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https://ndriresource.org/for-researchers/services-capabilities-sample/htorr

NDRI’s Human Tissue and Organs for Research Resource (HTORR) Program has been funded by the National Institutes of Health (NIH) for over 30 consecutive years to support research programs across multiple disciplines. It is through the HTORR program that NDRI provides academic biomedical investigators with donated normal and diseased human tissues and organs recovered from a diverse donor pool using customized procurement, processing, and preservation and distribution protocols. Our HTORR Program supports academic biomedical research investigators needs by providing: Access to a wide array of human biospecimens from any body system * Customized procurement in a variety of preservation formats including fresh, frozen, and fixed suitable for various analytical techniques * Reduced costs for tissue procurement * Technical support to design your studies utilizing human biospecimens * Letters of support and budgetary information for grant applications

Proper citation: Human Tissue and Organ for Research Resource (HTORR) (RRID:SCR_002859) Copy   

•   Source: SciCrunch Registry
  

http://www.epmba.org/

The Electronic Prenatal Mouse Brain Atlas, EPMBA, at present consists of two sets of annotated images of coronal sections from Gestational Day (GD) 12 heads and GD 16 brains of C57BL/6J mice. Ten micron thick sections were stained with hematoxylin and eosin. Images were prepared at various resolutions for annotations and for high resolution presentation. A subset of sections were annotated and linked to anatomical terms. Additionally, horizontal sections of a GD 12 head were aligned and re-assembled into a 3D volume for digital sectioning in arbitrarily oblique planes. These images were captured using a Nikon E800 stereomicroscope with a 10X objective. The resolution is 1.35 pixels/micrometer. The PC program used to grab the images, Microbrightfield's Neurolucida (version 6), stitched together a mosaic of between 10 and 50 high-res images for each tissue slice, while the user focused the scope for each mosaic tile. Since the nature of optic lenses is to focus on one central point, it was difficult to obtain a uniformly-focused field of vision; as such, small areas of these images are blurred. Images were then transferred to a Macintosh and processed in Adobe Photoshop (version 7). Color levels were adjusted for maximum clarity of the tissue, and areas surrounding the tissue were cleared of artifacts. Each image is approximately 3350 pixels wide by 2650 pixels high. A scale bar with a length of 1350 pixels/mm is visible in the lower right-hand corner of each image. The annotations have been completed for the Atlas of Developing Mouse Brain Gestational (Embryonic) Day 12 (7/5/07) as well as the Atlas of Developing Mouse Brain Embryonic Day 16 (4/26/07). The 3D EPMBA data set has been mounted on a NeuroTerrain Atlas Server (NtAS). (6/27/07).

Proper citation: EPMBA.ORG: Electronic Prenatal Mouse Brain Atlas (RRID:SCR_001882) Copy   

•   Source: SciCrunch Registry
  

http://www.bindingmoad.org/

Database of protein-ligand crystal structures that is a subset of the Protein Data Bank (PDB), containing every high-quality example of ligand-protein binding. The resolved protein crystal structures with clearly identified biologically relevant ligands are annotated with experimentally determined binding data extracted from literature. A viewer is provided to examine the protein-ligand structures. Ligands have additional chemical data, allowing for cheminformatics mining. The binding-affinity data ranges 13 orders of magnitude. The issue of redundancy in the data has also been addressed. To create a nonredundant dataset, one protein from each of the 1780 protein families was chosen as a representative. Representatives were chosen by tightest binding, best resolution, etc. For the 1780 best complexes that comprise the nonredundant version of Binding MOAD, 475 (27%) have binding data. This collection of protein-ligand complexes will be useful in elucidating the biophysical patterns of molecular recognition and enzymatic regulation. The complexes with binding-affinity data will help in the development of improved scoring functions and structure-based drug discovery techniques.

Proper citation: Binding MOAD (RRID:SCR_002294) Copy   

•   Source: SciCrunch Registry
  

http://bioinf.gen.tcd.ie/casbah/

Database which contains information pertaining to all currently known caspase substrates.

Proper citation: CASBAH (RRID:SCR_002728) Copy   

•   Source: SciCrunch Registry
  

http://www.gensat.org/retina.jsp

Collection of images from cell type-specific protein expression in retina using BAC transgenic mice. Images from cell type-specific protein expression in retina using BAC transgenic mice from GENSAT project.

Proper citation: Retina Project (RRID:SCR_002884) Copy   

•   Source: SciCrunch Registry
  

http://www.liu.se/hu/mdl/main/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. An on-line database and publically accessible depository that is dedicated to the omics of small biomolecules.

Proper citation: NMR metabolomics database of Linkoping (RRID:SCR_002758) Copy   

•   Source: SciCrunch Registry
  

https://sites.google.com/site/friaptamerstream/

The Aptamer Database is a comprehensive, annotated repository for information about aptamers and in vitro selection. This resource is provided to collect, organize and distribute all the known information regarding aptamer selection. Aptamers are DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules. Aptamers have been selected which bind nucleic acid, proteins, small organic compounds, and even entire organisms.

Proper citation: Aptamer Database - The Ellington Lab (RRID:SCR_001781) Copy   

•   Source: SciCrunch Registry
  

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

Database of annotations of functional units in proteins including multiple sequence alignment models for ancient domains and full-length proteins. This collection of models includes 3D structures that display the sequence/structure/function relationships in proteins. It also includes alignments of the domains to known three-dimensional protein structures in the MMDB database. The source databases are Pfam, Smart, and COG. Users can identify amino acids in protein sequences with the resources available as well as view single sequences embedded within multiple sequence alignments.

Proper citation: Conserved Domain Database (RRID:SCR_002077) Copy   

•   Source: SciCrunch Registry
  

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

A set of tools for deriving region of interest (ROI) atlases by whole brain clustering of task or resting state data. This resource also contains several atlases derived by parcellating publicly available resting state fMRI datasets. The initial release will include python scripts and ROI atlases developed to perform the analyses described in Craddock et. al., A whole brain fMRI atlas generated via spatially constrained spectral clustering, which is currently in revision in Human Brain Mapping. The scripts provide all of the tools necessary to derive an ROI atlases using spatially constrained Ncut spectral clustering. The scripts require python, numpy and scipy to run. Source code and parcellations now available! Go to http://ccraddock.github.io/cluster_roi/ for more information.

Proper citation: Spatially Constrained Parcellation (RRID:SCR_002198) Copy   

•   Source: SciCrunch Registry
  

http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-335

Cell signaling pathways can be explored using PathFinder, the interactive, online graphical representation of cell signaling pathways. The user can use PathFinder to explore the relationships between different cell signaling pathway components while being presented with our high quality small molecules, antibodies, enzymes, siRNA for gene knockdown and qPCR components to aid them in their research.

Proper citation: Cell Signaling Pathways (RRID:SCR_002070) Copy   

•   Source: SciCrunch Registry
  

http://www.escholarship.org/

Provides comprehensive publication services for Univeristy of California affiliated departments, research units, publishing programs, and individual scholars who seek to publish original, open access journals, books, conference proceedings, and other scholarship. Content is delivered via research platform and is available to scholars worldwide.

Proper citation: eScholarship (RRID:SCR_002624) Copy   

•   Source: SciCrunch Registry
  

http://hgc.rockefeller.edu/

An interactive web server that enables researchers to prioritize any list of genes by their biological proximity to defined core genes (i.e. genes that are known to be associated with the phenotype), and to predict novel gene pathways.

Proper citation: Human Gene Connectome Server (RRID:SCR_002627) Copy   

•   Source: SciCrunch Registry
  

http://microcircuit.epfl.ch/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 26, 2011. Neurons are characterized in terms of their morphological, physiological and gene expression profiles. Synaptic connections are characterized in terms of their physiological and anatomical profiles. Neuron morphology profiles are obtained from detailed morphometric breakdown of 3D reconstructed neurons (m-Profiles), neuron physiology profiles are obtained from detailed measurement of the electrophysiological responses to a series of stimulus protocols (e-Profiles), and neuron gene expression profiles are obtained from single cell RT-PCR data (g-Profiles) and in the near future from gene-chips. Synaptic connections are characterized by the identity of the pre and postsynaptic neurons (sn-Profile), the anatomy of synaptic connections as characterized by the axonal and dendritic location of light microscopically identified putative synapses (sm-Profile), and the physiology of synaptic connections as characterized by a profile of electrophysiological parameters obtained from a series of stimulation protocols applied to the presynaptic neuron (se-Profile).

Proper citation: Neocortical Microcircuit Database (RRID:SCR_002415) Copy   

•   Source: SciCrunch Registry
  

http://scholarlyoa.com/

Blog featuring critical analysis of scholarly open-access journals by Jeffrey Beale. Good tool to consult if you have suspicions that a journal is less than legit. Jeffrey Beall works as a librarian at Auraria Library, University of Colorado Denver, in Denver, Colorado.

Proper citation: Scholarly Open Access (RRID:SCR_002650) Copy   

•   Source: SciCrunch Registry
  

https://omictools.com/protein-interactions-and-molecular-information-database-tool

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. PRIME is a developed version of Kinase Pathway Database which is an integrated database concerning completed sequenced major eukaryotes, which contains the classification of protein kinases and their functional conservation and orthologous tables among species, protein-protein interaction data, domain information, structural information, and automatic pathway graph image interface. The protein-protein interactions are extracted by natural language processing (NLP) from abstracts using basic word pattern and protein name dictionary GENA: developed by our group. In this system, pathways are easily compared among species using protein interactions data more than 1,510,000 and orthologous tables. Further, using other organisms interaction data, interaction prediction is also possible.

Proper citation: Protein interaction and molecular information database (RRID:SCR_002096) Copy   

•   Source: SciCrunch Registry
  

http://www.HGPD.jp

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.The Human Gene and Protein Database presents SDS-PAGE patterns and other informations of human genes and proteins. The HGPD was constructed from full-length cDNAs. For conversion to Gateway entry clones, we first determined an open reading frame (ORF) region in each cDNA meeting the criteria. Those ORF regions were PCR-amplified utilizing selected resource cDNAs as templates. All the details of the construction and utilization of entry clones will be published elsewhere. Amino acid and nucleotide sequences of an ORF for each cDNA and sequence differences of Gateway entry clones from source cDNAs are presented in the GW: Gateway Summary window. Utilizing those clones with a very efficient cell-free protein synthesis system featuring wheat germ, we have produced a large number of human proteins in vitro. Expressed proteins were detected in almost all cases. Proteins in both total and supernatant fractions are shown in the PE: Protein Expression window. In addition, we have also successfully expressed proteins in HeLa cells and determined subcellular localizations of human proteins. These biological data are presented on the frame of cDNA clusters in the Human Gene and Protein Database. To build the basic frame of HGPD, sequences of FLJ full-length cDNAs and others deposited in public databases (Human ESTs, RefSeq, Ensembl, MGC, etc.) are assembled onto the genome sequences (NCBI Build 35 (UCSC hg17)). The majority of analysis data for cDNA sequences in HGPD are shared with the FLJ Human cDNA Database (http://flj.hinv.jp/) constructed as a human cDNA sequence analysis database focusing on mRNA varieties caused by variations in transcription start site (TSS) and splicing.

Proper citation: Human Gene and Protein Database (HGPD) (RRID:SCR_002889) Copy   

•   Source: SciCrunch Registry
  

http://network.bepress.com/

Bibliographic database that brings together free, full-text scholarly articles from hundreds of universities and colleges worldwide. Curated by university librarians and their supporting institutions, the Network includes a growing collection of peer-reviewed journal articles, book chapters, dissertations, working papers, conference proceedings, and other original scholarly work. A central discipline wheel features ten color-coded disciplines: law, social and behavioral sciences, arts and humanities, life sciences, physical sciences and mathematics, education, engineering, medicine and health sciences, business, and architecture. The size of each color-coded area reflects the size of each discipline's collection relative to the rest of DCN. Users can click on any segment of any layer of the wheel, with the selected discipline, subdiscipline, or subject navigating users to their chosen commons area where they can then proceed to a list of full-text PDFs. To be clear, typing a couple of keywords into the Search Entire Network box, also located on the homepage, might be a more efficient method than mousing around on this graphical browsing element. If you would like to contribute your institution's research to the Digital Commons Network, Use the form provided, http://network.bepress.com/about/

Proper citation: Digital Commons Network (RRID:SCR_002646) Copy   

•   Source: SciCrunch Registry
  

https://simtk.org/home/nmblmodels

The goal of the neuromuscular models library is to provide a resource for students, researchers, and clinicians to access, use, test, and develop models. The majority of models in this library are for use with OpenSIM and/or SIMM. Users who contribute models to the database can set up a project page where they can track who is using the model and contact with them.

Proper citation: Neuromuscular Models Library (RRID:SCR_002682) Copy   

•   Source: SciCrunch Registry
  

http://lepr.ofm-research.org/

Database of results of published experimental studies involving liquid-solid phase equilibria relevant to natural magmatic systems.

Proper citation: Library of Experimental Phase Relations (RRID:SCR_002202) Copy   

•   Source: SciCrunch Registry
  

http://bioinfo.au.tsinghua.edu.cn/dbRES/

dbRES is a web-oriented comprehensive database for RNA Editing Site. dbRES contain only experimental validated RNA Editing Site. All the data in dbRES was manually collected from literatures reporting related experiment result or the GeneBank database. dbRES now contains all together 5437 RNA edit site data. dbRES covers altogether 95 organisms from 251 transcripts. RNA editing is a post-transcriptional modification of RNA and markedly increases the complexity of the transcriptome. RNA editing occurs in the nucleus, as well as in mitochondria and plastids. To date such changes have been observed in prokaryotes, plants, animals and virus. The diversity of this widespread phenomenon includes nucleoside modifications, nucleotide additions and insertions, either in coding or non-coding sequences of RNA, which can occur concomitantly with transcription and splicing processes.

Proper citation: dbRES: A web-oriented database for annotated RNA Editing Site (RRID:SCR_002322) Copy   

•   Source: SciCrunch Registry