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http://databrary.org/

Project aims to promote data sharing, archiving, and reuse among researchers who study human development. Focuses on creating tools for scientists to store, manage, preserve, analyze and share video and related data.

Proper citation: Databrary (RRID:SCR_010471) Copy   

•   Source: SciCrunch Registry

http://uberon.org

An integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data. Uberon consists of over 10000 classes (March 2014) representing structures that are shared across a variety of metazoans. The majority of these classes are chordate specific, and there is large bias towards model organisms and human.

Proper citation: UBERON (RRID:SCR_010668) Copy   

•   Source: SciCrunch Registry

http://brainandsociety.org/the-brain-observatory

Formerly a topical portal studying the brain which collected and imaged 1000 human brains, the Brain Observatory has partnered with the Institute for Brain and Society to build virtual laboratories that will feed directly into the database of images and knowledge created in the context of the Human Brain Library. The Brain Observatory will also host exhibits, conferences, and events aimed at promoting a heightened awareness of brain research and how its results can benefit personal brain fitness and mental health.

Proper citation: Brain Observatory (RRID:SCR_010641) Copy   

•   Source: SciCrunch Registry

http://grassius.org/

A public resource composed of a collection of databases, computational and experimental resources that relate to the control of gene expression in the grasses, and their relationship with agronomic traits. As knowledge on the interactions of transcription factors (TFs) and cis-regulatory elements in the promoters of the genes that they regulate continues to accumulate, the information is acquired by GRASSIUS, either through contributions by the community, or by literature analysis. The overarching objective of GRASSIUS is to provide a one-stop resource that will facilitate research and communication within the plant community with regards to genome-wide regulation of gene expression processes.

Proper citation: GRASSIUS (RRID:SCR_012999) Copy   

•   Source: SciCrunch Registry

http://www.rcsb.org/#Category-welcome

Collection of structural data of biological macromolecules. Database of information about 3D structures of large biological molecules, including proteins and nucleic acids. Users can perform queries on data and analyze and visualize results.

Proper citation: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) (RRID:SCR_012820) Copy   

•   Source: SciCrunch Registry

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

A collection of software tools for high dimensional brain imaging genomics. These tools are designed to perform comprehensive joint analysis of heterogeneous imaging genomics data. HDBIG-SR is an HDBIG toolkit for sparse regression while HDBIG-SCCA is an HDBIG toolkit for sparse association.

Proper citation: HDBIG (RRID:SCR_014120) Copy   

•   Source: SciCrunch Registry

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

A Matlab tool to perform statistical analysis on cortical thickness signals on brain surfaces obtained from Freesurfer. It is used for multi-resolutional analysis of such cortical thickness signals and detecting group differences. It is based on the Spectral Graph Wavelet Transform (SGWT) toolbox and provides plug and play methods for deriving Wavelet Multiscale Descriptor (WMD), cortical thickness smoothing using SGWT, Multivariate General Linear Model (MGLM), and False Discovery Rate (FDR).

Proper citation: Wisconsin Cortical Thickness Analysis (CTA) Toolbox (RRID:SCR_014180) Copy   

•   Source: SciCrunch Registry

http://krasnow1.gmu.edu/CENlab/software.html

Stochastic reaction-diffusion simulator in Java which is used for simulating neuronal signaling pathways.

Proper citation: NeuroRD (RRID:SCR_014769) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/gscca_2013/

Group Sparse Canonical Correlation Analysis is a method designed to study the mutual relationship between two different types of data.

Proper citation: Group Sparse Canonical Correlation Analysis (RRID:SCR_014977) Copy   

•   Source: SciCrunch Registry

http://ccb.jhu.edu/software/hisat2/index.shtml

Graph-based alignment of next generation sequencing reads to a population of genomes.

Proper citation: HISAT2 (RRID:SCR_015530) Copy   

•   Source: SciCrunch Registry

http://avogadro.cc/

Software for semantic chemical editing, visualization, and analysis. It is designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.

Proper citation: Avogadro (RRID:SCR_015983) Copy   

•   Source: SciCrunch Registry

http://www.iu.edu/~beca/

Visualization and analysis software for interactive visual exploration and mining of fiber-tracts and brain networks with their genetic determinants and functional outcomes. BECA includes an fMRI and Diseases Analysis version as well as a Genome Explorer version.

Proper citation: BECA (RRID:SCR_015846) Copy   

•   Source: SciCrunch Registry

https://github.com/brain-life/encode

Software that implements a framework to encode structural brain connectomes into multidimensional arrays (tensors). Encoding Connectomes provides an agile framework for computing over connectome edges and nodes.

Proper citation: Linear Fascicle Evaluation (RRID:SCR_016153) Copy   

•   Source: SciCrunch Registry

http://hyphy.org/

Open source software package for comparative sequence analysis using stochastic evolutionary models. Used for analysis of genetic sequence data in particular the inference of natural selection using techniques in phylogenetics, molecular evolution, and machine learning.

Proper citation: HyPhy (RRID:SCR_016162) Copy   

•   Source: SciCrunch Registry

http://bids.neuroimaging.io

Standard specification for organizing and describing outputs of neuroimaging experiments. Used to organize and describe neuroimaging and behavioral data by neuroscientific community as standard to organize and share data. BIDS prescribes file naming conventions and folder structure to store data in set of already existing file formats. Provides standardized templates to store associated metadata in form of Javascript Object Notation (JSON) and tab-separated value (TSV) files. Facilitates data sharing, metadata querying, and enables automatic data analysis pipelines. System to curate, aggregate, and annotate neuroimaging databases. Intended for magnetic resonance imaging data, magnetoencephalography data, electroencephalography data, and intracranial encephalography data.

Proper citation: Brain Imaging Data Structure (BIDs) (RRID:SCR_016124) Copy   

•   Source: SciCrunch Registry

http://www.digimorph.org/

A dynamic archive of information on digital morphology and high-resolution X-ray computed tomography of biological specimens serving imagery for more than 750 specimens contributed by almost 150 collaborating researchers from the world''s premiere natural history museums and universities. Browse through the site and see spectacular imagery and animations and details on the morphology of many representatives of the Earth''s biota. Digital Morphology, part of the National Science Foundation Digital Libraries Initiative, develops and serves unique 2D and 3D visualizations of the internal and external structure of living and extinct vertebrates, and a growing number of ''invertebrates.'' The Digital Morphology library contains nearly a terabyte of imagery of natural history specimens that are important to education and central to ongoing cutting-edge research efforts. Digital Morphology visualizations are now in use in classrooms and research labs around the world and can be seen in a growing number of museum exhibition halls. The Digital Morphology site currently presents: * QuickTime animations of complete stacks of serial CT sections * Animated 3D volumetric movies of complete specimens * Stereolithography (STL) files of 3D objects that can be viewed interactively and rapidly prototyped into scalable physical 3D objects that can be handled and studied as if they were the original specimens * Informative introductions to the scanned organisms, often written by world authorities * Pertinent bibliographic information on each specimen * Useful links * A course resource for our ''Digital Methods for Paleontology'' course, in which students learn how to generate all of the types of imagery displayed on the Digital Morphology site

Proper citation: DigiMorph (RRID:SCR_004416) Copy   

•   Source: SciCrunch Registry

http://research.calacademy.org/redirect?url=http://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. The Catalog of Fishes is the authoritative reference for taxonomic fish names, featuring a searchable on-line database. The Catalog of Fishes covers more than 53,000 species and subspecies, over 10,000 genera and subgenera, and includes in excess of 16,000 bibliographic references. The Catalog of Fishes consists of three hardbound volumes of 900-1000 pages each, along with a CD-ROM. The online database is updated about every 8 weeks and is now about twice the size of the published version. It is one of the oldest and most complete databases for any large animal group. References are over 30,000. Valid species are over 30,000. This work is an essential reference for taxonomists, scientific historians, and for any specialist dealing with fishes. Entries for species, for example, consist of species/subspecies name, genus, author, date, publication, pages, figures, type locality, location of type specimen(s), current status (with references), family/subfamily, and important publication, taxonomic, or nomenclatural notes. Nearly all original descriptions have been examined, and much effort has gone into determining the location of type specimens. The Genera are updated from Eschmeyer''s 1990 Genera of Recent Fishes. Both genera and species are listed in a classification using recent taxonomic schemes. Also included are a lengthy list of museum acronyms, an interpretation of the International Code of Zoological Nomenclature, and Opinions of the International Commission involving fishes.

Proper citation: Catalog of Fishes (RRID:SCR_004408) Copy   

•   Source: SciCrunch Registry

http://pgn.cornell.edu/

Resource for the storage, retrieval and annotation of plant ESTs, with a focus on comparative genomics. PGN comprises an analysis pipeline and a website, and presently contains mainly data from the Floral Genome Project. However, it accepts submission from other sources. All data in PGN is directly derived from chromatograms and all original and intermediate data are stored in the database. The current datasets on PGN come from the floral genome project and includes the following species: Acorus americanus, Amborella trichopoda, Asparagus officinalis, Cucumis sativus, Eschscholzia californica, Eschscholzia californica, Illicium parviflorum, Ipomopsis aggregata, Liriodendron tulipifera, Mesembryanthemum crystallinum, Mimulus guttatus, Nuphar advena, Papaver somniferum, Persea americana, Prymnesium parvum, Ribes americanum, Saruma henryi, Stenogyne rugosa, Vaccinium corymbosa, Welwitschia mirabilis, Yucca filamentosa, Zamia fischeri. For functional annotation, blast is used to compare find the best match of each unigene sequence to in the Genbank NR database, and the in complete coding sequences from Arabidopsis. These annotations are stored in the database and serve as the primary source of annotation. The annotation framework will be extended to Gene Ontology annotations in the future.

Proper citation: PGN (RRID:SCR_004559) Copy   

•   Source: SciCrunch Registry

http://pdbml.pdb.org/

Markup Language that provides a representation of PDB data in XML format. The description of this format is provided in XML schema of the PDB Exchange Data Dictionary. This schema is produced by direct translation of the mmCIF format PDB Exchange Data Dictionary Other data dictionaries used by the PDB have been electronically translated into XML/XSD schemas and these are also presented in the list below. * PDBML data files are provided in three forms: ** fully marked-up files, ** files without atom records ** files with a more space efficient encoding of atom records * Data files in PDBML format can be downloaded from the RCSB PDB website or by ftp. * Software tools for manipulating PDB data in XML format are available.

Proper citation: Protein Data Bank Markup Language (RRID:SCR_005085) Copy   

•   Source: SciCrunch Registry

http://openneuro.org

Open platform for analyzing and sharing neuroimaging data from human brain imaging research studies. Brain Imaging Data Structure ( BIDS) compliant database. Formerly known as OpenfMRI. Data archives to hold magnetic resonance imaging data. Platform for sharing MRI, MEG, EEG, iEEG, and ECoG data.

Proper citation: OpenNeuro (RRID:SCR_005031) Copy   

•   Source: SciCrunch Registry