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

A comprehensive processing pipeline developed and used at University of North Carolina and University of Utah for brain MRIs. The processing pipeline includes image registration, filtering, segmentation and inhomogeneity correction. The tool is cross-platform and can be run within 3D Slicer or as a stand-alone program. The image segmentation algorithm is based on the EMS software developed by Koen van Leemput.

Proper citation: ABC (Atlas Based Classification) (RRID:SCR_005981) Copy   

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http://snnap.uth.tmc.edu/

SNNAP (Simulator for Neural Networks and Action Potentials) is a tool for rapid development and simulation of realistic models of single neurons and neural networks. It includes mathematical descriptions of ion currents and intracellular second messengers and ions. In addition, you can simulate current flow in multicompartment models of neurons by using the equations describing electric coupling. SNNAP also includes mathematical descriptions of intracellular second messengers and ions, and simulate the modulation of membrane currents and synaptic transmission, , either enhancement or inhibition. Other advantages of SNNAP include: * Written in JAVA and can run on virtually any type of computer system. * Graphical user interface * Ability to simulate common experimental manipulations. * Modular organizations of input files. Agencies: NCRR, FOSR grant F49620-93-1-0272, as well as NIH grants R01-RR11626 and P01-NS38310

Proper citation: Simulator for Neural Networks and Action Potentials (RRID:SCR_006031) Copy   

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http://www.stanford.edu/~nigam/cgi-bin/dokuwiki/doku.php?id=clench

Cluster Enrichment (CLENCH) allows A. thaliana researchers to perform automated retrieval of GO annotations from TAIR and calculate enrichment of GO terms in gene group with respect to a reference set. Before calculating enrichment, CLENCH allows mapping of the returned annotations to arbitrary coarse levels using GO slim term lists (which can be edited by the user) and a local installation of GO. Platform: Windows compatible, Linux compatible,

Proper citation: CLENCH (RRID:SCR_005735) Copy   

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http://www.sbur.org/

The Society for Basic Urologic Research (SBUR) is a society of scientists whose expertise includes the study of urologic cancers (prostate, bladder, kidney, testis, penis), the biology of prostate growth, kidney and bladder function, autoimmune urologic diseases, infectious diseases, neuro-urologic diseases, male reproductive biology, infertility and erectile dysfunction. Members include molecular biologists, immunologists, epidemiologists, oncologists, biochemists and clinical urologic scientists. SBUR members serve on a wide variety of advisory panels, study sections, editorial boards and in the pharmaceutical industry. The SBUR organizes two annual meetings to share new findings at a multidisciplinary level, to promote interaction among members and other interested scientists and to highlight new areas of research and funding opportunities. The Society was organized to address the following: * To provide a forum for the presentation and discussion of basic scientific topics related to urology * To develop educational forums concerning scientific advancements related to the field of urology * To promote collaborative investigations among member scientists with an emphasis on the interchange of expertise among clinical and basic scientists * To promote the communication and interests of urologic disease investigators with national funding agencies, industry representatives and academic institutions with regards to urology related research * To serve as a resource for research information and expertise to clinical urologists through the American Urological Association

Proper citation: SBUR - Society for Basic Urologic Research (RRID:SCR_005856) Copy   

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http://athina.biol.uoa.gr/DAM-Bio/

An integrated environment designed to support protein sequence and structure analysis on the web.

Proper citation: DAM-Bio (RRID:SCR_006226) Copy   

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http://bioinformatics.biol.uoa.gr/LepChorionDB/

A relational database of Lepidoptera chorion proteins. The proteinaceous Lepidopteran chorions are used in our lab, as a model system towards unraveling the routes and rules of formation of natural protective amyloids. Therefore, we constructed LepChorionDB a relational database, containing all Lepidoptera chorion proteins identified to date. Lepidoptera chorion proteins can be classified in two major protein families, A and B. This classification was based on multiple sequence alignments of conserved key residues, in the central domain of, well characterized, silkmoth chorion proteins. These alignments were used to build Hidden Markov Models in order to search various DataBases. This work was a collaboration of the Department of Cell Biology and Biophysics, University of Athens and the Centre of Immunology & Transplantation Biomedical Research Foundation, Academy of Athens.

Proper citation: LepChorionDB (RRID:SCR_006222) Copy   

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http://aias.biol.uoa.gr/OMPdb/

A database of Beta-barrel outer membrane proteins from Gram-negative bacteria. The web interface of OMPdb offers the user the ability not only to view the available data, but also to submit advanced queries for text search within the database''s protein entries or run BLAST searches against the database. The most up-to-date version of the database (as well as all past versions) can be downloaded in various formats (flat text, XML format or raw FASTA sequences). For constructing OMPdb, multiple freely accessible resources were combined and a detailed literature search was performed. The classification of OMPdb''s protein entries into families is based mainly on structural and functional criteria. Information included in the database consists of sequence data, as well as annotation for structural characteristics (such as the transmembrane segments), literature references and links to other public databases, features that are unique worldwide. Along with the database, a collection of profile Hidden Markov Models that were shown to be characteristic for Beta-barrel outer membrane proteins was also compiled. This set, when used in combination with our previously developed algorithms (PRED-TMBB, MCMBB and ConBBPRED) will serve as a powerful tool in matters of discrimination and classification of novel Beta-barrel proteins and whole-genome analyses., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: OMPdb (RRID:SCR_006221) Copy   

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http://michaeljfox.org/

A Parkinson's research foundation dedicated to finding a cure for Parkinson's disease and to ensuring the development of improved therapies. Pipeline Programs fund investigator-initiated proposals focused on the following critical points along the translational pathway to new therapies for Parkinson's disease.

Proper citation: Michael J. Fox Foundation for Parkinsons Research (RRID:SCR_006183) Copy   

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http://bioinformatics.biol.uoa.gr/

Laboratory focuses on research related to the elucidation of the principles governing protein structure and function, under the supervision of Professor Stavros J. Hamodrakas. In particular, original research is carried out along two main axes: # Algorithm development for the prediction of protein structure, function and interactions from amino acid sequence as well as construction of relevant databases. # Application of a variety of Biophysical methods and techniques for protein structure determination and for structural studies of complex, physiologically important, Biological tissues such as insect chorion and cuticle. More than 15 individuals (including post-doctoral researchers, PhD students, MSc and undergraduate students) are currently involved in several ongoing research projects. Apart from research, our lab offers undergraduate courses in Bioinformatics and Molecular Biophysics, which are elective for the degrees (BSc) in Biology (Faculty of Biology) and Physics (Faculty of Physics) of the University of Athens. At the same time, our lab is actively involved in the organization and co-ordination of the MSc Programme in Bioinformatics of the Faculty of Biology.

Proper citation: University of Athens Biophysics and Bioinformatics Laboratory (RRID:SCR_006180) Copy   

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http://athina.biol.uoa.gr/bioinformatics/GENEVITO/

A JAVA-based computer application that serves as a workbench for genome-wide analysis through visual interaction. GeneViTo offers an inspectional view of genomic functional elements, concerning data stemming both from database annotation and analysis tools for an overall analysis of existing genomes. The application deals with various experimental information concerning both DNA and protein sequences (derived from public sequence databases or proprietary data sources) and meta-data obtained by various prediction algorithms, classification schemes or user-defined features. Interaction with a Graphical User Interface (GUI) allows easy extraction of genomic and proteomic data referring to the sequence itself, sequence features, or general structural and functional features. Emphasis is laid on the potential comparison between annotation and prediction data in order to offer a supplement to the provided information, especially in cases of poor annotation, or an evaluation of available predictions. Moreover, desired information can be output in high quality JPEG image files for further elaboration and scientific use. GeneViTo has already been applied to visualize the genomes of two microbial organisms: the bacterion Chlamydia trachomatis and the archaeon Methanococcus jannaschii. The application is compatible with Linux or Windows ME-2000-XP operating systems, provided that the appropriate Java Runtime Environment (Java 1.4.1) is already installed in the system.

Proper citation: GeneVito (RRID:SCR_006211) Copy   

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http://www.sdbonline.org

Non-profit professional society dedicated to advancement of the field of developmental biology. Excellence in research and education in developmental biology is fostered; advice and resources on careers in developmental biology is provided; and information for the public on relevant topics in developmental biology is provided. Perhaps most importantly, a communication hub for all developmental biologists is provided. The SDB is associated with the journal Developmental Biology; the SDB organizes scientific meetings that focus on developmental biology; the SDB has established programs to interface with the international community of developmental biologists; and the SDB maintains this society web site that covers all aspects of developmental biology. Membership includes developmental biologists at all stages of their careers from around the world.

Proper citation: Society for Developmental Biology (RRID:SCR_006299) Copy   

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http://www.biomedbridges.eu/

Consortium of 12 Biomedical sciences research infrastructure (BMS RI) partners to develop a shared e-infrastructure to allow interoperability between data and services in the biological, medical, translational and clinical domains (providing a complex knowledge environment comprising standards, ontologies, data and services) and thus strengthen biomedical resources in Europe. The BMS RIs are on the roadmap of the European Strategy Forum on Research Infrastructures (ESFRI). Connecting several European research infrastructures brings a diversity of ethical, legal and security concerns including data security requirements for participating e-Infrastructures that are storing or processing patient-related data (or biosamples): EATRIS, ECRIN, BBMRI, EuroBioImaging and EMBL-EBI. In addition, INSTRUCT is interested in secure sample transport and in intellectual property rights; Infrafrontier stores high-throughput data from mice. BBMRI with its focus on the availability of biomaterials is currently emphasizing aspects like k-anonymity and metadata management for its data. Sharing of imaging data by Euro-BioImaging poses challenges with respect to anonymisation and intellectual property. Therefore, an ethical, regulatory and security framework for international data sharing that covers these diverse areas and different types of data (e.g. clinical trials data, mouse data, and human genotype and DNA sequence data) is of crucial importance. The outcomes will lead to real and sustained improvement in the services the biomedical sciences research infrastructures offer to the research community. Data curation and sample description will be improved by the adoption of best practices and agreed standards. Many improvements will emerge from new interactions between RIs created by data linkage and networking. Ensuring access to relevant information for all life science researchers across all BMS RIs will enable scientists to conduct and share cutting-edge research.

Proper citation: BioMedBridges (RRID:SCR_006179) Copy   

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https://array.nci.nih.gov/caarray/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on Sep 18, 2018. Open-source, web and programmatically accessible microarray data management system. caArray guides the annotation and exchange of array data using a federated model of local installations whose results are shareable across the cancer Biomedical Informatics Grid (caBIG). caArray furthers translational cancer research through acquisition, dissemination and aggregation of semantically interoperable array data to support subsequent analysis by tools and services on and off the Grid. As array technology advances and matures, caArray will extend its logical library of assay management.

Proper citation: caArray (RRID:SCR_006053) Copy   

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http://embryo.soad.umich.edu/

Complete three-dimensional data set of reference magnetic resonance microscopy (MRM) images of the human embryo representing 10 stages of development for each of 18 human embryos representing Carnegie stages 10 through 23, a critical embryonic time period for organogenesis. The users of the collection are able to manipulate the data on their own personal computers to view any slice from any plane of sectioning. Dynamic rotational views of whole embryos and time-lapse views of the growing embryo are accessible. Each embryo was imaged with three magnetic resonance pulse sequences to obtain fully-registered T1-weighted, T2-weighted, and diffusion-weighted image datasets. A complete set of coronal, sagittal, and axial images were produced from each image data set. Several major organs were isolated from each T1-weighted embryo data set using image segmentation methods and separate image data sets were created to represent each of these organs. Additionally, each embryo was optically photographed under a low-power microscope. The formalin-fixed specimens came from the highly respected Carnegie Collection of Human Embryos. This is the first distributable work to document in three dimensions the anatomy of the human embryonic time period. Pseudo- time-lapse movies were created using morphing software to represent the fourth dimension (time). Carnegie stages are a system used by embryologists to describe the apparent maturity of embryos. An embryo is assigned a Carnegie stage (numbered from 1 to 23) based on its external features. This staging system is not dependent on the chronological age nor the size of the embryo. The stages, are in a sense, arbitrary levels of maturity based on multiple physical features. Embryos that might have different ages or sizes can be assigned the same Carnegie stage based on their external appearance because of the natural variation which occurs between individuals. Postovulatory age is frequently used by clinicians to describe the maturity of an embryo. It refers to the length of time since the last ovulation before pregnancy. Postovulatory age is a good indication of embryonic age because the time of ovulation can be determined and fertilization must occur close to the time of ovulation. The terms gestation, pregnancy, and conception are usually avoided in describing embryonic age because fertilization is not universally accepted as the commencement of development (some consider implantation as the beginning of development). MRM was performed at the Center for In-vivo Microscopy at Duke University. Image processing and data managment was performed at the School of Art and Design, University of Michigan.

Proper citation: Multi-Dimensional Human Embryo (RRID:SCR_006296) Copy   

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http://mango.adult-neurogenesis.de

Database of genes concerning adult neurogenesis mapped to cell types and processes that have been curated from the literature. In its present state, the database is restricted to neurogenesis in the hippocampus.

Proper citation: Mammalian Adult Neurogenesis Gene Ontology (RRID:SCR_006176) Copy   

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https://syllabus.med.unc.edu/courseware/embryo_images/

Tutorial that uses scanning electron micrographs (SEMs) as the primary resource to teach mammalian embryology. The 3-D like quality of the micrographs coupled with selected line drawings and minimal text allow relatively easy understanding of the complex morphological changes that occur in utero. Because early human embryos are not readily available and because embryogenesis is very similar across mammalian species, the majority of micrographs that are utilized in this tutorial are of mouse embryos. The remainder are human. This tutorial is divided into units that may be studied in any order. All of the images have a legend that indicates the age of the embryo. If it is a mouse embryo, the approximate equivalent human age is indicated. To minimize labeling, color-coding is widely used. To view the micrographs without color, the cursor may be placed on the image. The SEMs used in this tutorial are from the Kathleen K. Sulik collection. The line drawings have been used with permission from Lippincott Williams & Wilkins and are from the 6th and 7th editions of Langman''s Medical Embryology by T.W. Sadler.

Proper citation: Embryo Images Normal and Abnormal Mammalian Development (RRID:SCR_006297) Copy   

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http://service.iris.edu/fdsnws/station/1/

Web service that returns International Federation of Digital Seismograph Networks (FDSN) station metadata in FDSN StationXML format or as delimited text. Results are available at multiple levels of granularity: network, station, channel and response. Metadata may be selected based on channel descriptors, time ranges, geographic regions, and more. This service is an implementation of the FDSN web service specification version 1.

Proper citation: IRIS DMC FDSNWS station Web Service (RRID:SCR_006177) Copy   

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http://www.ddduk.org/

The Deciphering Developmental Disorders (DDD) study aims to find out if using new genetic technologies can help doctors understand why patients get developmental disorders. To do this we have brought together doctors in the 23 NHS Regional Genetics Services throughout the UK and scientists at the Wellcome Trust Sanger Institute, a charitably funded research institute which played a world-leading role in sequencing (reading) the human genome. The DDD study involves experts in clinical, molecular and statistical genetics, as well as ethics and social science. It has a Scientific Advisory Board consisting of scientists, doctors, a lawyer and patient representative, and has received National ethical approval in the UK. Over the next few years, we are aiming to collect DNA and clinical information from 12,000 undiagnosed children in the UK with developmental disorders and their parents. The results of the DDD study will provide a unique, online catalogue of genetic changes linked to clinical features that will enable clinicians to diagnose developmental disorders. Furthermore, the study will enable the design of more efficient and cheaper diagnostic assays for relevant genetic testing to be offered to all such patients in the UK and so transform clinical practice for children with developmental disorders. Over time, the work will also improve understanding of how genetic changes cause developmental disorders and why the severity of the disease varies in individuals. The Sanger Institute will contribute to the DDD study by performing genetic analysis of DNA samples from patients with developmental disorders, and their parents, recruited into the study through the Regional Genetics Services. Using microarray technology and the latest DNA sequencing methods, research teams will probe genetic information to identify mutations (DNA errors or rearrangements) and establish if these mutations play a role in the developmental disorders observed in patients. The DDD initiative grew out of the groundbreaking DECIPHER database, a global partnership of clinical genetics centres set up in 2004, which allows researchers and clinicians to share clinical and genomic data from patients worldwide. The DDD study aims to transform the power of DECIPHER as a diagnostic tool for use by clinicians. As well as improving patient care, the DDD team will empower researchers in the field by making the data generated securely available to other research teams around the world. By assembling a solid resource of high-quality, high-resolution and consistent genomic data, the leaders of the DDD study hope to extend the reach of DECIPHER across a broader spectrum of disorders than is currently possible.

Proper citation: Deciphering Developmental Disorders (RRID:SCR_006171) Copy   

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http://www.crowdlabs.org/

A social visualization repository for the scientific workflow management system VisTrails providing a platform for sharing and executing computational tasks. It adopts the model used by social Web sites and that integrates a set of usable tools and a scalable infrastructure to provide an environment for scientists to collaboratively analyze and visualize data. crowdLabs aims to foster collaboration but was specifically designed to support the needs of computational scientists, including the ability to access high-performance computers and manipulate large volumes of data. By providing mechanisms that simplify the publishing and use of analysis pipelines, it allows IT personnel and end users to collaboratively construct and refine portals. This lowers the barriers for the use of scientific analyses and enables broader audiences to contribute insights to the scientific exploration process, without the high costs incurred by traditional portals. In addition, it supports a more dynamic environment where new exploratory analyses can be added on-the-fly.

Proper citation: crowdLabs (RRID:SCR_006294) Copy   

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http://vizhub.wustl.edu

A visualization hub displaying sequencing data from the Roadmap Epigenomics project. It hosts high volume of tracks from ENCODE and Roadmap Epigenomics projects, supports multiple organisms, visualizes chromatin-interaction data (e.g. Hi-C), performs gene set view, gene plot, and many others. All delivered on the web at high performance.

Proper citation: VizHub (RRID:SCR_006209) Copy   

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