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http://nsdl.org/

NSDL is a digital library of exemplary resource collections and services, organized in support of science education at all levels. Starting with a partnership of NSDL-funded projects, NSDL is emerging as a center of innovation in digital libraries as applied to education, and a community center for groups focused on digital-library-enabled science education. The National Science Digital Library (NSDL) was created by the National Science Foundation to provide organized access to high quality resources and tools that support innovations in teaching and learning at all levels of science, technology, engineering, and mathematics (STEM) education. As a national network of learning environments, resources, and partnerships, NSDL seeks to serve a vital role as STEM educational cyberlearning for the nation, meeting the informational and technological needs of educators and learners at all levels. Educators need efficient and reliable methods to discover and use science and math materials that help them meet the demands of instruction, assessment, and professional development in an increasingly complex technology-based world. NSDL provides an organized point of access to: -High-quality STEM content aggregated from a variety of other digital libraries, NSF-funded projects, and NSDL-reviewed web sites. -Services and tools that enhance the use of this content in a variety of contexts. NSDL is designed primarily for K-16 educators, but anyone can access NSDL.org and search the library at no cost. Access to most resources discovered through NSDL is free; however, some content providers may require a login, or a nominal fee or subscription to retrieve their specific resources. NSDL serves as a nexus for educators, researchers, policy makers and the public by building bridges: -Between private sector and public interests by providing access to resources such as publisher'' journal articles, teacher-created lesson plans and real-time data sets from scientists -Between the scientific, research and educational communities by applying advanced technologies to stimulate new ways for educators and learners to access and use scientific information -Between teachers and learners at all levels, in all locations by supplying content and tools in open-access, non-proprietary formats in an easily accessible online environment. Sponsors: This work supported by the National Science Foundation under Grant No. 0733600, Grant No. 0424671, Grant No. 0227648, Grant No. 0227656, and Grant No. 0227888.

Proper citation: NSDL: The National Science Digital Library (RRID:SCR_008215) Copy   

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http://www.uhnres.utoronto.ca/facilities/wcif/download.php

The ImageJ installations below correspond to the WCIF ImageJ manual. The manual is written for this particular installation of ImageJ. This ImageJ installation has, among other plugins, one that links to an online version of the manual. The online manual is more up-to-date than the PDF version. Windows users Download WCIF ImageJ bundle (~23Mb) v1.34i, 3rd March 2005 with J2SE 5.0 (formerly J2SE 1.5). For Windows: download and run program. Mac and Linux users Download your OS specific version of ImageJ from the ImageJ website then extract the following file to the plugins folder. Download WCIF ImageJ bundle plugins only (~2Mb) This contains only the plugins, IJ preferences, LUTs and plugin source code. Image Processing and Analysis Software ImageJ LSM Browser (*.lsm) Axiovision viewer (*.zvi) Manufacturers of our microscopes and related equipment Zeiss - Microscopes and imaging systems. P.A.L.M. Microlaser Technologies - Manufacturer of our laser capture system. Sutter Instruments - Micromanipulators. Uniblitz - Shutters. Ludl - Manufacturers of our motorised x-, y-stage Hamamatsu - Digital cameras. Molecular Probes - Dyes and reagents. Scanalytics - Image acquisition and processing software. MicroBrightField - Developers of the Neurolucida and Stereo Investigator software. DVC - Digital cameras. Bitplane - Developers of the Imaris suite of software. AutoQuant - Developers of the AutoDeblur deconvolution software

Proper citation: Wright Cell Imaging Facility (RRID:SCR_008488) Copy   

•   Source: SciCrunch Registry
  

http://qiime.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023.Software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data, but also supporting analysis of other types of data. QIMME analyzes and transforms raw sequencing data generated on Illumina or other platforms to publication quality graphics and statistics.

Proper citation: QIIME (RRID:SCR_008249) Copy   

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http://www.epidata.dk

Sustainability plan EpiData Software has since 2000 grown from securing the principles of Epi Info V6 to an independent and documentation based system with several translations and numerous downloads. To secure continued viability organisations and governments work is being done to secure for the future, see also the license principles - the ambition is to convert the programs to open-source within few years. Contributions are used for costs of development after version 1.5 (e.g. refining of programming, enhancing speed, maintenance of website, to pay for absence from paid work to do EpiData or other developmental and promotional efforts for EpiData). About the EpiData Association EpiData Software is from EpiData Entry version 2.0 and above released by the non-profit organisation The EpiData Association Odense, Denmark (In Danish: EpiData foreningen). The association receives NO baseline budget from anyone. The association has no employees Postal adress is: The EpiData Association, att. Jens Lauritsen, Enghavevej 34, DK5230 Odense M, Denmark, Europe The body of users of EpiData form the most important part of the basis of the EpiData Association. Those who choose to register as users will be asked when desicions are to made regarding additions to the program. Needs for documentation etc. Registration is done by adding your e-mail to the Information list. Supporting members or institutions adds to the foundation and development of EpiData by securing funding to pay for the associated costs. List of donors. The board of the association is made up of the core persons developing EpiData, currently Jens M.Lauritsen and Michael Bruus in collaboration with experienced users and the Friends Of EpiData group (FoED), comprising a group of international persons wishing to support the development of EpiData Sponsor. Without support from a number of NGO''s, Universities, Regional Health Authorities and other funding bodies EpiData development would have stopped

Proper citation: EpiData Software (RRID:SCR_008485) Copy   

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http://www.jax.org/imr/index.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 08, 2012. The function of the IMR is to select, import, cryopreserve, maintain, and distribute these important strains of mice to the research community. To improve their value for research, the IMR also undertakes genetic development of stocks, such as transferring mutant genes or transgenes to defined genetic backgrounds and combining transgenes and/or targeted mutations to create new mouse models for research. The function of the IMR is to: * select biomedically important stocks of transgenic, chemically induced, and targeted mutant mice * import these stocks into the Jackson Laboratory by rederivation procedures that rid them of any pathogens they might carry * cryopreserve embryos from these stocks to protect them against accidental loss and genetic contamination * backcross the mutation onto an inbred strain, if necessary * distribute them to the scientific community More than 1000 mutant stocks have been accepted by the IMR from 1992 through December 2006. Current holdings include models for research on cancer; breast cancer; immunological and inflammatory diseases; neurological diseases; behavioral, cardiovascular and heart diseases; developmental, metabolic and other diseases; reporter (e.g., GFP) and recombinase (e.g., cre/loxP) strains. About eight strains a month are being added to the IMR holdings. Research is being conducted on improved methods for assisted reproduction and speed congenic production. Most of the targeted mutants arrive on a mixed 129xC57BL/6 genetic background, and as many of these as possible are backcrossed onto an inbred strain (usually C57BL/6J). In addition, new mouse models are being created by intercrossing carriers of specific transgenes and/or targeted mutations. Simple sequence length polymorphism DNA markers are being used to characterize and evaluate differences between inbred strains, substrains, and embryonic stem cell lines.

Proper citation: Induced Mutant Resource (RRID:SCR_008366) Copy   

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http://www.osc.riken.jp/english/

Omics Science Center is aiming to develop a comprehensive system called Life Science Accelerator(LSA) for the advancement of omics research. The LSA is a comprehensive system consists of biological resources, human resources, technologies, know-how, and essential administrative ability. Ultimate goal of LSA is to support and accelerate the advancement in life science research. Omics is the comprehensive study of molecules in living organisms. The complete sequencing of genomes (the complete set of genes in an organism) has enabled rapid developments in the collection and analysis of various types of comprehensive molecular data such as transcriptomes (the complete set of gene expression data) and proteomes (the complete set of intracellular proteins). Fundamental omics research aims to link these omics data to molecular networks and pathways in order to advance the understanding of biological phenomena as systems at the molecular level.

Proper citation: RIKEN Omics Science Center (RRID:SCR_008241) Copy   

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http://www.theseed.org/DinsdaleSupplementalMaterial/

his table shows the metadata and links to sources of the data and citations associated with the publicly available metagenome sequences used in the Dinsdale, Edwards, et al., analysis of 87 different metagenomes. The links will take you to the annotated sequences in the metagenomics SEED, CAMERA, and the NCBI Short Read Archve. Please note that all metagenomes are currently available to download via the ftp links, some are available in the meta-RAST, and other links will be added as soon as they become available. Citations for individual metagenomes will also be added as and when they become available. DNA sequences for all metagenomes are avaialble via anonymous FTP. Sponsor. This project was supported by the Gordon and Betty Moore Foundation Marine Microbial Initiative, National Science Foundation grants (F.R. and D.L.V.), a Department of Commerce ATP grant (F.R.), a National Research Initiative Competitive Grant from the USDA Cooperative State Research, Education and Extension Service (B.W.), the National Institute of Allergy and Infectious Diseases, the National Institutes of Health and the Department of Health and Human Services (R.S.).

Proper citation: Metagenomes Used in The Statistical Analysis (RRID:SCR_008483) Copy   

•   Source: SciCrunch Registry
  

http://www.repairgenes.org/index.shtml

The aim of the repairGenes site is to be a source of information about DNA repair genes and a useful resource for research on DNA repair. At the moment, the site contains information about a number of DNA repair genes from a set of selected species. The information is organized by organism and by biological process term as defined by the Gene Ontology (GO) project. The coverage of DNA repair genes is not complete, but hopefully it satisfies to demonstrate the concept and generate ideas for future versions of the system. At present, the raw data about DNA repair genes is extracted from the SWISS-PROT database, and categorized using the GO system. SWISS-PROT entries are being annotated by the Gene Ontology Annotation project at EBI. GOA is an ongoing project which will become more complete with time. As more data is released, this will be fed into repairGenes to keep it up-to-date. In future versions, the user will be able to search freely among organisms and categories of repair genes, enabling easy comparisons between species. For a taste of this, please have a look at the overview of repair genes from five major organisms. The amount of information in the system will be increased and the quality will be improved in the future. So will the features of the system.

Proper citation: repairGenes (RRID:SCR_008240) Copy   

•   Source: SciCrunch Registry
  

http://www.dialog.com

Dialog provides critical information from the world''s most authoritative publishers, combined with the tools to search every bit of it with speed and precision. With direct operations in 27 countries, Dialog products and services are a combination of highly accurate online research tools offering access to unique and relevant databases designed to meet the specific needs of a wide range of users. Information professionals and end-users at business, professional, scientific, academic and government organizations in more than 100 countries prize Dialog services to meet their searching needs. As part of the Deep Web, which is estimated to be 500 times larger than the content accessible via Web search engines, Dialog products offer unparalleled depth and breadth of content coupled with the ability to search with precision and speed. Our collection of over 900 databases handles more than 700,000 searches and delivers over 17 million document page views per month. Searchable content on Dialog services includes articles and reports from thousands of real-time news feeds, newspapers, broadcast transcripts and trade publications, plus market research reports and analyst notes providing support for financial decision-making, as well as in-depth repositories of scientific and technical data, patents, trademarks and other intellectual property data. Additional content areas include government regulations, social sciences, food and agriculture, reference, energy and environment, chemicals, pharmaceuticals and medicine.

Proper citation: Dialog (RRID:SCR_008482) Copy   

•   Source: SciCrunch Registry
  

http://www.reciprocalnet.org/

Database of crystallographic information. Its membership includes crystallographic service facilities (that analyze crystals submitted by research chemists) located at major universities. These labs analyze anywhere from a few dozen to several hundred molecular structures each year and post the data online for the public to access. A distributed database engine takes care of shuttling this data across the Internet so that every structure can be located by the search engine. There may be a delay of a year or more between the time a structure is first analyzed and the time it finally becomes available for the public to see. This is due to intellectual property issues - the intervening time allows the chemists who first discovered the structure to publish it in a trade journal.

Proper citation: Reciprocal Net (RRID:SCR_008238) Copy   

•   Source: SciCrunch Registry
  

http://www.daylight.com/dayhtml/doc/theory/

Daylight provides enterprise-level cheminformatics software technologies to life science companies. Our superior chemistry, high performance, and open architecture have earned Daylight a reputation for delivering the state-of-the-art in chemical information processing since 1987. Daylight Chemical Information Systems, Inc. is a privately held company with corporate offices in Aliso Viejo, CA and research offices in Santa Fe, NM and Cambridge, England. Support At Daylight, support means a wide array of services that are designed to empower users to make the most of Daylight software. We offer detailed administration documentation and guides through this website. Our User Group Meetings allow in-depth exploration of our technology. And, of course, our support staff is available to assist you whenever the need occurs. Download - Downloading current releases as well as contributed code, system requirements, installation directions, and release information Reference Guides - List of available documentation such as programming guides and user manuals. Cheminformatics - List of additional general resources including introductory materials, theory manual, tutorials and user meeting archives. Sponsor. Daylight

Proper citation: Daylight (RRID:SCR_008474) Copy   

•   Source: SciCrunch Registry
  

http://www.sp2000.org/

Species 2000 is a federation of database organizations working closely with users, taxonomists and sponsoring agencies. The goal of the Species 2000 project is to create a validated checklist of all the world''s species (plants, animals, fungi and microbes). This is being achieved by bringing together an array of global species databases covering each of the major groups of organisms. Each database covers all known species in the group, using a consistent taxonomic system. The participating databases are widely distributed throughout the world and currently number 52. The existing global species databases presently account for some 60% of the total known species, so substantial investment in new databases will be needed for full coverage of all taxa to be achieved.

Proper citation: Species 2000 (RRID:SCR_008231) Copy   

•   Source: SciCrunch Registry
  

http://helixweb.nih.gov/dnaworks

DNAWorks automates the design of oligonucleotides for gene synthesis by PCR-based methods. The availability of sequences of entire genomes has dramatically increased the number of protein targets, many of which will need to be overexpressed in cells other than the original source of DNA. Gene synthesis often provides a fast and economically efficient approach. The synthetic gene can be optimized for expression and constructed for easy mutational manipulation without regard to the parent genome. DNAWorks accesses a computer program that automates the design of oligonucleotides for gene synthesis. The website provides forms for simple input information, i.e. amino acid sequence of the target protein and melting temperature (needed for the gene assembly) of synthetic oligonucleotides. The program outputs a series of oligonucleotide sequences with codons optimized for expression in an organism of choice. Those oligonucleotides are characterized by highly homogeneous melting temperatures and a minimized tendency for hairpin formation. The approach presented here simplifies the production of proteins from a wide variety of organisms for genomics-based studies.

Proper citation: DNAWorks at Helix Systems (RRID:SCR_008470) Copy   

•   Source: SciCrunch Registry
  

https://simtk.org/home/simtkcore

SimTK Core is one of the two packages that together constitute SimTK, the biosimulation toolkit from the Simbios Center. The other major component of SimTK is OpenMM which is packaged separately. This SimTK Core project collects together all the binaries needed for the various SimTK Core subprojects. These include Simbody, Molmodel, Simmath (including Ipopt), Simmatrix, CPodes, SimTKcommon, and Lapack. See the individual projects for descriptions. SimTK brings together in a robust, convenient, open source form the collection of highly-specialized technologies necessary to building successful physics-based simulations of biological structures. These include: strict adherence to an important set of abstractions and guiding principles, robust, high-performance numerical methods, support for developing and sharing physics-based models, and careful software engineering. Accessible High Performance Computing We believe that a primary concern of simulation scientists is performance, that is, speed of computation. We seek to build valid, approximate models using classical physics in order to achieve reasonable run times for our computational studies, so that we can hope to learn something interesting before retirement. In the choice of SimTK technologies, we are focused on achieving the best possible performance on hardware that most researchers actually have. In today''s practice, that means commodity multiprocessors and small clusters. The difference in performance between the best methods and the do-it-yourself techniques most people use can be astoundingeasily an order of magnitude or more. The growing set of SimTK Core libraries seeks to provide the best implementation of the best-known methods for widely used computations such as: Linear algebra, numerical integration and Monte Carlo sampling, multibody (internal coordinate) dynamics, molecular force field evaluation, nonlinear root finding and optimization. All SimTK Core software is in the form of C++ APIs, is thread-safe, and quietly exploits multiple CPUs when they are present. The resulting pre-built binaries are available for download and immediate use. Audience: Biosimulation application programmers interested in including robust, high-performance physics-based simulation in their domain-specific applications.

Proper citation: SimTKCore (RRID:SCR_008268) Copy   

•   Source: SciCrunch Registry
  

http://www.cabiatl.com/mricro/

MRIcro allows Windows and Linux computers view medical images. It is a standalone program, but includes tools to complement SPM (software that allows neuroimagers to analyze MRI, fMRI and PET images). MRIcro allows efficient viewing and exporting of brain images. In addition, it allows neuropsychologists to identify regions of interest (ROIs, e.g. lesions). MRIcro can create Analyze format headers for exporting brain images to other platforms. Some features of MRIcro are: - Converts medical images to SPM friendly Analyze format. - View Analyze format images (big or little endian). - Create Analyze format headers (big or little endian). - Create 3D regions of interest (with computed volume & intensity). - Overlap multiple regions of interest. - Rotate images to match SPM template images. - Export images to BMP, JPEG, PNG or TIF format. - Yoked images: linked viewing of multiple images (e.g. view same coordinates of PET and MRI scans). Users familiar with other Windows programs will find that this software is fairly straightforward to use. Resting the mouse cursor over a button will cause a text hint to appear over the button. However, a tutorial with a step by step guide of how to use MRIcro with SPM is available.

Proper citation: MRIcro Software (RRID:SCR_008264) Copy   

•   Source: SciCrunch Registry
  

http://www.amber.org.au/

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 6, 2016. AMBeR's aim is to bring together Australia's unique resources for genetic epidemiology and genomics with high level expertise in bioinformatics and statistical science, conduct advanced methodological research, develop new research capacity and competitiveness in cutting-edge techniques, bring them to bear on important medical research problems, train young Australians in bioinformatics and advanced biostatistics, and transfer this expertise to the medical research community.

Proper citation: Australian Medical Bioinformatics Resource (RRID:SCR_008385) Copy   

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https://simtk.org/home/isim_interface

A simple Java graphical user interface for running the program ISIM. ISIM is a package that simulates the thermodynamic ensemble of ions around a macromolecule using a grand canonical Monte Carlo scheme and simple hard sphere ion models. It is meant to provide an alternative mechanism to mean field approaches to allow the calculation of ion distributions around a highly charged molecule using a simple model that takes into account ion-ion correlations and steric interactions. The original source was created in the McCammon group at UCSD but is no longer available. The version of ISIM used is available in the ISIM project on simtk.org.

Proper citation: Ion Simulator Interface (RRID:SCR_008267) Copy   

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http://www.nia.nih.gov/research/dab/interventions-testing-program-itp

NIA''s ITP is a multi-institutional study investigating treatments with the potential to exte nd lifespan and delay disease and dysfunction in mice. Priority consideration will be given to the treatments that are easily obtainable, reasonably priced, and can be delivered in the diet (preferred) or water. Interventions that require labor intensive forms of administration, such as daily injections or gavage, are not feasible within the design of the ITP. Treatments currently under study include: - Pharmaceuticals - Nutraceuticals - Foods - Diets - Dietary supplements - Plant extracts - Hormones - Peptides - Amino acids - Chelators - Redox agents - Other agents or mixtures of agents Although the mice involved in this study will be housed at the University of Michigan, the Jackson Laboratories, and the University of Texas Health Sciences Center at San Antonio, the project is designed to involve collaborations with investigators at any university, institute, or other organization that has ideas about pharmacological interventions that might decelerate aging and wishes to test these in a lifespan study of mice. Sponsors: This program is supported by the National Institute of Aging.

Proper citation: Interventions Testing Program (RRID:SCR_008266) Copy   

•   Source: SciCrunch Registry
  

https://scicrunch.org/scicrunch/data/source/nlx_154697-16/search?q=%2A&l=&facet[]=Database:ResearchCrossroads

THIS RESOURCE IS NO LONGER IN SERVICE, documented on Feb. 05, 2014, however, NIF holds the Research Crossroads data and makes it available through Integrated Grants. World of publicly funded research aggregated into a database providing funding, publication, clinical trial and grant data from government and private research agencies. Advanced reporting and analysis tools are then used to connect research to researchers, organizations and topic areas to uncover non-obvious associations. Use ResearchCrossroads for: Researchers * Make your research visible to funding organizations and collaborators. * Connect with peers to stay up to date on their research progress * Update your investigator profile, biography and publications so funding organizations can find you * Discover available funding from private foundations and government funding organizations * Annotate your previous research grants with outcomes * Create a research diary and participate in discussions with your peers Foundations Participating in ResearchCrossroads is free if you share your research data. Send us a spreadsheet with your grant and investigator information. * Create a community for your researchers to learn from each other * Locate potential investigators and collaborators * Post available funding and be matched with investigator profiles * Access to analytical reporting of funding and research statistics * Update your personalized organization profile page * Display your logo in search results * Link to your ResearchCrossroads grants and investigator profiles from your own website Corporations, Academia & Governments Contact us about subscriptions to funding trend analytics and marketing opportunities. * In-depth reporting of 15 years of funding data from government and private institutions * Subscriptions available to advanced analysis & reporting tools * Display your corporate logo in search results * Update your organization profile page * Highly targeted marketing & advertising by research areas, keywords and categories of investigator * Register for notifications of the newest grants in your area of interest

Proper citation: ResearchCrossroads (RRID:SCR_008261) Copy   

•   Source: SciCrunch Registry
  

http://www.cdc.gov/nccdphp/ace/

A clinical study linking childhood maltreatment and later-life health and well-being. As a collaboration between the Centers for Disease Control and Prevention and Kaiser Permanente''s Health Appraisal Clinic in San Diego, Health Maintenance Organization (HMO) members undergoing a comprehensive physical examination provided detailed information about their childhood experience of abuse, neglect, and family dysfunction. Over 17,000 members chose to participate. To date, over 50 scientific articles have been published and over 100 conference and workshop presentations have been made. Future Directions: The ACE study is now in its 10th year and the prospective phase is currently underway. In this ongoing stage of the study, data are being gathered from various sources including outpatient medical records, pharmacy utilization records, and hospital discharge records to track the subsequent health outcomes and health care use of ACE Study participants. In addition, an examination of National Death Index records will be conducted to establish the relationship between ACE and mortality among the ACE Study population. The ACE Study findings suggest that these experiences are major risk factors for the leading causes of illness and death as well as poor quality of life in the United States. Progress in preventing and recovering from the nation''s worst health and social problems is likely to benefit from the understanding that many of these problems arise as a consequence of adverse childhood experiences. :Sponsors: This resource is supported by the Centers for Disease Control and Prevention and the Kaiser Permanente''s Health Appraisal Clinic in San Diego.

Proper citation: Adverse Childhood Experiences Study (RRID:SCR_008382) Copy   

•   Source: SciCrunch Registry