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http://ligand-expo.rutgers.edu/

An integrated data resource for finding chemical and structural information about small molecules bound to proteins and nucleic acids within the structure entries of the Protein Data Bank. Tools are provided to search the PDB dictionary for chemical components, to identify structure entries containing particular small molecules, and to download the 3D structures of the small molecule components in the PDB entry. A sketch tool is also provided for building new chemical definitions from reported PDB chemical components.

Proper citation: Ligand Expo (RRID:SCR_006636) Copy   

•   Source: SciCrunch Registry

http://rice.plantbiology.msu.edu/

Database and resource that provides sequence and annotation data for the rice genome. This website provides genome sequence from the Nipponbare subspecies of rice and annotation of the 12 rice chromosomes. All structural and functional annotation is viewable through our Rice Genome Browser which currently supports 75 tracks of annotation. Enhanced data access is available through web interfaces, FTP downloads and a Data Extractor tool developed in order to support discrete dataset downloads. Rice is a model species for the monocotyledonous plants and the cereals which are the greatest source of food for the world''s population. While rice genome sequence is available through multiple sequencing projects, high quality, uniform annotation is required in order for genome sequence data to be fully utilized by researchers. The existence of a common gene set and uniform annotation allows researchers within the rice community to work from a common resource so that their results can be more easily interpreted by other scientists. The objective of this project has always been to provide high quality annotation for the rice genome. They generated, refined and updated gene models for the estimated 40,000-60,000 total rice genes, provided standardized annotation for each model, linked each model to functional annotation including expression data, gene ontologies, and tagged lines. They have provided a resource to extend the annotation of the rice genome to other plant species by providing comparative alignments to other plant species. Analysis/Tools are available including: BLAST, Locus Name Search, Functional Term Search, Protein Domain Search, Anatomy Expression Viewer, Highly Expressed Genes

Proper citation: Rice Genome Annotation (RRID:SCR_006663) Copy   

•   Source: SciCrunch Registry

http://www.iedadata.org/

A community-based data facility to support, sustain, and advance the geosciences by providing data services for observational solid earth data from the Ocean, Earth, and Polar Sciences. IEDA systems enable these data to be discovered and reused by a diverse community now and in the future. Data services include data access, data analysis, data compliance, data publication, DOI search, and web services. Desktop apps GeoMapApp and Virtual Ocean are available to explore, visualize and analyze your own data within the context of hundreds of other earth science data from around the world. IEDA is a partnership between EarthChem and the Marine Geoscience Data System (MGDS). EarthChem and MGDS systems include the geochemical databases PetDB and SedDB, the geochemistry data network EarthChem, the Ridge2000 and MARGINS Data Portals, the Academic Seismic Portal field data collection, the Antarctic and Southern Ocean Data System, the Global Multi Resolution Topography synthesis, and the System for Earth Sample Registration SESAR.

Proper citation: Integrated Earth Data Applications (RRID:SCR_006739) Copy   

•   Source: SciCrunch Registry

http://redfly.ccr.buffalo.edu

Curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs). Includes experimentally verified fly regulatory elements along with their DNA sequence, associated genes, and expression patterns they direct. Submission of experimentally verified cis-regulatory elements that are not included in REDfly database are welcome.

Proper citation: REDfly Regulatory Element Database for Drosophilia (RRID:SCR_006790) Copy   

•   Source: SciCrunch Registry

http://www.openarchives.org/ore/

Initiative which defines standards for the description and exchange of aggregations of Web resources. The intent of the effort is to develop standards that generalize across all web-based information including the increasing popular social networks of web 2.0. The goal of these standards is to expose the rich content in these aggregations (sometimes called compound digital objects, they may combine distributed resources with multiple media types including text, images, data, and video) to applications that support authoring, deposit, exchange, visualization, reuse, and preservation. The specific aim of the ORE effort is to promote (through creation or endorsement) effective and consistent mechanisms which: facilitate discovery of compound digital objects; reference (or link to) these objects (as well as parts thereof); obtain a variety of disseminations of these objects; aggregate and disaggregate objects; and enable processing of objects by automated agents.

Proper citation: Open Archives Initiative - Object Reuse and Exchange Initiative (RRID:SCR_006982) Copy   

•   Source: SciCrunch Registry

http://smallrna.udel.edu/index.php

This project has developed a sequence dataset of plant small RNAs based on the hypothesis that most if not all plants utilize important small RNA signaling networks. Different plant families are likely to have both common and lineage-specific miRNAs or other small RNAs with important biological roles. Comparative genomics approaches can be applied to distinguish potential miRNAs from siRNAs and to match the miRNAs to the target sequences. This project develops an unparalleled resource of millions of plant small RNAs for comparative analyses. The project includes sequencing of small RNAs from a diverse and agronomically-relevant set of plant species, focused analyses of important members of the Solanaceae and Poaceae, and development of a small RNA database and web interface for public access and analysis of data. These data will allow the experimental characterization of the majority of biologically important small RNAs for a range of plant species, and will be tremendously useful to a broad set of plant biologists interested in development, stress responses, epigenetics, evolution, RNA biology and other traits impacted by small RNAs. We offer a variety of tools to query the small RNA data set, with options to identify sequences based on homology, expression levels, conservation, or potential function: 1. Small RNA mapping tool: searches for small RNAs perfectly matching a genomic sequence provided by the user. 2. Small RNA mismatch tool: searches the database for small RNAs or other short sequences provided by the user, allowing mismatches. 3. Library-comparison tool to identify conserved small RNAs. 4. Library-comparison tool to identify differentially regulated small RNAs. 5. Reverse Target Prediction.

Proper citation: Comparative Sequencing of Plant Small RNAs (RRID:SCR_007003) Copy   

•   Source: SciCrunch Registry

http://hendrix.imm.dtu.dk/software/lyngby/

Matlab toolbox for the analysis of functional neuroimages (PET, fMRI). The toolbox contains a number of models: FIR-filter, Lange-Zeger, K-means clustering among others, visualizations and reading of neuroimaging files.

Proper citation: Lyngby (RRID:SCR_007143) Copy   

•   Source: SciCrunch Registry

http://earthref.org/MAGIC/

Databases that accept and provide access to paleomagnetic and rock magnetic data. The paleomagnetic data range from individual measurements to specimen, sample or site level results, including a wide variety of derived parameters or associated rock magnetic measurements. The rock magnetic database includes data collected during rock magnetic experiments on remanence, anisotropy, hysteresis and susceptibility. The MagIC Console Software provides an effective environment in Microsoft Excel where users can collate and prepare their paleomagentic and rock magnetic data for uploading in the Online MagIC Database.

Proper citation: Magnetics Information Consortium (RRID:SCR_007098) Copy   

•   Source: SciCrunch Registry

http://www.genes2cognition.org/

A neuroscience research program that studies genes, the brain and behavior in an integrated manner, established to elucidate the molecular mechanisms of learning and memory, and shed light on the pathogenesis of disorders of cognition. Central to G2C investigations is the NMDA receptor complex (NRC/MASC), that is found at the synapses in the central nervous system which constitute the functional connections between neurons. Changes in the receptor and associated components are thought to be in a large part responsible for the phenomenon of synaptic plasticity, that may underlie learning and memory. G2C is addressing the function of synapse proteins using large scale approaches combining genomics, proteomics and genetic methods with electrophysiological and behavioral studies. This is incorporated with computational models of the organization of molecular networks at the synapse. These combined approaches provide a powerful and unique opportunity to understand the mechanisms of disease genes in behavior and brain pathology as well as provide fundamental insights into the complexity of the human brain. Additionally, Genes to Cognition makes available its biological resources, including gene-targeting vectors, ES cell lines, antibodies, and transgenic mice, generated for its phenotyping pipeline. The resources are freely-available to interested researchers.

Proper citation: Genes to Cognition: Neuroscience Research Programme (RRID:SCR_007121) 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://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://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://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://www.complex.iastate.edu/download/Picky/

A software tool for selecting optimal oligonucleotides (oligos) that allows the rapid and efficient determination of gene-specific oligos based on given gene sets, and can be used for large, complex genomes such as human, mouse, or maize.

Proper citation: Picky (RRID:SCR_010963) Copy   

•   Source: SciCrunch Registry

https://github.com/Benson-Genomics-Lab/TRF

Software tool to locate and display tandem repeats in DNA sequences. Program to analyze DNA sequences.

Proper citation: Tandem Repeats Finder (RRID:SCR_022193) Copy   

•   Source: SciCrunch Registry

https://github.com/marbl/MashMap

Software tool as fast approximate aligner for long DNA sequences. Used for computing local alignment boundaries between long DNA sequences.

Proper citation: MashMap (RRID:SCR_022194) Copy   

•   Source: SciCrunch Registry