff and uses ranks using a Wilcoxon test or either ranks or pvalues to score GOs using Kolmogorov-Smirnov statistics. * Gene Abundance GOstats - Takes input from all genes on microarray and sums up the gene abundances for each GO to compute statistics. * Two list GOstat - Compares GO statistics in two independent lists of genes, not necessarily one of them being the complete list the other list is sampled from. Platform: Online tool, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 17 years ago - by Anonymous

The Gregor Mendel Institute of Molecular Plant Biology (GMI) was founded by the Austrian Academy of Sciences in 2000 in the form of a company to promote research excellence within the field of plant molecular biology. It is the only international centre for basic plant research in Austria. The GMI is located at the Vienna Biocenter Campus within the purpose-built Austrian Academy of Sciences Life Sciences Center Vienna, completed in January 2006. The Vienna Biocenter Campus, which encompasses both independent and academic research institutes as well as biotechnology companies, provides an ideal environment for the GMI. Neighbouring institutes include the Research Institute of Molecular Pathology (IMP), the Institute of Molecular Biotechnology (IMBA), as well as the Max F. Perutz Laboratories of the University of Vienna and of the Medical University of Vienna. Research at the GMI is curiosity driven and covers many aspects of molecular genetics, from basic mechanisms of epigenetics to population genetics. Arabidopsis thaliana is used as the primary model organism, and research groups are evaluated annually by an international external Scientific Advisory Board. The working language of the GMI is English. Research at the GMI is carried out by independent research groups, led either by senior group leaders with contracts of unlimited duration, or junior group leaders with temporary (5 3 years) appointments. GMI''s research activities are supported by its administration and a platform consisting of the GMI''s own services, including state-of-the-art plant growth facilities, as well as joint services with the Research Institute of Molecular Pathology and the Institute of Molecular Biotechnology Funding Our employees are expected to apply for grants and additional financial support from various external national and international funding bodies. The list below provides an overview of the funding opportunities that could be relevant for GMI members. The Frderassistent of the FFG (in German) or the Frderkompass of the Federal Ministry of Transport, Innovation and Technology (in German) can also be used to find appropriate funding.

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• SciCrunch
• 17 years ago - by Anonymous

A computational biologist''s personal views on new technologies & publications on genomics & proteomics and their impact on drug discovery.

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• SciCrunch
• 13 years ago - by Anonymous

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.

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• SciCrunch
• 17 years ago - by Anonymous

A suite of web-based open source software programs for clinical and genetic study. The aims of this software development in the Laboratory of Neurogenetics, NIA, NIH are * Build retrievable clinical data repository * Set up genetic data bank * Eliminate redundant data entries * Alleviate experimental error due to sample mix-up and genotyping error. * Facilitate clinical and genetic data integration. * Automate data analysis pipelines * Facilitate data mining for genetic as well as environmental factors associated with a disease * Provide an uniformed data acquisition framework, regardless the type of a given disease * Accommodate the heterogeneity of different studies * Manage data flow, storage and access * Ensure patient privacy and data confidentiality/security. The GERON suite consists of several self contained and yet extensible modules. Currently implemented modules are GERON Clinical, Genotyping, and Tracking. More modules are planned to be added into the suite, in order to keep up with the dynamics of the research field. Each module can be used separately or together with others into a seamless pipeline. With each module special attention has been given in order to remain free and open to the academic/government user., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 17 years ago - by Anonymous

A program that opens a new perspective to the analysis of microarray data (e.g., gene expression profiling). Unlike traditional gene clustering software, GEDI is primarily sample-oriented rather than gene-oriented. By treating each high-dimensional sample, such as one microarray experiment, as an object, it accentuates the genome-wide response of a tissue or a patient and treats it as an integrated biological entity. Hence, GEDI honors the new spirit of a system-level approach in biology. Yet, it also allows the researcher to quickly zoom-in from global patterns onto individual genes that exhibit interesting expression behavior and retrieve gene-specific information. Therefore, GEDI unites a novel holistic perspective with the traditional gene-centered approach in molecular biology. GEDI allows experimental biologists or clinicians with no bioinformatics background to efficiently and intuitively navigate through a large number of expression profiles, each with a memorizable face, and inspect, group and collect them, like managing a stack of baseball cards. DYNAMIC ANALYSIS: The unique strength of GEDI, for which GEDI was originally developed, is that it can display the results of parallel monitoring of multiple high-dimensional time courses, such as the comparison of expression profile time evolution in response to a series of drugs. GEDI creates animated graphics showing how 10,000s of genes change their expression over time in response to 100s of separately tested drugs. STATIC ANAYLSIS: The signature graphical output of GEDI, the GEDI-mosaics provide a unique, one-glance visual engram that gives each microarray or other high-dimensional dataset a face. A characteristic of GEDI''s analysis is that it does not prejudicate any particular structure in the data (such as clusters or hierarchical organization). Thus, it allows the researcher to use human pattern recognition to perform a global first-level analysis of the data. Sponsor. The project was supported by the Air Force Office of Scientific Research and the National Health Institutes. It is distributed for free academic use by the Childrens Hospital, Boston., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 14 years ago - by Anonymous

GD library is an open source code library for the dynamic creation of images by programmers. GD is written in C, and wrappers are available for Perl, PHP and other languages. GD creates PNG, JPEG and GIF images, among other formats. GD is commonly used to generate charts, graphics, thumbnails, and most anything else, on the fly. While not restricted to use on the web, the most common applications of GD involve website development. gd is a graphics library. It allows your code to quickly draw images complete with lines, arcs, text, multiple colors, cut and paste from other images, and flood fills, and write out the result as a PNG or JPEG file. This is particularly useful in World Wide Web applications, where PNG and JPEG are two of the formats accepted for inline images by most browsers. gd is not a paint program. If you are looking for a paint program, you are looking in the wrong place. If you are not a programmer, you are looking in the wrong place, unless you are installing a required library in order to run an application. gd does not provide for every possible desirable graphics operation. It is not necessary or desirable for gd to become a kitchen-sink graphics package, but version 2.0 does include most frequently requested features, including both truecolor and palette images, resampling (smooth resizing of truecolor images) and so forth. What if I want to use another programming language? Not all of these tools are necessarily up to date and fully compatible with 2.0.33. PHP A variant of gd 2.x is included in PHP 4.3.0. It is also possible to patch PHP 4.2.3 for use with gd 2.0.33; see the gd home page for a link to that information. It would be a Good Idea to merge all of the things that are better in mainstream gd and all of the things that are better in PHP gd at some point in the near future. Perl gd can also be used from Perl, courtesy of Lincoln Stein''s GD.pm library, which uses gd as the basis for a set of Perl 5.x classes. Highly recommended. OCaml gd can be used from OCaml, thanks to Matt Gushee''s GD4O project. Tcl gd can be used from Tcl with John Ellson''s Gdtclft dynamically loaded extension package. Pascal Pascal enthusiasts should look into the freepascal project, a free Pascal compiler that includes gd support. REXX A gd interface for the REXX language is available. Any Language The fly interpreter performs gd operations specified in a text file. You can output the desired commands to a simple text file from whatever scripting language you prefer to use, then invoke the interpreter.

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• SciCrunch
• 17 years ago - by Anonymous

Although Haemophilus influenza type b (Hib) diseases and Hepatitis B (Hep B) infections are preventable with one combined life-saving vaccine, both continue to pose risks to the worlds most vulnerable populations, leading to life-long disabilities or even death. Vaccinating against Hib and Hepatitis B represents an essential step towards reaching Millennium Development Goal 4. The Hib bacterium causes meningitis and pneumonia and is considered the third vaccine-preventable cause of death in children aged under five. It is estimated that there are three million cases of serious Hib infection annually, of which 400,000 result in childhood death. The majority of survivors suffer paralysis, deafness, mental retardation and learning disabilities. Babies and young children are most at risk from Hep B, a viral disease, which attacks the liver and can cause both acute and chronic disease. This can lead to chronic liver disease and puts victims at high risk of death from cirrhosis of the liver and liver cancer in later life. More than two billion people are infected by Hep B worldwide of whom 360 million suffer from chronic Hep B infection; the latter is highly prevalent in all countries that GAVI supports. Children are most vulnerable to infection with 90 percent of infants infected in the first months of their lives developing chronic Hep B infection. Infections in the developing world are mostly from mother to child, or from child to child, mainly through cuts, bites, scrapes and scratches. Vaccinating against Hib and Hep B represents an essential step towards reaching Millennium Development Goal 4, which is to reduce the under-five mortality rate by two thirds by 2015. GAVI uses two mechanisms that draw heavily on private-sector thinking to help overcome historic limitations to development funding for immunisation. These mechanisms are the AMC and the IFFIm. The former reflects the need to meet disproportionately high costs in the early stages of implementing aid programmes; the latter developing countries'' need for sustainable predictable funding., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 14 years ago - by Anonymous

Software for visualization and Analysis of CGH arrays, transcriptome and other Molecular Profiles.

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• SciCrunch
• 13 years ago - by Anonymous

The Institute for Advanced Biosciences, Keio University, is an academic research institute pioneering the new life science field of Systems Biology, using both experimental and computational biology. There are several groups working in collaboration, focusing mainly on genome biology and engineering, genome design and synthetic biology, metabolic engineering, proteomics, metabolomics, RNA biology, bioinformatics and computational biology. Using cutting-edge technologies, intracellular components can be analyzed comprehensively to construct computer simulation models that can find numerous applications in fields such as biomedical, environmental, and agricultural science. Experimental and computational facilities are located in Tsuruoka, Yamagata prefecture, in northern Japan while the SFC campus, in the Tokyo area, hosts the bioinformatics laboratory and most undergraduate curricular activities. IAB has successfully attracted very significant funding for multiple research projects from major funding organizations including the New Energy and Industrial Technology Development Organization (NEDO) (2002-2006), for bioprocesses and cell modeling, the Ministry of Education, Culture, Sports, Science and Technology (MEXT) and its COE network, for biosimulation and systems biology (2003-2008), the Japan Science and Technology Agency (CREST, 2004-2009) for simulation and systems biology, the Ministry of Health, for cancer biology (2005), as well as from Yamagata prefecture and Tsuruoka city, 2001-2006 and 2006-2011). Over the past few years, IAB scientists have accumulated several awards including the 1st prize during the 5th Japan Biotechnology Business Competition (2005), the Minister of State for Science and Technology Policy award in recognition for industry-academia-government collaboration performance (2004), the IBM Shared University Research Award (2003), and the Nihon Kogyo Shimbunsha Award (2003) during the 17th Leading-edge Technology for Originality and Creativity. Sponsor. This study was supported by a grant from the Global COE Program entitled, Human Metabolomic Systems Biology and by a Grant-in-Aid for Scientific Research on Priority Areas Systems Genomes and on Lifesurveyor from the Ministry of Education, Culture, Sports, Science and Technology of Japan as well as research funds from the Yamagata prefectural government and the City of Tsuruoka.

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• SciCrunch
• 17 years ago - by Anonymous

A tool for mapping transcriptome data and for creating a database with an overview of the entire pathway, a web-based resource consisting of a web-application for the visualization of complex omics data onto KEGG pathways to overview all entities in the context of cellular pathways, and databases created with the software to visualize a series of microarray data. The web-application accepts transcriptome, proteome, metabolome, or the combination of these data as input, and because of this scalability it is advantageous for the visualization of cell simulation results. Several databases of transcriptome data obtained at Mori Laboratory, Nara Institute of Science and Technology, Japan, are also presented.

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• SciCrunch
• 17 years ago - by Anonymous

Fungal genomes available from the Sanger Institute. Data are accessible in a number of ways; for each organism there is a BLAST server, allowing search of the sequences. Sequences can also be down-loaded directly by FTP. In addition, for those organisms being sequenced using a cosmid approach, finished and annotated cosmids are submitted to EMBL and other public databases.

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• SciCrunch
• 17 years ago - by Anonymous

C. elegans Gene Knockout Project Containing information about the Gene Knockout consortium, an on-line version of targeted gene database, knockout submission form and oligo prediction software. C. elegans Gene Expression Project Members investigating C. elegans gene expression using promoter GFP fusions and serial analysis of gene expression (SAGE). Serial Analysis of Gene Expression View and download C. elegans SAGE data. Provided are tag to gene mappings, various filters (e.g. sequence quality, minimum tag count), and search by keyword or tag. Also available are supplemental data from publications. Microarray Data Download C. elegans expression data generated from the Affymetrix GeneChipTM or a NimbleGen custom array. These experiments were done in parallel with the SAGE experiments, and there is data available for the six major developmental stages. Expression Patterns for promoter GFP fusions View and search expression patterns of C. elegans promoter GFP fusions. Tools for automated PCR primer design PCR-based screening for deletions in C. elegans genes, including the ''poison primer'' strategy Construction of promoter GFP fusions using PCR stitching (fusion PCR) Fosmid Clone Search We have created a C. elegans fosmid library. Use this site to search for fosmid clones for your gene or region of interest, and request clones.

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• SciCrunch
• 17 years ago - by Anonymous

A computer algorithm that provides a fast and quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes. The predictive power of FOLDEF has been tested on a very large set of point mutants (1088 mutants) spanning most of the structural environments found in proteins . FoldX uses a full atomic description of the structure of the proteins. The different energy terms taken into account in FoldX have been weighted using empirical data obtained from protein engineering experiments.

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• SciCrunch
• 17 years ago - by Anonymous

FlowingData explores how designers, statisticians, and computer scientists are using data to understand ourselves better - mainly through data visualization. Money spent, reps at the gym, time you waste, and personal information you enter online are all forms of data. How can we understand these data flows? Data visualization lets non-experts make sense of it all. About Nathan As for me, I''m a PhD candidate in statistics. I live and breathe data. I also have a background in computer science and design. I do some freelancing from time to time, but mostly I''m just trying to work on my dissertation. You can find more about me here. For the New Readers If you''re new here, welcome to FlowingData. A good place to start is the archives where you''ll find FlowingData''s most popular posts or take a look at the FlowingData beginner''s guide. If you like what you see, subscribe to the feed, follow on Twitter, or fan on Facebook More specifically, I''m most interested in Social data visualization Self-surveillance Data for non-professionals FlowingData readers are data-savvy people who are interested in visualization, statistics, design, analysis, and programming. If you have a product or service that is of interest to them, then FD sponsorship is a great way for you to connect with them. There are two exclusive ways for you or your group to connect with readers. The first is through a banner ad, which appears in the top right of every page. The second is via a bimonthly sponsorship of the FlowingData RSS feed. Both sponsorship types also include a mention in the monthly thank you post.

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• SciCrunch
• 17 years ago - by Anonymous

Software for single-cell flow cytometry analysis. Its functions include management, display, manipulation, analysis and publication of the data stream produced by flow and mass cytometers.

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• SciCrunch
• 17 years ago - by Anonymous

Welcome to Flintbox, an application that revolutionizes the way the innovation community can share technologies, distribute new materials and software, and collaborate on research projects. Hundreds of research institutions are participating in the Flintbox open innovation network. Become a member to contribute and explore We are excited to present the Flintbox Application Programming Interface (API) to provide users with an easy way to upload data from any system to Flintbox. This freely available tool for synchronized information exchange will be a valuable resource to the open innovation community. The Flintbox API gives you the power to: Import existing technology postings directly into Flintbox Avoid duplicate data entry to market your technologies, ideas, and materials Create postings from any database Export project information to other websites For more information about using and implementing the Flintbox API, please see the About the Flintbox API page. Featured Project The New Flintbox offers expanded transactional capabilities: credit cards, purchase orders, purchase authorizations, donations, and much more The global Flintbox community is ideal for marketing new technologies, creative works, course materials, and innovative ideas. Flintbox enables universities to maximize their outreach to a broad spectrum of the innovation community. Plus, Wellspring provides expertise in assisting TTOs, inventors, and industrial liaison offices to promote their technologies, research programs, and partnering opportunities to Flintbox. Flintbox for Corporations Corporations turn to Flintbox to cultivate existing relationships and engage in new opportunities for collaborative research and solution sourcing from universities and other companies. For example, a pharmaceutical firm uses Flintbox to provide researchers and physicians software to assess patient outcomes. Flintbox for Technology Communities Flintbox empowers technology communities to connect effectively in a geographic region, building a Sphere of Innovation to truly recognize and capitalize on the valuable relationships and innovation assets in your community. For example, by creating or joining a community Group of members with common interests, say tissue engineering or artificial intelligence, you can link to other groups and explore common interests and complementary resources, for a dynamic collaborative effort and to efficiently share related technology projects. Flintbox is a registered trademark of Wellspring Worldwide, LLC