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https://www.msu.edu/~brains/index.html
The Brain Biodiversity Bank refers to the repository of images of and information about brain specimens contained in the collections associated with the National Museum of Health and Medicine at the Armed Forces Institute of Pathology in Washington, DC. Atlases and brain sections are available for a variety of mammals, and we are also developing a series of labeled atlases of stained sections for educators, students, and researchers. These collections include, besides the Michigan State University Collection, the Welker Collection from the University of Wisconsin, the Yakovlev-Haleem Collection from Harvard University, the Meyer Collection from the Johns Hopkins University, and the Huber-Crosby and Crosby-Lauer Collections from the University of Michigan. What we are doing currently at Michigan State is a series of demonstration projects for publicizing the contents of the collections and ways in which they can be used. For example, the images from the collection can be used for comparative brain study. We have prepared databases of the contents of the collections for presentation and use on this site, as well as for downloading by users in several formats. We are also developing a series of labeled atlases of stained sections for educators, students, and researchers. This internet site is associated with the Comparative Mammalian Brain Collections site. All of the images are in JPEG or GIF format.
Proper citation: Michigan State University Brain Biodiversity Bank (RRID:SCR_003289) Copy
http://www.yaleruddcenter.org/
A non-profit research and public policy organization devoted to improving the worlds diet, preventing obesity, and reducing weight stigma.
Proper citation: Yale Rudd Center for Food Policy and Obesity (RRID:SCR_003283) Copy
http://www.brainbank.mclean.org/
Biomaterial supply resource that acquires, processes, stores, and distributes postmortem brain specimens for brain research. Various types of brain tissue are collected, including those with neurological and psychiatric disorders, along with their parents, siblings and offspring. The HBTRC maintains an extensive collection of postmortem human brains from individuals with Huntington's chorea, Alzheimer's disease, Parkinson's disease, and other neurological disorders. In addition, the HBTRC also has a collection of normal-control specimens.
Proper citation: Harvard Brain Tissue Resource Center (RRID:SCR_003316) Copy
http://www.physiol.ucl.ac.uk/research/silver_a/nclamp/
Data acquisition software that runs in conjunction with neuromatic. configured to work with Igor Pro on PC or Mac, instrutech or national instrument acquisition devices. Funded by The Medical Research Council (UK) Compatibility with WaveMetrics Igor Pro 5 and 6. Compatibility with Mac or PC. NIDAQ interfacing multifunction DAQ boards from National Instruments. Requires Igor NIDAQ Tools MX. ITC interfacing - data acquisition systems from InstruTech / Heka. Requires Igor ITC XOPs. Episodic acquisition (stim and sample). Continuous acquisition (currently for ITC users only). Online analysis, with ability to create your own analysis functions. Notes and Log Files which can be displayed within a table or notebook. Automatic saving of data and log folders to your hard drive. Flexible stimulus pulse generator with ability to use your own pulse waveforms. Instant accessibility to all of NeuroMatics and Igor Pros pre-existing data analysis functions.
Proper citation: Nclamp - data acquisition software for electrophysiology (RRID:SCR_003750) Copy
Database of images of putative biological pathways, macromolecular structures, gene families, and cellular relationships. It is of use to those who are working with large sets of genes or proteins using cDNA arrays, functional genomics, or proteomics. The rationale for this collection is that: # Except in a few cases, information on most biological pathways in higher eukaryotes is non-existent, incomplete, or conflicting. # Similar biological pathways differ by tissue context, developmental stages, stimulatory events, or for other complex reasons. This database allows comparisons of different variations of pathways that can be tested empirically. # The goal of this database is to use images created directly by biomedical scientists who are specialists in a particular biological system. It is specifically designed to NOT use average, idealized or redrawn pathways. It does NOT use pathways defined by computer algorithm or information search approaches. # Information on biological pathways in higher eukaryotes generally resides in the images and text of review papers. Much of this information is not easily accessible by current medical reference search engines. # All images are attributable to the original authors. All pathways or other biological systems described are graphic representations of natural systems. Each pathway is to be considered a work in progress. Each carries some degree of error or incompleteness. The end user has the ultimate responsibility to determine the scientific correctness and validity in their particular biological system. Image/pathway submissions are welcome.
Proper citation: Biological Biochemical Image Database (RRID:SCR_003474) Copy
Computing resources structural biologists need to discover the shapes of the molecules of life, it provides access to web-enabled structural biology applications, data sharing facilities, biological data sets, and other resources valuable to the computational structural biology community. Consortium includes X-ray crystallography, NMR and electron microscopy laboratories worldwide.SBGrid Service Center is located at Harvard Medical School.SBGrid's NIH-compliant Service Center supports SBGrid operations and provides members with access to Software Maintenance, Computing Access, and Training. Consortium benefits include: * remote management of your customized collection of structural biology applications on Linux and Mac workstations; * access to commercial applications exclusively licensed to members of the Consortium, such as NMRPipe, Schrodinger Suite (limited tokens) and the Incentive version of Pymol; remote management of supporting scientific applications (e.g., bioinformatics, computational chemistry and utilities); * access to SBGrid seminars and events; and * advice about hardware configurations, operating system installations and high performance computing. Membership is restricted to academic/non-profit research laboratories that use X-ray crystallography, 2D crystallography, NMR, EM, tomography and other experimental structural biology technologies in their research. Most new members are fully integrated with SBGrid within 2 weeks of the initial application.
Proper citation: Structural Biology Grid (RRID:SCR_003511) Copy
http://www.cellimagelibrary.org/
Freely accessible, public repository of vetted and annotated microscopic images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes. Explore by Cell Process, Cell Component, Cell Type or Organism. The Cell includes images acquired from historical and modern collections, publications, and by recruitment.
Proper citation: Cell Image Library (CIL) (RRID:SCR_003510) Copy
http://www.stjohns.edu/academics/schools-and-colleges/college-pharmacy-and-health-sciences
The College of Pharmacy and Allied Health Professions equips students with the education, training and support they need to meet the present and future demands professionals encounter as pharmacists, physician assistants, clinical laboratory scientists, toxicologists and radiologic technologists. The College is committed to helping students: * Focus on the responsibilities of public health and service * Appreciate the ever-changing character of the health professions * Enjoy a broad, general education * Pursue graduate study in specialized fields of interest Facilities Laboratory facilities in the College of Pharmacy and Allied Health Professions include state-of-the-art equipment used in pharmacology/toxicology, medicinal chemistry, industrial pharmacy and drug information. Our facilities include: GC-mass spectrophotometers; transmission and scanning electron microscopes; Mrs.; capillary GCs; preparative and analytical HPLCs; liquid scintillation and gamma counters; luminometers; dissolution apparatus; membrane potentiometers; atomic absorption spectrophotometers; polygraphs; high-speed and ultracentrifuges. In addition, we have sophisticated tissue-cultures laboratories, molecular pharmacology and molecular biology laboratories, as well as an AAALAC accredited animal facility. In addition to the main University computer, a fully equipped microcomputer laboratory is located adjacent to the main science complex.
Proper citation: St. John's College of Pharmacy and Allied Health Professions (RRID:SCR_003752) Copy
https://services.healthtech.dtu.dk/
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.
Proper citation: DTU Center for Biological Sequence Analysis (RRID:SCR_003590) Copy
http://www.investigatordatabank.org/
Consortium between several pharmaceutical companies to develop a database that shares clinical trial investigator information that each company has on file to reduce administrative burden for investigators and to increase visibility of qualified investigators to research sponsors. Hosted by a 3rd party, DrugDev, it is the one place where pharmaceutical companies can share investigator and site information and investigators can view, edit, and comment on their own information. Industry members will be able share information from their clinical trial management systems including investigator / site contact details, GCP training records, past trial participation, and recruitment history. Upon investigator opt-in, this information is used by each participating company to identify sites for upcoming studies; to help set recruitment targets and timelines; and to share start-up documents such as CV, GCP, and site profile forms. The Databank has grown to include nearly 180,000 investigators (May 2014) and is already bringing benefits to its member companies in identifying qualified investigators for their studies. It also reported the inclusion of 7,335 protocols and 50K sites, representing a patient population around 1.9M.
Proper citation: Investigator Databank (RRID:SCR_003866) Copy
http://solstice.eplt.washington.edu/
A Web application development framework for Perl. Based on the MVC programming paradigm, it provides a sensible layout for Web applications that helps you write applications faster and with fewer mistakes. Solstice serves as the foundation for a suite of enterprise communication and collaboration tools used at the University of Washington. Many of these tools, such as the WebQ survey and quiz creation application, the UMail anonymous email form, and the CrowdControl module for managing groups of users, are available for download now. More are on the way. They will offer you rich starting points, examples, and solutions for your own applications. Solstice is designed to support large, complex applications that have a serious need for structured navigation. Its state-machine based navigation system ensures that users stay on the paths they need to follow within your Web application. With any mod_perl enabled Apache server, Solstice offers easy installation and proven scalability. Specifically, Solstice provides your application with: * a state-machine based navigation system, * integrated validation, * highly reusable and embeddable page elements, * session management, * user and group models for flexible, built-in authorization, * a development mode for realtime diagnostics, and * a focus on scalability. When you work with Solstice, you can also use Majere, a Web-based development tool that automates the creation of applications and manages their configuration. Majere frees you to focus on the more interesting parts of application development and is available along with Solstice on our Download page. Solstice provides support for RESTful development.
Proper citation: Solstice (RRID:SCR_003463) Copy
A nonprofit devoted to spreading ideas, usually in the form of short, powerful talks (18 minutes or less). TED began as a conference where Technology, Entertainment and Design converged, and today covers almost all topics - from science to business to global issues - in more than 100 languages. Meanwhile, independently run TEDx events help share ideas in communities around the world.
Proper citation: TED (RRID:SCR_003739) Copy
A dropbox like model cloud-based, commercial data management and collaboration system designed specifically for research scientists. It helps manage and annotate data, track provenance and share this with colleagues.
Proper citation: Ovation (RRID:SCR_003737) Copy
An Antibody supplier
Proper citation: Eton Bioscience (RRID:SCR_003533) Copy
A not-for-profit membership organization and educational charity that facilitates collaborative data sharing projects in the pharmaceutical, cosmetics and chemistry-related industries specializing in the development of expert computer systems for toxicity and metabolism prediction. They provide a number of extensive and continually updated knowledge bases and the software needed to interrogate them. Its charitable aims include the sponsorship of activities that advance scientific knowledge and understanding and they regularly support computational chemistry events and initiatives that are of interest to Lhasa Limited members and the wider scientific community. All applications for sponsorship will be considered on their individual merits.
Proper citation: Lhasa Limited (RRID:SCR_003775) Copy
http://www.transformproject.eu/portfolio-item/d6-2-clinical-research-information-model/
A clinical research information model for the integration of clinical research covering randomized clinical trials (RCT), case-control studies and database searches into the TRANSFoRm application development. TRANSFoRm clinical research is based on primary care data, clinical data and genetic data stored in databases and electronic health records and employs the principle of reusing primary care data, adapting data collection by patient reported outcomes (PRO) and eSource based Case Report Forms. CRIM was developed using the TRANSFoRm clinical use cases of GORD and Diabetes. Their use case driven approach consisted of three levels of modelling drawing heavily on the clinical research workflow of the use cases. Different available information models were evaluated for their usefulness to represent TRANSFoRm clinical research, including for example CTOM of caBIG, Primary Care Research Object Model (PRCOM) of ePCRN and BRIDG of CDISC. The PCROM model turned out to be the most suitable and it was possible to extend and modify this model with only 12 new information objects, 3 episode of care related objects and 2 areas to satisfy all requirements of the TRANSFoRm research use cases. Now the information model covers Good Clinical Practice (GCP) compliant research, as well as case control studies and database search studies, including the interaction between patient and GP (family doctor) during patient consultation, appointment, screening, patient recruitment and adverse event reporting.
Proper citation: TRANSFoRm Clinical Research Information Model (RRID:SCR_003889) Copy
Videos and podcasts presenting the latest innovative research being conducted by the Stein Institute for Research on Aging medical faculty, with the aim of promoting healthy aging. Additionally, many of the public lectures from the Public Lecture Series are also available on UCSD-TV's website video on demand programming. The Lecture series allows affiliated faculty members of the Stein Institute for Research on Aging and other scientists from the UCSD School of Medicine, as well as individuals from surrounding academic and research institutions, to present the latest findings in their respective fields of expertise and share their present work with the general community. All of these lectures focus on topics related to healthy aging or age-related diseases.
Proper citation: Stein Institute for Research on Aging Video Archive (RRID:SCR_003761) Copy
Collection of pathways and pathway annotations. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways (signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism) . Provides website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets.
Proper citation: Reactome (RRID:SCR_003485) Copy
Research informatics and analytics platform for the IMI OncoTrack consortium.
Proper citation: eTRIKS (RRID:SCR_003765) Copy
http://mimi.ncibi.org/MimiWeb/main-page.jsp
MiMi Web gives you an easy to use interface to a rich NCIBI data repository for conducting your systems biology analyses. This repository includes the MiMI database, PubMed resources updated nightly, and text mined from biomedical research literature. The MiMI database comprehensively includes protein interaction information that has been integrated and merged from diverse protein interaction databases and other biological sources. With MiMI, you get one point of entry for querying, exploring, and analyzing all these data. MiMI provides access to the knowledge and data merged and integrated from numerous protein interactions databases and augments this information from many other biological sources. MiMI merges data from these sources with deep integration into its single database with one point of entry for querying, exploring, and analyzing all these data. MiMI allows you to query all data, whether corroborative or contradictory, and specify which sources to utilize. MiMI displays results of your queries in easy-to-browse interfaces and provides you with workspaces to explore and analyze the results. Among these workspaces is an interactive network of protein-protein interactions displayed in Cytoscape and accessed through MiMI via a MiMI Cytoscape plug-in. MiMI gives you access to more information than you can get from any one protein interaction source such as: * Vetted data on genes, attributes, interactions, literature citations, compounds, and annotated text extracts through natural language processing (NLP) * Linkouts to integrated NCIBI tools to: analyze overrepresented MeSH terms for genes of interest, read additional NLP-mined text passages, and explore interactive graphics of networks of interactions * Linkouts to PubMed and NCIBI's MiSearch interface to PubMed for better relevance rankings * Querying by keywords, genes, lists or interactions * Provenance tracking * Quick views of missing information across databases. Data Sources include: BIND, BioGRID, CCSB at Harvard, cPath, DIP, GO (Gene Ontology), HPRD, IntAct, InterPro, IPI, KEGG, Max Delbreuck Center, MiBLAST, NCBI Gene, Organelle DB, OrthoMCL DB, PFam, ProtoNet, PubMed, PubMed NLP Mining, Reactome, MINT, and Finley Lab. The data integration service is supplied under the conditions of the original data sources and the specific terms of use for MiMI. Access to this website is provided free of charge. The MiMI data is queryable through a web services api. The MiMI data is available in PSI-MITAB Format. These files represent a subset of the data available in MiMI. Only UniProt and RefSeq identifiers are included for each interactor, pathways and metabolomics data is not included, and provenance is not included for each interaction. If you need access to the full MiMI dataset please send an email to mimi-help (at) umich.edu.
Proper citation: Michigan Molecular Interactions (RRID:SCR_003521) Copy
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