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http://eyegene.ophthy.med.umich.edu/madeline/

Software tool designed for preparing, visualizing, and exploring human pedigree data used in genetic linkage studies. It converts pedigree and marker data into formats required by popular linkage analysis packages, provides powerful ways to query pedigree data sets, and produces Postscript pedigree drawings that are useful for rapid data review.

Proper citation: MADELINE (RRID:SCR_001979) Copy   

•   Source: SciCrunch Registry
  

http://bioinformatics.charite.de/superdrug/

Public database of the structures of active ingredients in marketed drugs. It utilizes a web-query system with various search options, such as drug names, trade name, and synonyms.

Proper citation: Super Drug Database (RRID:SCR_002703) Copy   

•   Source: SciCrunch Registry
  

https://scicrunch.org/scicrunch/Resources/record/nlx_144509-1/f2172664-1499-555d-9e84-3b7768695e4d/search?q=integrated&l=integrated

Virtual database of individual data sources, maintained by SciCrunch participating groups. Database topics are varied, including animals, grants, software, brain gene expression, and clinical trials.

Proper citation: Integrated (RRID:SCR_002187) Copy   

•   Source: SciCrunch Registry
  

http://giladlab.uchicago.edu/orthoExon/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database of orthologous exon regions in the genomes of human, chimpanzee, and rhesus macaque. It can be used in analysis of multi-species RNA-seq expression data, allowing for comparisons of exon-level expression across primates, as well as comparative examination of alternative splicing and transcript isoforms.

Proper citation: Primate Orthologous Exon Database (RRID:SCR_002065) Copy   

•   Source: SciCrunch Registry
  

http://atgc.lbl.gov/atgc/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. ATGC stands for Alignable Tight Genomic Cluster, which is cluster of closely related prokaryotic genomes. ATGC is the principal notion of this web resource. The purpose of this web resource is to prepare ATGC-derived data sets for a variety of research projects in functional and evolutionary genomics. Unique features of ATGC include: * Reliable identification of orthologs (high degree of similarity between the genomes in the set allow an extensive use of synteny in ortholog identification); * Fine granularity of protein classification (in comparisons of more distant genomes, proteins belonging to families of paralogs are often lumped into a singlegroup; under the ATGC approach, comparison of genomic sequences from highly similar genomes allows one to track each set of orthologs separately); * Relative rarity of changes of any kind (in sequence, genome organization and gene content) allows the use of parsimony-related methods of analysis.

Proper citation: Alignable Tight Genomic Cluster (RRID:SCR_001894) Copy   

•   Source: SciCrunch Registry
  

http://www.wormatlas.org/

Anatomical atlas about structural anatomy of Caenorhabditis elegans. Provides simple interface allowing user to easily navigate through every anatomical structure of worm. Contains set of images which can be sorted by different characteristics: sex, genotype, age, body portion or tissue type. Includes links to other major worm websites and databases. Application for viewing and downloading thousands of unpublished electron micrographs and associated data. These images have been generated by several labs in the C. elegans community, including the MRC, the Hall lab (Center for C. elegans Anatomy), and the Culotti and Riddle labs.

Proper citation: WormAtlas (RRID:SCR_002861) Copy   

•   Source: SciCrunch Registry
  

http://www.arabidopsisreactome.org

Curated database of core pathways and reactions in plant biology that covers biological pathways ranging from the basic processes of metabolism to high-level processes such as cell cycle regulation. While it is targeted at Arabidopsis pathways, it also includes many biological events from other plant species. This makes the database relevant to the large number of researchers who work on other plants. Arabidopsis Reactome currently contains both in-house curated pathways as well as imported pathways from AraCyc and KEGG databases. All the curated information is backed up by its provenance: either a literature citation or an electronic inference based on sequence similarity. Their ontology ensures that the various events are linked in an appropriate spatial and temporal context.

Proper citation: Arabidopsis Reactome (RRID:SCR_002063) Copy   

•   Source: SciCrunch Registry
  

http://ibvd.virtualbrain.org/

A database of brain neuroanatomic volumetric observations spanning various species, diagnoses, and structures for both individual and group results. A major thrust effort is to enable electronic access to the results that exist in the published literature. Currently, there is quite limited electronic or searchable methods for the data observations that are contained in publications. This effort will facilitate the dissemination of volumetric observations by making a more complete corpus of volumetric observations findable to the neuroscience researcher. This also enhances the ability to perform comparative and integrative studies, as well as metaanalysis. Extensions that permit pre-published, non-published and other representation are planned, again to facilitate comparative analyses. Design strategy: The principle organizing data structure is the "publication". Publications report on "groups" of subjects. These groups have "demographic" information as well as "volume" information for the group as a whole. Groups are comprised of "individuals", which also have demographic and volume information for each of the individuals. The finest-grained data structure is the "individual volume record" which contains a volume observation, the units for the observation, and a pointer to the demographic record for individual upon which the observation is derived. A collection of individual volumes can be grouped into a "group volume" observation; the group can be demographically characterized by the distribution of individual demographic observations for the members of the group.

Proper citation: Internet Brain Volume Database (RRID:SCR_002060) Copy   

•   Source: SciCrunch Registry
  

http://viperdb.scripps.edu/

Database for icosahedral virus capsid structures. The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration. In addition, all virus capsids are placed in a single icosahedral orientation convention, facilitating comparison between different structures. The web site includes powerful search utilities , links to other relevant databases, background information on virus capsid structure, and useful database interface tools. It is an information source for the analysis of high resolution virus structures. VIPERdb is a one-stop site dedicated to helping users around the world examine the many icosahedral virus structures contained within the Protein Data Bank (PDB) by providing them with an easy to use database containing current data and a variety of analytical tools. Sponsors: VIPERdb is funded by the NIH., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: VIPERdb (RRID:SCR_002853) Copy   

•   Source: SciCrunch Registry
  

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