Curator Dashboard

Blog investigating a light-weight way of publishing scientific, academic and technical knowledge on the web where you can read about current events. It is used in a number of different ways: hosting tutorials on ontologies and bioinformatics; as a conference website; and as a mechanism for documenting Knowledge Blog. They also provide software for extending WordPress, enabling referencing, adding metadata to posts, and supporting mathematics on the web. Together, these pieces of software have had many thousands of downloads, representing 100s of installations; it can be used to provide a formal personal publication framework for the researcher. Finally, they provide Greycite, a service which provides bibliographic metadata for any website, supporting their referencing plugin, and helping authors to link to the many web archiving services, enabling increased digital preservation. Blogs and blog technology has been designed to allow people to discuss, share and disseminate their opinion in a simple and light-weight way. Adding a little formality to this, and we have a journal.

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• SciCrunch
• 17 years ago - by Anonymous

An R package designed to simulate RNA sequencing experiments with differential transcript expression. Given a set of annotated transcripts, it will simulate the steps of an RNA-seq experiment (fragmentation, reverse-complementing, and sequencing) and produce files containing simulated RNA-seq reads. Simulated reads can be analyzed using a choice of downstream analysis tools. Polyester has a built-in wrapper function to simulate a case/control experiment with differential transcript expression and biological replicates. Users are able to set the levels of differential expression at transcripts of their choosing. This means they know which transcripts are differentially expressed in the simulated dataset, so accuracy of statistical methods for differential expression detection can be analyzed. Polyester offers several unique features: * Built-in functionality to simulate differential expression at the transcript level * Ability to explicitly set differential expression signal strength * Simulation of small datasets, since large RNA-seq datasets can require lots of time and computing resources to analyze * Generation of raw RNA-seq reads, as opposed to alignments or transcript-level abundance estimates * Transparency/open-source code

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• SciCrunch
• 12 years ago - by Anonymous

The objective of this human tissue repository is to systematically collect, store, and distribute brain and other tissues for research dedicated to the improved understanding, care, and treatment of individuals with developmental disorders. Brain sections are primarily frozen in isopentane / dry ice. Tissues are stored in 10% formalin and frozen at -85 degrees C. Of special interest are individuals with Down syndrome and other chromosomal defects, mitochondrial encephalopathies, phenylketonuria and other aminoacidopathies, maternal PKU, Rett syndrome, leukodystrophies, lysosomal disorders, dyslexia, autism, and other neurodevelopmental disorders. The brain and tissue banks have extensive experience in arranging for the rapid retrieval of tissue upon the death of individuals who die while at home, in hospitals or hospice care. As a special service, the brain and tissue banks are able to assist researchers who are working with patients who intend to donate tissues at the time of their death. Immediately after retrieval of the tissue, the brain and tissue banks will forward needed tissue to the referring investigators and ensure proper storage and cataloging of any additional tissues as part of the brain and tissue banks. The recipient of tissue and the brain and tissue banks are required to sign a Tissue Transfer Agreement before any tissues are transferred.

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• SciCrunch
• 17 years ago - by Anonymous

Developed as part of the BioText project at the University of California, Berkeley, the BioText Search Engine is a freely available Web-based application that provides biologists with new ways to access the scientific literature. The system indexes all open access articles available at PubMed Central. New articles are indexed daily. The current collection consists of more than 300 journals, 40,000 articles, 100,000 figures, and 60,000 tables. The Full Text & Abstract view searches the full text of articles (in addition to title, author, and abstract information) and returns full-text excerpts that match users' queries. Three selection boxes at the top (ABSTRACTS, FULL-TEXT EXCERPTS and FIGURES allow users to choose what the view displays. The BioText Search Engine allows users to search in tables. When the table view is selected, BioText searches in article titles, table captions, and table contents. The Grid View allows users to search over captions. It returns figures and truncated captions in a grid arrangement.

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• SciCrunch
• 16 years ago - by Anonymous

The EuroBioBank network is the first operating network of biobanks in Europe providing human DNA, cell and tissue samples as a service to the scientific community conducting research on rare diseases. It is the only network dedicated to rare disease research in Europe. By creating a critical mass of collections and facilitating the exchange of biological material, the EuroBioBank network helps accelerate research on these diseases. * Over 440,000 samples are available across the network and can be requested via the online catalogue. Approximately 13,000 samples are collected each year and 7,000 samples distributed in Europe and beyond. The biological samples are obtained from patients affected by rare diseases, including rare neuromuscular disorders. * The EuroBioBank Network is currently composed of 18 members, of which 16 biobanks from 8 European countries (France, Germany, Hungary, Italy, Malta, Slovenia, Spain and the United-Kingdom) as well as Israel and Canada. Goals * Identify and localize biological material of interest to researchers * Build a critical mass of rare disease sample collections * Distribute high quality material and associated data to users * Promote best-practice guidelines for biobanking activities * Disseminate knowledge and know-how to the scientific community through training courses * Enhance collaboration with the medical and scientific community in the field of rare diseases EuroBioBank acts as a clearing house or virtual bank, with all samples listed in the central online catalogue remaining in the possession of the member biobanks, where they are located and can be requested. The network was established by patients and researchers to facilitate research on rare diseases by guaranteeing quick and easy access to samples via an online catalogue. The catalogue lists the samples available throughout the EuroBioBank network by type of biomaterial. A search engine enables a search by disease or by bank contact. Once a sample has been located in the catalogue, it can be requested by email. Therefore, the biological material is exchanged faster. If a sample does not appear in the EuroBioBank catalogue, help can be provided to further search it at: eurobiobank (at) telethon.it Funding and Collaboration Originally funded by the EC between 2003-2006, the EuroBioBank received further EC support between 2007-2011 within the European Network of Excellence TREAT-NMD (FP6), which covered the cost sustained by Eurordis for the network coordination and website hosting. Each biobank of the network is financed by its own Institution or charitable organization. As of January 2012, the Fondazione Telethon provides the administrative support for coordinating the EuroBioBank network and hosting the website.

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• SciCrunch
• 16 years ago - by Anonymous

Organization to lead the integration of ocean, coastal, and Great Lakes observing capabilities, in collaboration with Federal and non-Federal partners, to maximize access to data and generation of information products, inform decision making, and promote economic, environmental, and social benefits to the nation and the world. This national-regional partnership is working to provide new tools and forecasts to improve safety, enhance the economy, and protect the environment. Integrated ocean information is available in near real time, as well as retrospectively. Easier and better access to this information is improving their ability to understand and predict coastal events - such as storms, wave heights, and sea level change. Such knowledge is needed for everything from retail to development planning. The Integrated Ocean Observing System (IOOS) program achieves its objectives by funding organizations through a competitive process.

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• SciCrunch
• 13 years ago - by Anonymous

A web-based software tool offering an integrated analysis of transcriptome data under genomic, proteomic and metabolic context.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6,2023. Code used for analysis of TwoPhoton data.

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• SciCrunch
• 13 years ago - by Anonymous

Software library for manipulating neural data files generated in Andreas Tolias Lab.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. Code and algorithms produced by the Andreas Tolias lab (Baylor College of Medicine, Department of Neuroscience) where the goal is to understand the rules by which networks of nerves cells in the neocortex orchestrate their activity to process information; to decipher the neural code.

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• SciCrunch
• 13 years ago - by Anonymous

Database designed to capture experimental or inferential results that support submitter-provided annotation for sequence data that the submitter did not directly determine but derived from GenBank primary data. Records are divided into two categories: * TPA:experimental: Annotation of sequence data is supported by peer-reviewed wet-lab experimental evidence. * TPA:inferential: Annotation of sequence data by inference (where the source molecule or its product(s) have not been the subject of direct experimentation) TPA records are retrieved through the Nucleotide Database and feature information on the sequence, how it was cataloged, and proper way to cite the sequence information.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. Database and atlas of transgenic mouse lines that are generated by random insertion of enhancer trap probes. The trapped lines have highly restricted expression of tet transcription activator (some lines also have Cre DNA recombinase), which enables genetic manipulations in specific cell types.

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• SciCrunch
• 13 years ago - by Anonymous

Web server to search for genes involved in given phenotypic difference between mammalian species. The mouse-referenced multiple alignment data files used to perform the forward genomics screen is also available. The webserver implements one strategy of a Forward Genomics approach aiming at matching phenotype to genotype. Forward genomics matches a given pattern of phenotypic differences between species to genomic differences using a genome-wide screen. In the implementation, the divergence of the coding region of genes in mammals is measured. Given an ancestral phenotypic trait that is lost in independent mammalian lineages, it is shown that searching for genes that are more diverged in all trait-loss species can discover genes that are involved in the given phenotype.

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• SciCrunch
• 13 years ago - by Anonymous

Center for Biological Sequence Analysis of the Technical University of Denmark conducts basic research in the field of bioinformatics and systems biology and directs its research primarily towards topics related to the elucidation of the functional aspects of complex biological mechanisms. A large number of computational methods have been produced, which are offered to others via WWW servers. Several data sets are also available. The center also has experimental efforts in gene expression analysis using DNA chips and data generation in relation to the physical and structural properties of DNA. The on-line prediction services at CBS are available as interactive input forms. Most of the servers are also available as stand-alone software packages with the same functionality. In addition, for some servers, programmatic access is provided in the form of SOAP-based Web Services. The center also educates engineering students in biotechnology and systems biology and offers a wide range of courses in bioinformatics, systems biology, human health, microbiology and nutrigenomics.

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• SciCrunch
• 16 years ago - by Anonymous

Core facility that provides the following services: Printed circuit fabrication, Printed circuit board assembly, System design and fabrication. <BR/> <BR/>David Collins is NASA certified for electrical assembly.

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• SciCrunch
• 13 years ago - by Anonymous

Data set of up-to-date data on attitudes, behavior, and social structure in Germany. Every two years since 1980 a representative cross section of the population is surveyed using both constant and variable questions. The ALLBUS data become available to interested parties for research and teaching as soon as they are processed and documented.

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• SciCrunch
• 13 years ago - by Anonymous

Free, Java-based video coding and data visualization tool for collecting behavioral data from video. It supports all video formats that Quicktime or VLC can play, including .asf, .wmv, .avi, .flv, .mov, .mpf, .ogg, .mpg, .nsc, .wav, and .dts. It exports data in a variety of forms depending on analysis needs.

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• SciCrunch
• 13 years ago - by Anonymous

Mount Sinai Allograft Technologies, a department of Mount Sinai Hospital formerly known as the The Rubinoff Bone Bank, has been a leader in advanced tissue innovations since 1972. We are committed to providing the highest quality bone and tissue allograft products as well as continued innovation in the development of allograft implants for transplantation. We are dedicated to meeting all surgical needs and to exceed all client expectations. We work closely with the Trillium Gift of Life Network to promote their mission of increasing donor awareness and to ensure that the wishes of Ontario donor families' are carried out with the utmost care and respect. Our allograft implants are 100% Ontario produced, human allograft tissues. To produce the safest and highest quality Canadian produced allograft implants, Mount Sinai Allograft Technologies leverages the expertise of a variety of medical experts, state-of-the art laboratory testing, proven bio-processing techniques, validated irradiation methods and preferred packaging systems.

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• SciCrunch
• 16 years ago - by Anonymous

A set of Python software packages that takes large sets of overlapping images in 2D and 3D and produces registered (aligned) 3D volumes at any size and scale. These tools were originally designed to construct 3D connectomics volumes from terabytes of image data for the Marc lab at the University of Utah Moran Eye Center.

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• SciCrunch
• 13 years ago - by Anonymous

Software package that constructs 2D and 3D datasets from 2D image mosaics using the nornir tools. This produces a set of images and transforms on disk which can be accessed via Viking, HTTP, or written as a stack of images.

• Resource
• SciCrunch
• 13 years ago - by Anonymous