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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

http://science.kqed.org/quest/

An award-winning multimedia science and environment series created by KQED, San Francisco, the public media station serving Northern California. Launched in February 2007, by the end of its fourth season (in September 2010), QUEST had reached approximately 36 million viewers and listeners through its traditional TV and radio broadcasts and its growing Web audience. QUEST''s ultimate aim is to raise science literacy in the San Francisco Bay Area and beyond, inspiring audiences to discover and explore science and environment issues for themselves. Every season, KQED''s QUEST produces: * half-hour television episodes episodes that air weekly, exploring the cutting-edge work of Northern California scientists and researchers (QUEST airs Wednesdays 7:30pm on KQED Public Television 9); * weekly radio reports covering urban environmental issues which often include multimedia slide shows, and interactive online maps (QUEST airs Mondays 6:30am and 8:30am on KQED Public Radio 88.5 FM); * Educational resources, for use by formal and informal educators; QUEST also provides professional development for science educators to support multimedia and technology integration in science classrooms and programs; * 20 six-minute stories for its new web only series, Science on the SPOT, which takes a fresh, fast and curious look at science with stories about albino redwoods, the science of fog and banana slugs, to name a few. (launched in 2010); * A daily science blog written by Northern California scientists, QUEST producers and science enthusiasts; * Exclusive web extras, featuring extended interviews with scientists; Flickr photos, and science hikes. Formal and informal Educators who would like to become involved withthe educational outreach program should contact: ScienceEd (at) kqed.org.

Proper citation: QUEST (RRID:SCR_005210) 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

http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:DelPhi

DelPhi provides numerical solutions to the Poisson-Boltzmann equation (both linear and nonlinear form) for molecules of arbitrary shape and charge distribution. The current version is fast, accurate, and can handle extremely high lattice dimensions. It also includes flexible features for assigning different dielectric constants to different regions of space and treating systems containing mixed salt solutions. DelPhi takes as input a coordinate file format of a molecule or equivalent data for geometrical objects and/or charge distributions and calculates the electrostatic potential in and around the system, using a finite difference solution to the Poisson-Boltzmann equation. DelPhi is a versatile electrostatics simulation program that can be used to investigate electrostatic fields in a variety of molecular systems. Features of DelPhi include solutions to mixtures of salts of different valence; solutions to different dielectric constants to different regions of space; and estimation of the best relaxation parameter at run time.

Proper citation: DelPhi (RRID:SCR_008669) Copy   

•   Source: SciCrunch Registry

http://plantgrn.noble.org/LegumeIP/

LegumeIP is an integrative database and bioinformatics platform for comparative genomics and transcriptomics to facilitate the study of gene function and genome evolution in legumes, and ultimately to generate molecular based breeding tools to improve quality of crop legumes. LegumeIP currently hosts large-scale genomics and transcriptomics data, including: * Genomic sequences of three model legumes, i.e. Medicago truncatula, Glycine max (soybean) and Lotus japonicus, including two reference plant species, Arabidopsis thaliana and Poplar trichocarpa, with the annotation based on UniProt TrEMBL, InterProScan, Gene Ontology and KEGG databases. LegumeIP covers a total 222,217 protein-coding gene sequences. * Large-scale gene expression data compiled from 104 array hybridizations from L. japonicas, 156 array hybridizations from M. truncatula gene atlas database, and 14 RNA-Seq-based gene expression profiles from G. max on different tissues including four common tissues: Nodule, Flower, Root and Leaf. * Systematic synteny analysis among M. truncatula, G. max, L. japonicus and A. thaliana. * Reconstruction of gene family and gene family-wide phylogenetic analysis across the five hosted species. LegumeIP features comprehensive search and visualization tools to enable the flexible query on gene annotation, gene family, synteny, relative abundance of gene expression.

Proper citation: LegumeIP (RRID:SCR_008906) Copy   

•   Source: SciCrunch Registry

http://www.readout.info

Matlab toolbox that makes it easy to apply decoding analyses to neural data. The design of the toolbox revolves around four abstract object classes which enables users to interchange particular modules in order to try different analyses while keeping the rest of the processing stream intact. The toolbox is capable of analyzing data from many different types of recording modalities, and examples are given on how it can be used to decode basic visual information from neural spiking activity and how it can be used to examine how invariant the activity of a neural population is to stimulus transformations.

Proper citation: Neural Decoding Toolbox (RRID:SCR_009012) Copy   

•   Source: SciCrunch Registry

https://kepler-project.org/

Kepler is a software application for analyzing and modeling scientific data. Using Kepler''s graphical interface and components, scientists with little background in computer science can create executable models, called scientific workflows, for flexibly accessing scientific data (streaming sensor data, medical and satellite images, simulation output, observational data, etc.) and executing complex analyses on this data. Kepler is developed by a cross-project collaboration led by the Kepler/CORE team. The software builds upon the mature Ptolemy II framework, developed at the University of California, Berkeley. Ptolemy II is a software framework designed for modeling, design, and simulation of concurrent, real-time, embedded systems. The Kepler Project is dedicated to furthering and supporting the capabilities, use, and awareness of the free and open source, scientific workflow application, Kepler. Kepler is designed to help scien��tists, analysts, and computer programmers create, execute, and share models and analyses across a broad range of scientific and engineering disciplines. Kepler can operate on data stored in a variety of formats, locally and over the internet, and is an effective environment for integrating disparate software components, such as merging R scripts with compiled C code, or facilitating remote, distributed execution of models. Using Kepler''s graphical user interface, users simply select and then connect pertinent analytical components and data sources to create a scientific workflowan executable representation of the steps required to generate results. The Kepler software helps users share and reuse data, workflows, and compo��nents developed by the scientific community to address common needs. Kepler is a java-based application that is maintained for the Windows, OSX, and Linux operating systems. The Kepler Project supports the official code-base for Kepler development, as well as provides materials and mechanisms for learning how to use Kepler, sharing experiences with other workflow developers, reporting bugs, suggesting enhancements, etc. The Kepler Project Leadership Team works to assure the long-term technical and financial viability of Kepler by making strategic decisions on behalf of the Kepler user community, as well as providing an official and durable point-of-contact to articulate and represent the interests of the Kepler Project and the Kepler software application. Details about how to get more involved with the Kepler Project can be found in the developer section of this website.

Proper citation: Kepler (RRID:SCR_005252) Copy   

•   Source: SciCrunch Registry

http://www.bioextract.org/GuestLogin

An open, web-based system designed to aid researchers in the analysis of genomic data by providing a platform for the creation of bioinformatic workflows. Scientific workflows are created within the system by recording tasks performed by the user. These tasks may include querying multiple, distributed data sources, saving query results as searchable data extracts, and executing local and web-accessible analytic tools. The series of recorded tasks can then be saved as a reproducible, sharable workflow available for subsequent execution with the original or modified inputs and parameter settings. Integrated data resources include interfaces to the National Center for Biotechnology Information (NCBI) nucleotide and protein databases, the European Molecular Biology Laboratory (EMBL-Bank) non-redundant nucleotide database, the Universal Protein Resource (UniProt), and the UniProt Reference Clusters (UniRef) database. The system offers access to numerous preinstalled, curated analytic tools and also provides researchers with the option of selecting computational tools from a large list of web services including the European Molecular Biology Open Software Suite (EMBOSS), BioMoby, and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The system further allows users to integrate local command line tools residing on their own computers through a client-side Java applet.

Proper citation: BioExtract (RRID:SCR_005397) Copy   

•   Source: SciCrunch Registry

http://www.biokepler.org

A Comprehensive Bioinformatics Scientific Workflow Module for Distributed Analysis of Large-Scale Biological Data that is distributed on top of the core Kepler scientific workflow system.

Proper citation: bioKepler (RRID:SCR_005385) Copy   

•   Source: SciCrunch Registry

http://cvcweb.ices.utexas.edu/cvcwp/?page_id=100

VolumeRover (a.k.a VolRover) is an interactive multi-purpose image processing software that can visualize three dimensional imaging data of any size (as big as terabyte) in a commodity PC or workstation and additionally supports the following image processing operations. Image Contrast Enhancement, Filtering/Noise Reduction, Image Segmentation, Isocontouring, Symmetry Detection (for Virus Maps, Boundary-free Image Skeletonization. VolRover provides a user interface to a number of CVC software packages including Segmentation, Contrast Enhancement, and Motif Elucidation.

Proper citation: VolumeRover (RRID:SCR_005457) Copy   

•   Source: SciCrunch Registry

http://bioimage.ucsb.edu/bisque

Open source database for exchange and exploration of biological images. Used to store, visualize, organize and analyze images in cloud. Centered around database of images and metadata.

Proper citation: Bisque database (RRID:SCR_005559) Copy   

•   Source: SciCrunch Registry

http://carringtonlab.org/resources/cashx

Software pipeline to parse, map, quantify and manage large quantities of sequence data. CASHX is a set of tools that can be used together, or as independent modules on their own. The reference genome alignment tools can be used with any reference sequence in fasta format. The pipeline was designed and tested using Arabidopsis thaliana small RNA reads generated using an Illumina 1G.

Proper citation: CASHX (RRID:SCR_005477) Copy   

•   Source: SciCrunch Registry

http://mcbc.usm.edu/gofetcher/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 29, 2012. We developed a web application, GOfetcher, with a very comprehensive search facility for the GO project and a variety of output formats for the results. GOfetcher has three different levels for searching the GO: Quick Search, Advanced Search, and Upload Files for searching. The application includes a unique search option which generates gene information given a nucleotide or protein accession number which can then be used in generating gene ontology information. The output data in GOfetcher can be saved into several different formats; including spreadsheet, comma-separated values, and the Extensible Markup Language (XML) format. Platform: Online tool

Proper citation: GOfetcher (RRID:SCR_005681) Copy   

•   Source: SciCrunch Registry