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http://openconnectomeproject.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. Connectomes repository to facilitate the analysis of connectome data by providing a unified front for connectomics research. With a focus on Electron Microscopy (EM) data and various forms of Magnetic Resonance (MR) data, the project aims to make state-of-the-art neuroscience open to anybody with computer access, regardless of knowledge, training, background, etc. Open science means open to view, play, analyze, contribute, anything. Access to high resolution neuroanatomical images that can be used to explore connectomes and programmatic access to this data for human and machine annotation are provided, with a long-term goal of reconstructing the neural circuits comprising an entire brain. This project aims to bring the most state-of-the-art scientific data in the world to the hands of anybody with internet access, so collectively, we can begin to unravel connectomes. Services: * Data Hosting - Their Bruster (brain-cluster) is large enough to store nearly any modern connectome data set. Contact them to make your data available to others for any purpose, including gaining access to state-of-the-art analysis and machine vision pipelines. * Web Viewing - Collaborative Annotation Toolkit for Massive Amounts of Image Data (CATMAID) is designed to navigate, share and collaboratively annotate massive image data sets of biological specimens. The interface is inspired by Google Maps, enhanced to allow the exploration of 3D image data. View the fork of the code or go directly to view the data. * Volume Cutout Service - RESTful API that enables you to select any arbitrary volume of the 3d database (3ddb), and receive a link to download an HDF5 file (for matlab, C, C++, or C#) or a NumPy pickle (for python). Use some other programming language? Just let them know. * Annotation Database - Spatially co-registered volumetric annotations are compactly stored for efficient queries such as: find all synapses, or which neurons synapse onto this one. Create your own annotations or browse others. *Sample Downloads - In addition to being able to select arbitrary downloads from the datasets, they have also collected a few choice volumes of interest. * Volume Viewer - A web and GPU enabled stand-alone app for viewing volumes at arbitrary cutting planes and zoom levels. The code and program can be downloaded. * Machine Vision Pipeline - They are building a machine vision pipeline that pulls volumes from the 3ddb and outputs neural circuits. - a work in progress. As soon as we have a stable version, it will be released. * Mr. Cap - The Magnetic Resonance Connectome Automated Pipeline (Mr. Cap) is built on JIST/MIPAV for high-throughput estimation of connectomes from diffusion and structural imaging data. * Graph Invariant Computation - Upload your graphs or streamlines, and download some invariants. * iPad App - WholeSlide is an iPad app that accesses utilizes our open data and API to serve images on the go.

Proper citation: Open Connectome Project (RRID:SCR_004232) Copy   

•   Source: SciCrunch Registry

http://www.cure.med.ucla.edu/

Center whose interests and activities encompass several facets of gastrointestinal regulatory physiology and cell biology. It provides an infrastructure to support basic, translational and clinical research and to facilitate interdisciplinary research and training activities in digestive diseases.

Proper citation: CURE - Digestive Diseases Research Center (RRID:SCR_004238) Copy   

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http://www.euadr-project.org/

Consortium that created the capability to detect Adverse Drug Response (ADR) signals by creating the infrastructure for large-scale monitoring of drug safety using electronic health records (EHR). The platform leverages EHR''''s comprising demographics, drug use and clinical data of over 30 million patients from several European countries. Special attention was given to patient groups that are not routinely involved in clinical trials, for ethical or practical reasons (e.g. pregnant women, elderly people, people using many drugs simultaneously, and children). This project also studies and compares a number of different techniques that all aim to detect unexpected or disproportional rates of events. The algorithms that they studied originate not only from the field of (pharmaco)epidemiology, but also from fields such as bio-terrorism, machine learning, and classical signal detection. EU-ADR specific objectives are: To detect events, To relate these events to drugs, To develop hypothesis that explain adverse events, To detect adverse events earlier, and To avoid false positives. The web-based platform is available at https://bioinformatics.ua.pt/euadr/ EU-ADR has contributed to the ability to conduct better drug safety studies based on the re-use of healthcare data. By facilitating the early detection of adverse drug reactions, but also providing key information on populations at risk, potential drug interactions, potential underlying mechanisms and intervening pathways in adverse events, etc., the project will allow for improved and more complete information to be available for drug and healthcare delivery, leading to increased patient safety and its associated cost savings. The EU-ADR system can be considered as a complementary tool to already existing pharamcovigilance systems. Should the system be widespread in the long term, it has the potential to contribute to the development of future electronic health record systems, insofar as the expected benefits of these IT tools are only fully attainable when EHRs develop themselves in consistency, richness and formats that allow them to be subject of such tools. In anticipation, EU-ADR has been designed to be modular and scalable, so that different EHR databases (other than those participating in the Consortium) can be progressively enlisted in the future, adopt the software for data extraction and therefore become susceptible of exploitation by the system, for maximum global effect.

Proper citation: EU-ADR (RRID:SCR_004028) Copy   

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http://www.mcewencentre.com/

Center aiming to be a catalyst for regenerative medicine by facilitating collaboration, supporting research, and promoting awareness of the field. The center includes 15 scientists at five Toronto hospitals, as well as the University of Toronto, currently working to accelerate the development of more effective treatments for conditions such as heart disease, diabetes, respiratory disease and spinal cord injury. They collaborate with many other research institutions throughout North America, Europe and the Asia / Pacific region. The research is powered by a team of recent doctoral graduates recruited from around the world that are selected through a competitive process. They are a critical tool for supporting the work of McEwen Centre, allowing them to find medical breakthroughs faster.

Proper citation: McEwen Centre for Regenerative Medicine (RRID:SCR_004020) Copy   

•   Source: SciCrunch Registry

https://sfari.org/

Launched in 2005, the Simons Foundation Autism Research Initiative (SFARI) is a research campaign within the Simons Foundation''s overall suite of programs. SFARI''s mission is to improve the diagnosis and treatment of autism spectrum disorders by funding, catalyzing and driving innovative research of the greatest quality and relevance. Although SFARI''s priority is to benefit individuals challenged by these disorders, its efforts are certain to yield insights into the neural mechanisms of fundamental human capabilities, thereby promoting the broader mission of the Simons Foundation to advance the frontiers of research in the basic sciences and mathematics. Autism spectrum disorders are a set of complex developmental disorders characterized by persistent deficits in social communication and interaction, as well as restricted behaviors, interests or activities. The Centers for Disease Control and Prevention estimates that roughly 1 in 110 children in the U.S. have autism, with many more boys affected than girls. These disorders cost the U.S. economy an estimated $35 billion dollars each year in direct care costs and lost productivity, and extract an incalculable human toll.

Proper citation: SFARI - Simons Foundation Autism Research Initiative (RRID:SCR_004261) Copy   

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http://webvision.med.utah.edu/

Online textbook that has evolved into an interactive, dynamic blog that covers all things related to the bioscience of the visual system. It summarizes recent advances in knowledge and understanding of the visual system through dedicated chapters and evolving discussion to serve as a clearing house for all things related to retina and vision science.

Proper citation: Webvision - The Organization of the Retina and Visual System (RRID:SCR_004254) Copy   

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http://www.cclg.org.uk/index.php

THIS RESORUCE IS NO LONGER IN SERVICE. Documented on April 27,2023. CCLG is an association of healthcare professionals involved in the treatment and care of children and younger teenagers with cancer, and underpins all the activity in pediatric oncology in the British Isles. CCLG is committed to research and development in the treatment of cancer in this age group, the ultimate goal of which is to maximize cure while minimizing the early and late side effects of treatment. Provision of information for patients and families is a core activity. The Children''s Cancer and Leukaemia Group was formed in 2006 as a result of the merger of the UK Children''s Cancer Study Group and the UK Childhood Leukaemia Working Party, both of which had been in existence since the 1970s.

Proper citation: CCLG (RRID:SCR_004137) Copy   

•   Source: SciCrunch Registry

http://www.fishbase.org/home.htm

A global species database and encyclopedia of over 32,800 species and subspecies of fishes that is searchable by common name, genus, species, geography, family, ecosystem, references literature, tools, etc. It links to other, related databases such as the Catalog of Fishes, GenBack, and LarvalBase. It is associated with a partner journal, Acta Ichthyologica et Piscatoria. It is available in English, Greek, Spanish, Portuguese, French, Dutch, Italian, and German. Photo and video submissions are welcome. FishBase 2004 is also available on DVD or CD-ROMs with full information on 28,500 species. It comes together with the FishBase 2000 book and can be ordered for 95 US$ including air-mail.

Proper citation: FishBase (RRID:SCR_004376) Copy   

•   Source: SciCrunch Registry

http://www.penta-id.org/

A Level 1 network for pediatric infectious disease in Europe recognized by the European networks of paediatric research at the European Medicines Agency (EnprEMA) whose activities vary from clinical trials, to cohort studies and training. It is currently developing a portfolio of clinical trials in antimicrobials in children, including antibiotics, antivirals and antifungals.

Proper citation: PENTA-ID (RRID:SCR_004092) Copy   

•   Source: SciCrunch Registry

https://zenodo.org/

Repository for all research outputs from across all fields of science in any file format as well as both positive and negative results. They assign all publicly available uploads a Digital Object Identifier (DOI) to make the upload easily and uniquely citeable. They further support harvesting of all content via the OAI-PMH protocol. They promote peer-reviewed openly accessible research, and curate uploads. ZENODO allows users to create their own collection and accept or reject all uploads to it. They allow for uploading under a multitude of different licenses and access levels.

Proper citation: ZENODO (RRID:SCR_004129) Copy   

•   Source: SciCrunch Registry

http://www.brainarchitecture.org/mouse-home

An atlas project whose goal is to enerate brainwide maps of inter-regional neural connectivity that specify the inputs and outputs of every brain region, at a "mesoscopic" level of analysis. A 3D injection viewer is used to view the mouse brain. To determine the outputs of a brain region, anterograde tracers are used which are taken up by neurons locally ("the input"), then transported actively down the axons to the "output regions." The whole brain is then sliced thinly, and each slice is digitally imaged. These 2-D images are reconstructed in 3D. The majority of the resulting 3-D brain image is unlabeled. Only the injected region and its output regions have tracer in them, allowing for identification of this small fraction of the connectivity map. This procedure is repeated identically, to account for individual variability. To determine the inputs to the same brain region as above, a retrograde tracer is injected in the same stereotaxic location ("the input"), and the process is repeated. In order to accumulate data from different mice (each of whom has a slightly different brain shape and size), 3-D spatial normalization is performed using registration algorithms. These gigapixel images of whole-brain sections can be zoomed to show individual neurons and their processes, providing a "virtual microscope." Each sampled brain is represented in about 500 images, each image showing an optical section through a 20 micron-thick slice of brain tissue. A multi-resolution viewer permits users to journey through each brain, following the pathways taken through three-dimensional brain space by tracer-labeled neuronal pathways. A key point is that at the mid-range "mesoscopic" scale, the team expects to assemble a picture of connections that are stereotypical and probably genetically determined in a species-specific manner. By dividing the volume of a hemisphere of the mouse brain into 250 equidistant, predefined grid-points, and administering four different kinds of tracer injections at each grid point -- in different animals of the same sex and age a complete wiring diagram that will be stitched together in "shotgun" fashion from the full dataset.

Proper citation: Mouse Brain Architecture Project (RRID:SCR_004683) Copy   

•   Source: SciCrunch Registry

http://www.taverna.org.uk/

An open source and domain independent Workflow Management System ����?? a suite of tools used to design and execute scientific workflows and aid in silico experimentation. Taverna Workbench now has support for service sets, offline workflow editing, workflow validation, improved workflow run monitoring, and the pausing and canceling of workflow runs. The command line tool allows you to run workflows outside of the workbench and is available as a stand-alone download or bundled with the Taverna Workbench 2.2.0 download. The Taverna suite is written in Java and includes the Taverna Engine (used for enacting workflows) that powers both the Taverna Workbench (the desktop client application) and the Taverna Server (which allows remote execution of workflows). Taverna is also available as a Command Line Tool for a quick execution of workflows from a terminal. Taverna 2.2.0 includes * Copy/paste, shortcuts, undo/redo, drag and drop * Animated workflow diagram * Remembers added/removed services * Secure Web services support * Secure access to resources on the web * Up-to-date R support * Intermediate values during workflow runs * myExperiment integration * Excel and csv spreadsheet support * Command line tool

Proper citation: Taverna (RRID:SCR_004437) Copy   

•   Source: SciCrunch Registry

http://dkcoin.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented October 13, 2014. The resource has moved to the NIDDKInformation Network (dkNET) project. Contact them at info_at_dknet.org with any questions. Database of large pools of data relevant to the mission of NIDDKwith the goal of developing a community-based network for integration across disciplines to include the larger DKuniverse of diseases, investigators, and potential users. The focus is on greater use of this data with the objective of adding value by breaking down barriers between sites to facilitate linking of different datasets. To date (2013/06/10), a total of 1,195 resources have been associated with one or more genes. Of 11,580 total genes associated with resources, the ten most represented are associated with 359 distinct resources. The main method by which they currently interconnect resources between the providers is via EntrezGene identifiers. A total of 780 unique genes provide the connectivity between 3,159 resource pairs across consortia. To further increase interconnectivity, the groups have been further annotating their data with additional gene identifiers, publications, and ontology terms from selected Open Biological and Biomedical Ontologies (OBO).

Proper citation: dkCOIN (RRID:SCR_004438) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/Structure/cblast/cblast.cgi?

The NCBI Related Structures tool allows you to find 3D structures from the Molecular Modeling Database (MMDB) that are similar in sequence to a query protein. Although the query protein may not yet have a resolved structure, the 3D shape of a similar protein sequence can shed light on the putative shape and biological function of the query protein. CBLAST is a tool that compares a query protein sequence against all protein sequences from resolved 3D structures by using protein BLAST against the PDB data set. The purpose is to find representative 3D structures for the query and/or its homologs, as available. Each record in the Entrez Protein database has been CBLAST''ed and the search results are available as Related Structures in the Links menu of Entrez Protein records. You can also enter a protein query sequence directly into the CBLAST search page in order to find its sequence-similar 3D structure records. The search results can be viewed in Cn3D (hence the name CBLAST), which displays an alignment of the query protein to the related structure''s sequence and allows you to interactively examine the sequence-structure relationship.

Proper citation: CBLAST (RRID:SCR_004711) Copy   

•   Source: SciCrunch Registry

http://www.sbgn.org/Main_Page

The Systems Biology Graphical Notation (SBGN) project aims to develop high quality, standard graphical languages for representing biological processes and interactions. Each SBGN language is based on the consensus of the broad international SBGN community of biologists, curators and software developers. Over the course of its development many individuals, organizations and companies made invaluable contributions to the SBGN through participating in discussions and meetings, providing feedback on the documentation and worked examples, adopting the standard and spreading the word. Circuit diagrams and Unified Modeling Language diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity, removing ambiguity and enabling software tool support for communication of complex information. Ironically, despite having one of the highest ratios of graphical to textual information, biology still lacks standard graphical notations. The recent deluge of biological knowledge makes addressing this deficit a pressing concern. Toward this goal, we present the Systems Biology Graphical Notation (SBGN), a visual language developed by a community of biochemists, modelers and computer scientists. SBGN consists of three complementary languages: process diagram, entity relationship diagram and activity flow diagram. Together they enable scientists to represent networks of biochemical interactions in a standard, unambiguous way. We believe that SBGN will foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling. A list of software packages known to provide (or have started to develop) support for SBGN notations is available.

Proper citation: Systems Biology Graphical Notation (RRID:SCR_004671) Copy   

•   Source: SciCrunch Registry

http://magnet.c2b2.columbia.edu/

The mission of the Center for the Multiscale Analysis of Genomic and Cellular Networks (MAGNet) is to develop novel Structural and Systems Biology methods and tools for the dissection of molecular interactions in the cell and for the interaction-based elucidation of cellular phenotypes. These tools are made freely available to the the members of the research community. They are also validated in the context of the Center''''s own research program through collaborative projects with experimental biologists. MAGNet is one of 7 National Centers for Biomedical Computing (NCBC). These Centers, in conjunction with individual investigator awards, are creating a networked effort to build the computational infrastructure for biomedical computing in the nation. The NCBC program is devoted to all facets of biomedical computing, from basic research in computational science to providing the tools and resources that biomedical and behavioral researchers need to do their work. In addition to carrying out fundamental research the NCBCs play a major role in educating and training researchers to engage in biomedical computing. MAGNet is also one of 12 inter-disciplinary Centers for Cancer Systems Biology (CCSBs), a component of the National Cancer Institute''''s Integrative Cancer Biology Program. The CCSBs provide a core framework for applying systems biology approaches to cancer research through the development and implementation of computational models of processes relevant to cancer prevention, diagnostics and therapeutics. The CCSBs seek to integrate experimental biology with mathematical modeling to foster new insights in the biology and new approaches to the management of cancer. MAGNet''''s Training Core ensures that the methods developed by the Center are integrated into the educational offerings of Columbia University''''s Medical School.

Proper citation: MAGNet - Multiscale Analysis of Genomic and Cellular Networks (RRID:SCR_004399) Copy   

•   Source: SciCrunch Registry

http://www.uca.edu.ar/index.php/home/index/en/universidad/facultades/buenos-aires/cs-medicas/investigacion/iib/

The Biomedical Research Program (PIB) of the School of Medical Sciences was created in 2007, after a Collaboration Protocol was established between UCA and the National Council of Scientific and Technical Research (CONICET). Research at PIB aims at unraveling the molecular, biochemical and genetic aspects of human diseases, therefore contributing to understanding complex pathologies. Research Groups include: * Molecular and Cell Biology Lab (LBCM) - Group leader: Tom��s A. Santa Coloma, Ph.D. * Nanotechnology Lab - Group leader: Tom��s A. Santa Coloma, Ph.D. * Molecular Neurobiology Lab - Group leader: Francisco J. Barrantes, Ph.D.

Proper citation: Biomedical Research Program UCA (RRID:SCR_004395) Copy   

•   Source: SciCrunch Registry

http://www.openanesthesia.org/

OpenAnesthesia.org is a wiki promoting evidence-based medicine in anesthesiology, critical care and pain management. It is divided into several, major Units (Anesthesia Text, Critical Care Manual, Practice-Changing Articles, Controversies in Anesthesia, ABA keywords, Audio/Video Archives, CME, GME, Pharmacology...), each of which is subdivided into Chapters (or in some cases, even smaller subdivisions, such as sections, individual key words, topics, points of interest, or bibliographic references). The goal of Anasthesia Text is to collect and distribute evidence-based information regarding all aspects of anesthesia. This section is similar to a traditional textbook in the broad range of topics covered, but different in that it will provide this information in the form of a wiki (i.e. anyone can edit, add, or subtract to it). OpenAneshesia.org provides anesthesia residents with GME credit and Program Directors with a tool to document core competency activities for Accreditation Council for Graduate Medical Education (ACGME)-mandated learning portfolios. Residents are invited invited to read the Anesthesia & Analgesia article of the month and listen to an interview with one of the article''s authors. During the interview, the author will discuss the specifics of the article as well as general topics geared towards improving each resident''s appreciation of basic or clinical research. After listening to the podcast and reading the article, residents can answer 5 questions in order to demonstrate their mastery of the topics discussed (similar to the Anesthesia & Analgesia Continuing Medical Education (CME) section). Like the CME section, after demonstrating proficiency, a resident will receive a printable certificate that will specify which ACGME core competencies were addressed in the article and interview. The certificates can be put in each resident''s ACGME-required learning portfolio.

Proper citation: OpenAnesthesia.org (RRID:SCR_004547) Copy   

•   Source: SciCrunch Registry

http://kingdevicktest.com/

An accurate and reliable method for identifying athletes with head trauma, and a strong candidate rapid sideline screening test for concussion. The test is able to capture impairments of eye movement, attention, language and other symptoms of impaired brain function. It is a physical method of evaluating visual tracking and saccadic eye movements is based on the time to perform rapid number naming. It involves reading aloud a series of single digit numbers from left to right on three test cards. Participants are asked to read the numbers on each card from left to right as quickly as possible but without making any errors. The sum of the three test card time scores constitutes the summary score for the entire test. The test is a proven indicator of oculomotor inefficiencies regarding eye movements during reading. Published medical studies have determined that deficiencies in saccadic eye movements can be an indicator of mild Traumatic Brain Injury (mTBI) or concussions. Studies have shown that there is a significant relationship between poor oculomotor functions and learning disabilities (including dyslexia detection). Saccadic eye movement deficiencies can be improved with training and correspondingly reading performance also can be improved. Simply put, subjects who don''t perform well on this test are not efficient readers, although because there are many reasons for poor reading unrelated to eye movements, some poor readers do fine on the test. They believe that the test should be in the hands of teachers in order to help them determine if a student''s poor reading performance is related to deficiencies in their ability to move their eyes efficiently.

Proper citation: King-Devick Test (RRID:SCR_004500) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/pcsubstance?db=pcsubstance

As one of three primary databases of PubChem (Pcsubstance, Pccompound, and PCBioAssay), PubChem Substance Database contains descriptions of chemical samples, from a variety of sources, and links to PubMed citations, protein 3D structures, and biological screening results that are available in PubChem BioAssay. If the contents of a chemical sample are known, the description includes links to PubChem Compound. A PubChem FTP is available and new data is accepted into the repository. Pcsubstance contains more than 81 million records (2011).

Proper citation: PubChem Substance (RRID:SCR_004742) Copy   

•   Source: SciCrunch Registry