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The objectives of Open Science Summit are to create an annual flagship event and news hub to build and maintain the identity of the international Open Science Movement as well as organize the various sub-communities into an effective, global, socio-technological force for rapid change in science/innovation policy. The Open Science Summit is the first and only event examining the full spectrum of the most crucial policy questions affecting the future of science. We consider the disruptive changes required to improve the functioning of 21st science, including institutional changes, new infrastructure for data driven science, and new practices. Scientists, Hackers, Students, Patients, and Activists, Entrepreneurs, Funders, Citizens should attend. Anyone who cares passionately about unleashing the full potential of Open Science to solve the big problems confronting humanity. Topics include: Synthetic Biology, Open Data, Open Access, Microfinance for Science, Citizen science, DIY Biology, Alternative Funding for Research, Open Source Drug Discovery, The Future of Patents, Accelerating Innovation, Open Genomics/Medicine, and More!

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• SciCrunch
• 16 years ago - by Anonymous

bioView3D is an open source and cross-platform application intended for biologists to visualize 3D stack (laser scanning confocal, etc.) imagery. It runs on Windows, MacOS X and Linux. Features include: - Cross-platform with binaries for Windows, Mac, Linux - Reads many bio image and video formats - Reads meta-data from BioRad PIC, TIFF, Metamorph STK (uncompressed and LZW compressed), Fluoview TIFF, Carl Zeiss LSM 5, PSIA TIFF, Nanoscope II/III - Has two modes of rendering: textures and voxels - On-the-fly 3D visualization (mapping/enhancement) of multi-channel data - Export of fly-over video to several popular formats: QuickTime, WMV, AVI, Flash, MPEG1/2/4 - Visualization of graphical annotations: XML GObjects Sponsors: This work is supported in part by an NSF infrastructure award No. EIA-0080134 and IIS-0808772.

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• SciCrunch
• 17 years ago - by Anonymous

A markup language and a set of technologies for capturing, storing and operationalizing structured biological knowledge. It also makes the knowledge available to other applications, such as the GTP, as a navigable network of biological facts. The BEL Framework assembles biological facts recorded using BEL syntax. BEL is a use-neutral format for unambiguously capturing biological entities and their inter-relationships and associating them with external vocabularies and ontologies. To facilitate context-based analysis, BEL syntax captures causal (e.g., AKT1 phosphorylates SKP2 at serine 72) and correlative relationships (e.g., increased LRG1 levels in serum are correlated with ovarian cancer) along with the experimental context in which the relationships were observed (e.g., AKT1 phosphorylates SKP2 at serine 72 in HeLa cells) and citations in which the peer reviewed knowledge has been reported (Pubmed ID 19270695 illustrates AKT1 phosphorylation of SKP2 and Pubmed ID 20831812 discusses the correlation between LRG1 and ovarian cancer). The BEL Framework provides an environment for managing and operationalizing biological facts stored in the BEL format (BEL document) and consists of the following components: * A user-friendly, web-based, knowledge-capture and knowledge-management application * A compiler that can assemble composite knowledge networks from multiple sources containing BEL statements from the BEL document store * A portable storage format for compiled BEL statements * Application Programming Interfaces (APIs) to allow applications such as the GTP to access and use the knowledge The BEL Framework is unique in that it is designed to deal with the fundamental contradictions and ambiguities associated with assimilating scientific findings from disparate biological experiments and quality issues associated with manual and algorithm-driven collation methods. Following eight years of development and proprietary use, BEL has proven to be an intuitive and effective language for scientists, supporting the creation of a large knowledgebase used in the interpretation of ''omics data sets via causal relationship-based analytics. BEL and supporting tools are now being made publicly available to the research community through the introduction of the BEL Web Portal. The BEL Web Portal provides public access to BEL language specifications, documentation, knowledge representation examples, and BEL software tools.

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• SciCrunch
• 16 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19,2022. The BAMS Thesaurus is a part of the larger BAMS The Foundational Model of Connectivity (FMC). The principle of constructing the resource are: 1. Systematic attempts to produce internally consistent classifications and taxonomies require theoretical frameworks for deciding between alternatives. 2. Alternate classification and taxonomy schemes are always possible and must be accommodated. 3. The FMC is based on evidence, not authority. All components are justified by reference to the best observational or experimental evidence from the literature, combined with reference to priority when possible, not by undocumented statements from textbooks, the Web, or elsewhere. 4. The FMC is based on evolving evidence and concepts, revisions are based on enforced rules, and versioning is systematic and historical. The first version of FMC and the foundation of this online version was published in Swanson & Bota (2010). Please cite this reference whenever any part of the FMC is used in any way. This online version of FMC has the following main parts: 1. Thesaurus, which includes an alphabetical list of all concepts and terms used in FMC to date. The preferred terms are in bold. Clicking on each term of the Thesaurus will retrieve its definition, reference, list of synonyms, and a comment form that can be used by registered users. 2. References, which includes an alphabetical list of the literature used to construct FMC. Listed references are associated with the definitions included in the Thesaurus, and PubMed links. 3. Search form that can be used to search for terms defined in FMC, included in their definitions, their abbreviations, and references (search by authors). We strongly recommend to read FMC rules and notations before starting to use the online version.

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• SciCrunch
• 16 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented October 4, 2017.<br/><br/>A sub-project of the Cell Centered Database (http://ccdb.ucsd.edu) providing a public repository for animal imaging data sets from MRI and related techniques. The public AIDB website provides the ability for browsing, visualizing and downloading the animal subjected MRI data. The AIDB is a pilot project to serve the current need for public imaging repositories for animal imaging data. The Cell Centered Database (CCDB) is a web accessible database for high resolution 2D, 3D and 4D data from light and electron microscopy. The AIDB data model is modified from the basic model of the CCDB where microscopic images are combined to make 2D, 3D and 4D reconstructions. The CCDB has made available over 40 segmented datasets from high resolution magnetic resonance imaging of inbred mouse strains through the prototype AIDB. These data were acquired as part of the Mouse BIRN project by Drs. G. Allan Johnson and Robert Williams. More information about these data can be found in Badea et al. (2009) (Genetic dissection of the mouse CNS using magnetic resonance microscopy - Pubmed: 19542887)

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• SciCrunch
• 17 years ago - by Anonymous

Software application to create gene maps using either radiation hybrid data or linkage data (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

EyeBrowse displays expressed sequence tag (EST) cDNA clones from eye tissues (derived from NEIBank and other sources) aligned with current versions of the human, rhesus, mouse, rat, dog, cow, chicken, or zebrafish genomes, including reference sequences for known genes. This gives a simplified view of gene expression activity from different parts of the eye across the genome. The data can be interrogated in several ways. Specific gene names can be entered into the search window. Alternatively, regions of the genome can be displayed. For example, entering two STS markers separated by a semicolon (e.g. RH18061;RH80175) allows the display of the entire chromosomal region associated with the mapping of a specific disease locus. ESTs for each tissue can then be displayed to help in the selection of candidate genes. In addition, sequences can be entered into a BLAT search and rapidly aligned on the genome, again showing eye derived ESTs for the same region. EyeBrowse includes a custom track display SAGE data for human eye tissues derived from the EyeSAGE project. The track shows the normalized sum of SAGE tag counts from all published eye-related SAGE datasets centered on the position of each identifiable Unigene cluster. This indicates relative activity of each gene locus in eye. Clicking on the vertical count bar for a particular location will bring up a display listing gene details and linking to specific SAGE counts for each eye SAGE library and comparisons with normalized sums for neural and non-neural tissues. To view or alter settings for the EyeSAGE track on EyeBrowse, click on the vertical gray bar at the left of the display. Other custom tracks display known eye disease genes and mapped intervals for candidate loci for retinal disease, cataract, myopia and cornea disease. These link back to further information at NEIBank. For mouse, there is custom track data for ChIP-on-Chip of RNA-Polymerase-II during photoreceptor maturation.<BR

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• SciCrunch
• 17 years ago - by Anonymous

An integrated exploration of biomedical literature and data. An anatomy viewer can be accessed and searches of PubMed literature are visualized as to the anatomical regions that they effect. PubAnatomy takes advantage of the 25-micron voxel level mouse brain structure annotation generated by the Allen Brain Institute and integrates Allen Brain Atlas gene expression data, relationships between brain regions and diseases for more efficient exploration of Medline database and gene expression data.

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• SciCrunch
• 17 years ago - by Anonymous

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• SciCrunch
• 16 years ago - submitted by Stephen Larson

The CMTA is a 501(C)(3)nonprofit organization founded in 1983 whose goals are patient support, public education, promotion of research and ultimately the treatment and cure of CMT. Charcot-Marie-Tooth, or CMT, is the most commonly inherited neurological disorder and is found world-wide in all races and ethnic groups. Discovered in 1886 by three physicians, Jean-Martin-Charcot, Pierre Marie, and Howard Henry Tooth, CMT affects an estimated 2.6 million people. CMT patients slowly lose normal use of their feet/legs and hands/arms as nerves to the extremities degenerate and the muscles in the extremities become weakened because of the loss of stimulation by the affected nerves. Many patients also have some loss of sensory nerve function. CMT is one of the 40 diseases covered by the MDA, but unlike muscular dystrophy, in which the defect is in the muscles, CMT is a disorder in which the defect is in the nerves that control the muscles. CMT usually isnt life-threatening and almost never affects brain function. It is not contagious, but it is hereditary and can be passed down from one generation to the next. CMT... * ...is also known as peroneal muscular atrophy (PMA) and hereditary motor sensory neuropathy (HMSN). * ...is slowly progressive, causing deterioration of peripheral nerves which control sensory information and muscle function of the foot/lower leg and hand/forearm. * ...causes degeneration of peroneal muscles (located on the front of the leg below the knees). * ...causes foot-drop walking gait, foot bone abnormalities, high arches and hammertoes, problems with balance, problems with hand function, occasional lower leg and forearm muscle cramping, loss of some normal reflexes, scoliosis (curvature of the spine) and sometimes, breathing difficulties. * ...does not affect life expectancy, but can, in rare instances, cause severe disability. * ...has no cure, although physical therapy, occupational therapy and moderate physical activity are beneficial. * ...is sometimes surgically treated. * ...is usually inherited in an autosomal dominant pattern, which means if one parent has CMT there is a 50/50 chance of each child inheriting the disorder. * ...may become worse if certain neurotoxic drugs are taken. * ...can vary greatly in severity, even within the same family. * ...can now be diagnosed by a blood test (CMT types: 1A, 1B, 1C, 1D, 1E, 1F, 1X, 2A, 2B, 2E, 2F, 2I, 2J, 2K, 4A, 4C, 4E, 4F, 4J, HNPP, CHN, and DSN).

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• SciCrunch
• 17 years ago - by Anonymous

BrainWeb provides information and links to validated sites about brain diseases and disorders. These include outside resources reviewed by scientific advisers, as well as articles in Dana publications. Sites listed in BrainWeb detail common brain diseases and disorders, and include general neuroscience and health resources. They offer descriptions of conditions, frequently asked questions, organization contacts, and sources for more information. BrainWeb and its links are suitable for lay readers, including students and educators, as well as people with brain disorders, their families, and caregivers.

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• SciCrunch
• 14 years ago - by Anonymous

STRFPak is a Matlab toolbox for estimating the linear and nonlinear stimulus-response mapping function of sensory systems. This mapping function is commonly called the spatio- or spectro-temporal receptive field (STRF). A quantitative estimate of the STRF can be used in subsequent computational modeling studies or to predict future responses of the system. STRFPak implements several general STRF estimation techniques and can be used with any stimuli (including natural scenes and sounds). The theoretical basis for STRF estimation has been known for some time, but estimation software has not been widely available. This project aims to develop appropriate software and make it available to the wider community of sensory neuroscientists. Although STRFPak is based on established methods it incorporates two important innovations. First, STRFPak can be used to characterize a sensory system from its response to arbitrary stimuli including natural signals (e.g., vocalizations, natural scenes). Second, STRFPak incorporates several methods for estimating nonlinear STRFs. STRFPak also includes tutorial examples and documentation.

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• SciCrunch
• 17 years ago - by Anonymous

George Washington University is a pioneer in the field of pharmacogenomics offering the only Bachelor''s degree program in the country. Students are admitted into this full-time program in their Junior year. The program strives to educate a new generation of health science graduates who are acutely aware of the interface between human genetic variability and drug action. Our mission is to offer a world-class education to students and equip future pharmacists, scientists, physicians, policy makers and health care professionals with concrete knowledge and unparalleled experience in pharmacogenomics. Our graduates play integral roles in the resolution of the scientific, policy and ethical issues surrounding personalized medicine. The program will uniquely prepare individuals for a variety of positions in the biopharmaceutical industry and allied health professions as well as continued advanced education in health policy, medicine, pharmacological/genomic research and pharmacy.

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• SciCrunch
• 16 years ago - by Anonymous

A professional organization focused on advancing neurosurgery by providing members with the educational and career development opportunities. They have an annual meeting and offer CME opportunities. The Congress of Neurological Surgeons seeks to improve the quality of healthcare through: * The development of educational programs that convey knowledge, enhance self-directed learning and improve patient outcomes. * Advancing the science of medical education. * Promoting original inquiry and the exchange of clinical and scientific evidence. * Public advocacy for the enhancement of quality, safety and access to neurosurgical care. The Congress of Neurological Surgeons seeks to advance the profession of neurosurgery through: * Refining neurosurgical practice based on evidence. * Promoting volunteerism and leadership development within our specialty. * Development of programs to promote safety, quality and efficiency in practice for domestic and international members.

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• SciCrunch
• 16 years ago - by Anonymous

A computational hosting resource which assissts with lab organization by splitting functions into four modules. “Order requests” is a module where users can view and track order requests. The module “Inventory” allows users to track commercial and lab-made products. “Documents” allows users to organize and share protocols and other documents. “Equipment sign-up” allows users to manage shared equipment. An active help system, video guides, and 1-on-1 demos are available for assistance when setting up.

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• SciCrunch
• 16 years ago - by Anonymous

This is a blog about post genomic knowledge. The website''s goal is to make public datasets from the bioinformatics community available in RDF format via standard SPARQL endpoints.

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• SciCrunch
• 17 years ago - by Anonymous

Resources and tools from a project to automatically extract useful information from texts written by scientists to help overcome the problems caused by information overload. The primary annotated resource created is the GENIA corpus, a collection of biomedical literature which consists of multiple layers of annotation, encompassing both syntactic and semantic annotation. The project also created or coordinated the annotation of multiple other corpus resources. Additionally, a rich set of automatic tools are available for various annotation tasks, most trained on various parts of the GENIA corpus annotations. The GENIA corpus was developed to provide a reference material for the development of bio-TM systems. The corpus currently contains 1,999 Medline abstracts which were collected using the three MeSH terms, human, blood cells, and transcription factors. The corpus has been annotated with various levels of linguistic and semantic information. The GENIA corpus includes the following: * POS annotation * Treebank * Coreference Annotation * Term annotation * Event annotation * Relation annotation * Cellular localization * Disease-Gene association * Pathway corpus The GENIA Project initiated the BioNLP Shared Task series and has organized a number of tasks in three different shared task events, many using resources based on GENIA Corpus annotations. Tools include: * XConc suite: a collection of XML-based tools which are integrated to support the corpus development and annotation.

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• SciCrunch
• 16 years ago - by Anonymous

Gene Expression Atlas is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. The EBI Gene Expression Atlas Blog discusses ideas, features and problems of creating a large scale meta-analytical atlas of gene expression from publicly available microarray data. Atlas REST API provides all the results available in the main web application in a pragmatic, easy to use form - simple HTTP GET queries as input and either JSON or XML formats as output. Gene Expression Atlas goals: 1. Provision of a statistically robust framework for integration of gene expression experiment results across different platforms at a meta-analytical level 2. A simple interface for identifying strong differential expression candidate genes in conditions of interest 3. Integration of ontologies for high quality annotation of gene and sample attributes 4. Construction of new gene expression summarized views, with a view to analysis of putative signaling pathway targets, discovery of correlated gene expression patterns and the identification of condition/tissue-specific patterns of gene expression.

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• SciCrunch
• 16 years ago - by Anonymous

The Wisconsin Primate Research Center supports one of the largest colonies of common marmosets (Callithrix jacchus) in the United States. Through the Callicam, anyone with web access can observe one of the WPRC''s common marmoset families. The Callicam webcam allows site visitors to pan, zoom, and manipulate the camera themselves for two minutes at a time. Accompanying links to comprehensive information about the species along with sample exercises for use with the Callicam provide the opportunity to learn about this engaging primate while observing it live online.

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• SciCrunch
• 16 years ago - by Anonymous

The UK Crop Plant Bioinformatics Network (UK CropNet) was established in 1996 as part of the BBSRC''s Plant and Animal Genome Analysis special initiative. Our focus is the development, management, and distribution of information relating to comparative mapping and genome research in crop plants. Find out more about our background or read our UK CropNet paper published in Nucleic Acids Research (pdf reader required).This site hosts a wide range of databases and software developed by UK CropNet, as well as hosting many other plant databases developed in the USA. You can perform a keyword text search across all of these databases or use our UK CropNet BLAST server to search against all of the sequences in these databases.

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• SciCrunch
• 17 years ago - by Anonymous