Curator Dashboard

Software that performs sequence alignment for protein and translated DNA searches and functions. Used for high performance analysis of big sequence data, protein-protein search, and DNA-protein search.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

A curated knowledge base of the circuitry of the hippocampus of normal adult, or adolescent, rodents at the mesoscopic level of neuronal types. Knowledge concerning dentate gyrus, CA3, CA2, CA1, subiculum, and entorhinal cortex is distilled from published evidence and is continuously updated as new information becomes available. Each reported neuronal property is documented with a pointer to, and excerpt from, relevant published evidence, such as citation quotes or illustrations. Please note: This is an alpha-testing site. The content is still being vetted for accuracy and has not yet undergone peer-review. As such, it may contain inaccuracies and should not (yet) be trusted as a scholarly resource. The content does not yet appear uniformly across all combinations of browsers and screen resolutions.

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• SciCrunch
• 14 years ago - by Anonymous

Database of organelle proteins, and subcellular structures / complexes from compiled protein localization data from organisms spanning the eukaryotic kingdom. All data may be downloaded as a tab-delimited text file and new localization data (and localization images, etc) for any organism relevant to the data sets currently contained in Organelle DB is welcomed. The data sets in Organelle DB encompass 138 organisms with emphasis on the major model systems: S. cerevisiae, A. thaliana, D. melanogaster, C. elegans, M. musculus, and human proteins as well. In particular, Organelle DB is a central repository of yeast protein localization data, incorporating results from both previous and current (ongoing) large-scale studies of protein localization in Saccharomyces cerevisiae. In addition, we have manually curated several recent subcellular proteomic studies for incorporation in Organelle DB. In total, Organelle DB is a singular resource consolidating our knowledge of the protein composition of eukaryotic organelles and subcellular structures. When available, we have included terms from the Gene Ontologies: the cellular component, molecular function, and biological process fields are discussed more fully in GO. Additionally, when available, we have included fluorescent micrographs (principally of yeast cells) visualizing the described protein localization. Organelle View is a visualization tool for yeast protein localization. It is a visually engaging way for high school and undergraduate students to learn about genetics or for visually-inclined researchers to explore Organelle DB. By revealing the data through a colorful, dimensional model, we believe that different kinds of information will come to light.

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• SciCrunch
• 17 years ago - by Anonymous

Software application as a single-core implementation of frequency-based substring mining. It can be used in bioinformatics to extract substrings that discriminate two (or more) datasets inside high-throughput sequencing data.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. The Annotator is an open-source JavaScript library and tool that can be added to any webpage to make it annotatable. Annotations can have comments, tags, users and more. Moreover, the Annotator is designed for easy extensibility so its a cinch to add a new feature or behavior. Adding annotation to your webpage using the Annotator is easy. Full instructions are in the Getting Started section of the docs, but it is just two short steps. First, you need to download the Annotator library (or link to the hosted version), include it on your page along with jQuery. Then add the following line to initialize the annotator. $("#content").annotator(); Plug-ins can be included for adding functionality such as user accounts, tags, filtering and formatting. You'll need to store your data somewhere, luckily we've made this very simple to do using AnnotateIt, a hosted web service for storing annotations. Alternatively if you'd like to integrate the annotator with your own storage system check out the Docs for more information on the annotation format and store plugin. The bookmarklet is a simple tool that allows you to add the annotator to any webpage and save your annotations to AnnotateIt. Check it out at http://annotateit.org/.

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• SciCrunch
• 15 years ago - by Anonymous

Java library and a web service for extracting metadata and content from scientific articles in born-digital form. The system analyses the entire content of a PDF file containing a publication and attempts to extract information such as: the title of the article, journal information (title, etc.), bibliographic information (volume, issue, page numbers, etc.), authors and affiliations, keywords, abstract, bibliographic references and structured sections hierarchy.

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• SciCrunch
• 14 years ago - by Anonymous

A fast and accurate multiple sequence alignment algorithm.

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• SciCrunch
• 13 years ago - by Anonymous

A database that focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. The curated data can be analyzed in the context of the high throughput data and viewed graphically with the MINT Viewer. This collection of molecular interaction databases can be used to search for, analyze and graphically display molecular interaction networks and pathways from a wide variety of species. MINT is comprised of separate database components. HomoMINT, is an inferred human protein interatction database. Domino, is database of domain peptide interactions. VirusMINT explores the interactions of viral proteins with human proteins. The MINT connect viewer allows you to enter a list of proteins (e.g. proteins in a pathway) to retrieve, display and download a network with all the interactions connecting them.

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• SciCrunch
• 15 years ago - by Anonymous

Biomedicine can only be understood in the context of genomics and with the concourse of bioinformatics. Our department aims to tackle biomedical problems from a system's biology perspective. Following this, the general objective we seek through the main lines of research is to relate the mutations (Pharmacogenomics and Comparative Genomics) to their effect at cellular and phenotypic level (Functional Genomics) trying to understand the mechanism of action (Structural Genomics). Systems Biology Genes operate within an intricate network of interactions that we have only recently started to envisage. Many higher-order levels of interaction are continuously being discovered. In this scenario we are interested in developing methods and tools which can help to understand large-scale experiments from a systems biology perspective. Comparative genomics We are interested in the analysis of patterns and processes occurred during the evolution of our genome, and in the application of the evolutionary thought in human health and disease. * Adaptive Human Evolution * Evolutionary Pharmacogenetics * SNP's and Human Disease Structural genomics Our Unit aims to develop and apply computational methods for understanding the molecular mechanisms of cell regulation beyond proteins. In particular, we apply our methods to study the interaction of small chemical compounds with proteins and to characterize their molecular actions. We are also developing methods for RNA 3D structure prediction with the aim of applying them to understand the effects of non-coding RNA molecules. Finally, in collaboration with experimentalists, we are working in determining the first ever 3D structure of a genomic domain in human.

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• SciCrunch
• 15 years ago - by Anonymous

A XML format that enables genomics researchers to store critical information on PCR experiments. Accompagnying perl scripts are written to read from (dbSTS) or write to a MIPE XML file.

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• SciCrunch
• 12 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The World Parkinson's Disease Association is an alliance of members from all over the world who have come together to share information about Parkinson's disease. In order to further Parkinson's research and better the condition of those diagnosed with the disease, the Association: establishes computerized connections; takes part in and/or finances research activities; urges pharmaceutical companies and government institutions of the various countries to support the guidelines recommended by the associations of Parkinson's patients; and coordinates and promotes interchange of information among its members with the aim of solving problems of mutual interest.

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• SciCrunch
• 17 years ago - by Anonymous

DICOMscope is a free DICOM viewer which can display uncompressed, monochrome DICOM images from all modalities and which supports monitor calibration according to DICOM part 14 as well as presentation states. The application is rather a feasibility study for DICOM presentation states. DICOMscope offers a print client (DICOM Basic Grayscale Print Management) which also implements the optional Presentation LUT SOP Class.

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• SciCrunch
• 17 years ago - by Anonymous

A free package of software programs for inferring phylogenies (evolutionary trees). The source code is distributed (in C), and executables are also distributed. In particular, already-compiled executables are available for Windows (95/98/NT/2000/me/xp/Vista), Mac OS X, and Linux systems. Older executables are also available for Mac OS 8 or 9 systems.

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• SciCrunch
• 17 years ago - by Anonymous

The Office of Scientific and Technical Information's mission is to advance science and sustain technological creativity by making R&D findings available and useful to Department of Energy (DOE) researchers and the public. At OSTI you can find research results and science information from the Manhattan Project to the present, download documents, view energy citations, discover patents and e-prints, read about ongoing research projects and amazing accomplishments, search science conference proceedings and software, and connect to U.S. and global science portals. You can do this by using special online tools, such as: * Key Resources * DOE Science Accelerator * Science.gov * WorldWideScience.org Strategies for accomplishing the OSTI mission: * Collaborate within DOE through the Scientific and Technical Information Program to develop and maintain efficient, state-of-the-art access and delivery of research results. * Partner with others to facilitate alliances for national and international cooperation and information exchange. * Develop, deliver, and maintain customized information products and services for a variety of constituencies. * Implement Department-wide STI policy and best business practices. * Preserve STI, in tangible copies or electronically, as appropriate. * Accelerate the diffusion of knowledge to advance science. OSTI develops and maintains search tools that use a special technology called federated search. KEY RESOURCES Research Documents/Information Information Bridge Find DOE R&D full-text documents and bibliographic citations. DOE R&D Accomplishments Find information about the outcomes of past DOE R&D. DOE patents Find patents resulting from DOE-sponsored research and development. E-print Network Find e-prints in basic and applied sciences . Energy Citations Database (ECD) Find bibliographic records and full-text where available. Adopt-A-Doc? is an on-demand service that provides individuals the option to sponsor the digitization of full-text DOE technical reports. Science Conference Proceedings Find select science and technology conference papers and proceedings. EnergyFiles Find databases and websites of interest to DOE. Research Summaries DOE R&D Project Summaries Find R&D projects underway at DOE. Federal R&D Project Summaries Find R&D projects underway at federal agencies. Science Information from U.S. Agencies Science.gov Find selected science information provided by U.S. Government agencies. Science Information from Global Sources WorldWideScience.org Find science from participating nations of every inhabited continent. ETDEWEB Register for access to worldwide energy technology discoveries. International Nuclear Information System Find International bibliographic records related to peaceful applications of nuclear science and technology. Science Education Resources ScienceLab A portal listing numerous education resources within DOE and beyond Scientific Research Data About Scientific Research Data Learn about the Department of Energys data discovery tool as well as data centers, forums, and publications. DOE Data Explorer Find scientific research data - such as computer simulations, numeric data files, figures and plots, interactive maps, multimedia, and scientific images - generated in the course of DOE-sponsored research in various science disciplines. Scientific and Technical Software Energy Science and Technology Software Center Find federally funded scientific and technical software developed by the national laboratories, other facilities and DOE contractors. SCIENCE ACCELERATOR Science Accelerator is a gateway to science, including R&D results, project descriptions, accomplishments, and more, via resources made available by the Office of Scientific and Technical Information (OSTI), U.S. Department of Energy. Science Accelerator was developed and is made available by OSTI as a free public service. SCIENCE.GOV Science.gov searches over 40 databases and 1,950 selected websites, offering 200 million pages of authoritative U.S. government science information, including research and development results. WORLDWIDESCIENCE.ORG WorldWideScience.org is a global science gatewayaccelerating scientific discovery and progress through a multilateral partnership to enable federated searching of national and international scientific databases and portals.

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• SciCrunch
• 17 years ago - by Anonymous

A commercial software for computerized physician order entry and electronic health record system (EHR) enhancements for data analysis, along with other software products and services.

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• SciCrunch
• 17 years ago - by Anonymous

Software application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. It examines sequencing alignment data in SAM / BAM files according to the features of the mapped reads and provides an overall view of the data that helps to the detect biases in the sequencing and/or mapping of the data and eases decision-making for further analysis.

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• SciCrunch
• 13 years ago - by Anonymous

An application ontology built for the Beta Cell Genomics database aiming to support database annotation, complicated semantic queries, and automated cell type classification. The ontology is developed using Basic Formal Ontology (BFO) as upper ontology, Ontology for Biomedical Investigations (OBI) as ontology framework and integrated subsets of multiple OBO Foundry (candidate) ontologies. Current the BCGO contains 2383 classes including terms referencing to 24 various OBO Foundry ontologies including CL, CLO, UBERON, GO, PRO, UO, etc.

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• SciCrunch
• 13 years ago - by Anonymous

Northern Eclipse 6.0 software is a Windows based full Image Analysis and Archiving System with a full suite of Image Processing techniques, Morphological and Densitometry measuring routines, digital and analogue camera control, SDK for custom camera driver solutions, 3D-Reconstruction, De-Convolution and programmable via 3 levels of automation plus access to hundreds of OLE applications and thousands of scripts.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package for Multipoint QTL Mapping in Genetically Heterogeneous Animals (entry from Genetic Analysis Software) The method is implemented in a C-program and there is now an R version of HAPPY. You can run HAPPY remotely from their web server using your own data (or try it out on the data provided for download).

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• SciCrunch
• 14 years ago - by Anonymous

An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the adult Drosophila melanogaster brain.

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• SciCrunch
• 16 years ago - by Anonymous