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http://www.cis.rit.edu/htbooks/mri/

An interesting and exhaustive explanation of how the technology works and is applied. It is an online book on principles and practice of magnetic resonance imaging. This educational package requires a hyper text markup language (HTML) 3.0 compatible browser, such as Mozilla Firefox, Microsoft Internet Explorer, or Apple Safari. This type of browser allows the user to view frames. Three frames will be used in this package to simultaneously display text, graphics, and navigation aids. You are reading this in the text window. The graphics window is in the upper left hand corner of your screen. This window will be used to display animations, static figures, references, symbol definitions, and the glossary. The navigation window appears in the lower left corner of the screen and has one line of options. To experience the full potential of the frames, a screen capable of displaying at least 1024 by 768 pixels with 256 colors is recommended. You may be able to gain a few extra pixels in the vertical direction on your monitor by turning off the show toolbar, show location, and show directory buttons under options at the top of your browser. A computer mouse is necessary to access the contents of this package. The mouse allows you to move up and down in a frame by either moving the slider, or holding the mouse button down on the up or down arrows located at the right of the frame.

Proper citation: The Basics of MRI (RRID:SCR_002287) Copy   

•   Source: SciCrunch Registry

http://fiji.sc

Software package as distribution of ImageJ and ImageJ2 together with Java, Java3D and plugins organized into coherent menu structure. Used to assist research in life sciences.

Proper citation: Fiji (RRID:SCR_002285) Copy   

•   Source: SciCrunch Registry

http://amedeo.com/

A service created to allow healthcare professionals to access timely, relevant information within their respective fields. Users can subscribe to receive weekly emails with bibliographic lists about new scientific publications, personal web pages for one-time download of available abstracts, and an overview of the medical literature published in relevant journals over the past 12 to 24 months.

Proper citation: AMEDEO: The Medical Literature Guide (RRID:SCR_002284) Copy   

•   Source: SciCrunch Registry

http://www.iris.edu/hq/

Passive and active source waveform data, event (earthquake) catalog, channel response data is available. This comprehensive data store of raw geophysical time-series data is collected from a large variety of sensors, courtesy of a vast array of US and International scientific networks, including seismometers (permanent and temporary), tilt and strain meters, infrasound, temperature, atmospheric pressure and gravimeters, to support basic research aimed at imaging the Earth's interior. IRIS also provides data and software for educational purposes. This consortium of over 100 US universities is dedicated to the operation of science facilities for the acquisition, management, and distribution of seismological data. IRIS programs contribute to scholarly research, education, earthquake hazard mitigation, and verification of the Comprehensive Nuclear-Test-Ban Treaty. Data is stored at the IRIS Data Management Center in Seattle, Washington. They currently manage a large archive from over tens of thousands of seismic stations and ship hundreds of terabytes of data yearly.

Proper citation: Incorporated Research Institutions for Seismology (RRID:SCR_002201) Copy   

•   Source: SciCrunch Registry

http://mips.gsf.de/genre/proj/yeast/index.jsp

The MIPS Comprehensive Yeast Genome Database (CYGD) aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition, the data of various projects on related yeasts are used for comparative analysis.

Proper citation: CYGD - Comprehensive Yeast Genome Database (RRID:SCR_002289) Copy   

•   Source: SciCrunch Registry

http://microbes.ucsc.edu/cgi-bin/hgGateway?db=neisMeni_MC58_1

Portal contains detailed information for Neisseria meningitidis MC58. Information include DNA molecule summary, primary annotation summary, and taxonomy. It is a tool that allows the researcher to access all of the bacterial genome sequences completed to date. Users may access information on all of the bacterial genomes or any subset of them. Information in the website about its DNA molecule includes: total number of DNA molecules, total size of all DNA molecules, number of primary annotation coding bases, and number of G + C bases. Its primary annotation summary include: total genes, protein coding genes, tRNA genes, and rRNA genes. Sponsors: The CMR was previously funded by two grants, one from the U.S. Department of Energy (DOE) and one from the National Science Foundation (NSF). It is currently partially funded by a Microbial Sequence Center (MSC) grant from the National Institute of Allergy and Infectious Diseases (NIAID)

Proper citation: Neisseria meningitidis MC58 Genome Page (RRID:SCR_002200) Copy   

•   Source: SciCrunch Registry

http://www.cmelist.com/

Links to, and descriptions of, every web site that offers AMA-approved Continuing Medical Education (CME) online. At this time, there are over 325 sites listed. These sites offer over 16,000 separate activities and over 26,000 hours of credit. Using this list, you can find online CME web sites arranged by their: # dominant medical specialty or medical topic; or # alphabetically by the first letter of the site name; or # you can scroll this list until you find a course or site of interest. Find sites by medical specialty or topic: Allergy, Anesthesia, Bioterrorism, Cardiology, Critical Care, Dermatology, Diabetes/Endocrinology, Ear, Nose and Throat, Emergency Medicine, Family Practice, Gastroenterology, Genetics, Geriatrics, Hematology / Oncology, HIV / Infectious Disease, Imaging / Radiology, Internal Medicine, Neurology, Neurosurgery, Obstetrics / Gynecology, Oncology/Hematology, Ophthalmology, Orthopedic Surgery, Pain Management, Pathology / Lab Medicine, Pediatrics, Psychiatry, Pulmonary, Quality/Management, Radiology / Imaging, Rheumatology, Surgery, Urology, Wellness / Prevention.

Proper citation: CMEList.com (RRID:SCR_002288) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/miva/

Software package that is a powerful graphical interface that displays, segments, aligns, manipulates, and blends image (pixel) and geometry (real-world coordinates) data simultaneously. Several applications are directly built into MIVA. Registration modes include interactive affine transformations. Fiducial registration tools facilitate rapid alignments for inter-modality volumes. Interactive Region of Interst (ROI) and Volume-of-Interest (VOI) tools exist to segment medical images. Virtually unique to MIVA are its 3D geometry tools and their compatibility with pixel based medical images. A full 3D interactive rat brain atlas is in an fMRI module which walks one through the necessary steps of fMRI. A multiple material surface routine takes segmented medical slices and creates 3D triangulated surfaces that align along all region boarders without overlap or gaps. These surfaces are the direct input into the MIVA tetrahedral mesh generator.

Proper citation: Medical Image Visualization and Analysis (RRID:SCR_002315) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/mriwatcher/

This simple visualization tool allows to load several images at the same time. The cursor across all windows are coupled and you can move/zoom on all the images at the same time. Very useful for quality control, image comparison.

Proper citation: MriWatcher (RRID:SCR_002318) Copy   

•   Source: SciCrunch Registry

http://mpss.danforthcenter.org/

Informational portal that aggregates information about databases for next gen sequencing.

Proper citation: NextGen Sequence Databases (RRID:SCR_002152) Copy   

•   Source: SciCrunch Registry

http://insulatordb.uthsc.edu/

A comprehensive collection of experimentally determined and computationally predicted CCCTC-binding factor (CTCF) binding sites (CTCFBS) from the literature. The database is designed to facilitate the studies on insulators and their roles in demarcating functional genomic domains. The CTCFBS Prediction Tool allows users to scan sequences for the single best match to CTCF position weight matrices. Currently (March 2014), the database contains almost 15 million experimentally determined CTCF binding sites across several species. CTCF binding sites were collected from published papers containing CTCF binding sites identified using ChIPSeq or similar methods, data from the ENCODE project, and a set of approximately 100 manually curated binding sites identified by low-throughput experiments. Users can browse insulator sequence features, function annotations, genomic contexts including histone methylation profiles, flanking gene expression patterns and orthologous regions in other mammalian genomes. Users can also retrieve data by text search, sequence search and genomic range search.

Proper citation: CTCFBSDB (RRID:SCR_002279) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/mgdm/

An efficient level set framework for multi-object segmentation. Its representation inherently prevents overlaps and gaps and it readily preserves object topology and object relationships. MGDM is efficient, storing only a fixed number of functions for any number of objects, and therefore scales well to segmentation problems with many classes and large images. It's representation also avoids some instabilities in other multi-class level set methods. MGDM is cross-platform; MATLAB wrappers, Java source and API are provided, with MIPAV plugins forthcoming.

Proper citation: MGDM: Multi Geometric Deformable Model (RRID:SCR_002311) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/HTGS/

Database of high-throughput genome sequences from large-scale genome sequencing centers, including unfinished and finished sequences. It was created to accommodate a growing need to make unfinished genomic sequence data rapidly available to the scientific community in a coordinated effort among the International Nucleotide Sequence databases, DDBJ, EMBL, and GenBank. Sequences are prepared for submission by using NCBI's software tools Sequin or tbl2asn. Each center has an FTP directory into which new or updated sequence files are placed. Sequence data in this division are available for BLAST homology searches against either the htgs database or the month database, which includes all new submissions for the prior month. Unfinished HTG sequences containing contigs greater than 2 kb are assigned an accession number and deposited in the HTG division. A typical HTG record might consist of all the first-pass sequence data generated from a single cosmid, BAC, YAC, or P1 clone, which together make up more than 2 kb and contain one or more gaps. A single accession number is assigned to this collection of sequences, and each record includes a clear indication of the status (phase 1 or 2) plus a prominent warning that the sequence data are unfinished and may contain errors. The accession number does not change as sequence records are updated; only the most recent version of a HTG record remains in GenBank.

Proper citation: High Throughput Genomic Sequences Division (RRID:SCR_002150) Copy   

•   Source: SciCrunch Registry

http://cibex.nig.ac.jp/data/

Gene expression database system in compliance with MIAME, which is a standard that the MGED Society has developed for comparing and data produced in microarray experiments at different laboratories worldwide. It serves as a public repository for a wide range of high-throughput experimental data in gene expression research, including microarray-based experiments measuring mRNA, serial analysis of gene expression (SAGE tags), and mass spectrometry proteomic data.

Proper citation: CIBEX: Center for Information Biology gene EXpression database (RRID:SCR_002307) Copy   

•   Source: SciCrunch Registry

https://www.usap-dc.org/

Assists scientists in finding Antarctic scientific data of interest and submitting data for long-term preservation in accordance with their obligations under the National Science Foundation (NSF) Office of Polar Programs (OPP) Data Policy.

Proper citation: U.S. Antarctic Program Data Coordination Center (RRID:SCR_002221) Copy   

•   Source: SciCrunch Registry

https://github.com/BRAINSia/BRAINSTools/tree/master/BRAINSFit

A program for registering images with with mutual information based metric. Several registration options are given for 3,6, 9,12,16 parameter (i.e. translate, rigid, scale, scale/skew, full affine) based constraints for the registration. The program uses the Slicer3 execution model framework to define the command line arguments and can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3

Proper citation: BRAINSFit (RRID:SCR_002340) Copy   

•   Source: SciCrunch Registry

http://www.pathwaycommons.org/pc

Database of publicly available pathways from multiple organisms and multiple sources represented in a common language. Pathways include biochemical reactions, complex assembly, transport and catalysis events, and physical interactions involving proteins, DNA, RNA, small molecules and complexes. Pathways were downloaded directly from source databases. Each source pathway database has been created differently, some by manual extraction of pathway information from the literature and some by computational prediction. Pathway Commons provides a filtering mechanism to allow the user to view only chosen subsets of information, such as only the manually curated subset. The quality of Pathway Commons pathways is dependent on the quality of the pathways from source databases. Pathway Commons aims to collect and integrate all public pathway data available in standard formats. It currently contains data from nine databases with over 1,668 pathways, 442,182 interactions,414 organisms and will be continually expanded and updated. (April 2013)

Proper citation: Pathway Commons (RRID:SCR_002103) Copy   

•   Source: SciCrunch Registry

https://arvados.org/

Bioinformatics platform for storing, organizing, processing, and sharing genomic and other biomedical big data. Designed to make it easier for bioinformaticians to develop analyses, developers to create genomic web applications and IT administers to manage large-scale compute and storage genomic resources. Designed to run on top of cloud operating systems such as Amazon Web Services and OpenStack. Currently, there are implementations that work on AWS and Xen+Debian/Ubuntu. Functionally, Arvados has two major sets of capabilities: (a) data management and (b) compute management.

Proper citation: Arvados (RRID:SCR_002223) Copy   

•   Source: SciCrunch Registry

http://www.nodc.noaa.gov/

Accepts and provides access to biology data, buoy data, chlorophyll, nutrients, ocean currents, oxygen, plankton, profile data, salinity, satellite data, sea level, snow and ice, temperature, waves. Please note that routine underway oceanographic shipboard data collected with standard equipment aboard the UNOLS fleet (e.g. CTD, ADCP, XBT, MET, TSG) are routinely transmitted to NODC via Rolling Deck to Repository (R2R). NODC Provides: * The World's largest collection of freely available oceanographic data * Water temperatures dating back to the late 1700's and measuring thousands of meters deep * A State of the Ocean Climate from NODC's Ocean Climate Lab and Satellite Team's scientific analyses * Scientific journals, rare books, historical photo collections and maps through the NOAA Central Library, a division of NODC * Data management expertise including metadata training through NODC's National Coastal Data Development Center

Proper citation: National Oceanographic Data Center (RRID:SCR_002189) Copy   

•   Source: SciCrunch Registry

http://ftp://ftp.ncbi.nlm.nih.gov/pub/mhc/rbc/Final Archive

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 23, 2019.BGMUT was database that provided publicly accessible platform for DNA sequences and curated set of blood mutation information. Data Archive are available at ftp://ftp.ncbi.nlm.nih.gov/pub/mhc/rbc/Final Archive.

Proper citation: Blood Group Antigen Gene Mutation Database (RRID:SCR_002297) Copy   

•   Source: SciCrunch Registry