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http://www.hbpp.org/

An open international project under the patronage of the Human Proteome Organisation (HUPO) that aims: To analyze the brain proteome of human as well as mouse models in healthy, neurodiseased and aged status with focus on Alzheimer's and Parkinson's Disease; To perform quantitative proteomics as well as complementary gene expression profiling on disease-related brain areas and bodily fluids; To advance knowledge of neurodiseases and aging in order to push new diagnostic approaches and medications; To exchange knowledge and data with other HUPO projects and national / international initiatives in the neuroproteomic field; To make neuroproteomic research and its results available in the scientific community and society. Recent work has shown that standards in proteomics and especially in bioinformatics are mandatory to allow comparable analyses, but still missing. To address this challenge, the HUPO BPP is closely working together with the HUPO Proteome Standards Initiative (HUPO PSI).

Proper citation: HUPO Brain Proteome Project (RRID:SCR_007302) Copy   

•   Source: SciCrunch Registry

http://celldesigner.org/

CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks. Networks are drawn based on the process diagram, with graphical notation system proposed by Kitano, and are stored using the Systems Biology Markup Language (SBML), a standard for representing models of biochemical and gene-regulatory networks. Networks are able to link with simulation and other analysis packages through Systems Biology Workbench (SBW). By using CellDesigner, you can browse and modify existing SBML models with references to existing databases, simulate and view the dynamics through an intuitive graphical interface. Sponsors: ERATO-SORST program (JST); International Standard Development area of the International Joint Research Grant (NEDO); Strategic Japanese-Swedish Cooperative Program on Multidisciplinary BIO (JST-VINNOVA/SSF); Establishment of a Human Genome Network Platform (MEXT) and through the special coordination funds for promoting science and technology from the Japanese government''s Ministry of Education, Culture, Sports, Science and Technology (MEXT) Keywords: Cell, Designer, Gene, Biochemical, Network, Diagram, Biology, System, Gene, Biolohy, Database,

Proper citation: CellDesigner: A modeling tool of biochemical networks (RRID:SCR_007263) Copy   

•   Source: SciCrunch Registry

http://www.andp.org/

The mission of the Association for Neuroscience Departments and Programs is to advance education and research training in academic neuroscience. We serve member programs and their trainees by maintaining a searchable directory of neuroscience training programs in North America and around the globe. An important goal for the ANDP is disseminate information about neuroscience education and training, and this is achieved through Fall and Spring meetings as well as electronic resource development. We perform a biannual survey of neuroscience education and training that provides key information on current trends in trainees, faculty and programs. Outstanding neuroscience educators are recognized with an annual ANDP award. Active ANDP members create an advocacy group for neuroscience that informs policy makers about neuroscience research and workforce needs. We work to be the stewards of the discipline..

Proper citation: Association of Neuroscience Departments and Programs (RRID:SCR_007386) Copy   

•   Source: SciCrunch Registry

http://www.aesnet.org/

The American Epilepsy Society promotes research and education for professionals dedicated to prevention, treatment and cure of epilepsy. American Epilepsy Society members work to improve the quality of life for people with epilepsy. In the support of its members, AES is committed to providing those engaged in research with information and assistance of potential benefit in advancing their work. AES also has formed alliances with other organizations that provide research funding, including the Grass Foundation, Epilepsy Foundation, and other funding sources. Keywords: American, Epilepsy, Society, Research, Education, Professional, Prevention, Treatment, Cure, Member, Benefit,

Proper citation: American Epilepsy Society (RRID:SCR_007262) Copy   

•   Source: SciCrunch Registry

http://www.thoracic.org

The roots of the American Thoracic Society reach back to 1905, when a small group of physicians decided that the best way to improve care for tuberculosis patients was to share their experiences and discoveries. Today, the ATS has grown into an international society with more than 15,000 members. In this introductory section, you will find information about the people and programs that make the ATS the world''s leading medical association dedicated to advancing our clinical and scientific understanding of pulmonary diseases, critical illnesses and sleep-related breathing disorders. It created a new program to enhance the Societys commitment to discovering new knowledge and advancing patient care. Over the last seven years, the ATS Research Program has grown tremendously, providing more than 7.5 million in grants to 76 young researchers investigating a wide spectrum of lung diseases, ranging from asthma and COPD to pulmonary fibrosis and alpha-1 antitrypsin. The program has also funded the career development of 24 pulmonary and critical care fellows. A main purpose of the American Thoracic Society is to foster the gathering, evaluating, and disseminating of scientific and clinical information. This part of the ATS Website contains clinical information arranged by topic. Most of the information is developed and contributed by the scientific assemblies of the American Thoracic Society.

Proper citation: American Thoracic Society (RRID:SCR_007261) Copy   

•   Source: SciCrunch Registry

http://ndg.sfn.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on September 06, 2013. Resource aimed at promoting awareness and facilitating access to online neuroscience databases.

Proper citation: Neuroscience Database Gateway (RRID:SCR_007297) Copy   

•   Source: SciCrunch Registry

http://www.birncommunity.org/collaborators/function-birn/

The FBIRN Federated Informatics Research Environment (FIRE) includes tools and methods for multi-site functional neuroimaging. This includes resources for data collection, storage, sharing and management, tracking, and analysis of large fMRI datasets. fBIRN is a national initiative to advance biomedical research through data sharing and online collaboration. BIRN provides data-sharing infrastructure, software tools, strategies and advisory services - all from a single source.

Proper citation: Function BIRN (RRID:SCR_007291) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/evora/

R package for quantifying variation in DNA methylation as a cancer biomarker.

Proper citation: EVORA (RRID:SCR_007329) Copy   

•   Source: SciCrunch Registry

http://www.nntc.org/

Collects, stores, and distributes samples of nervous tissue, cerebrospinal fluid, blood, and other tissue from HIV-infected individuals. The NNTC mission is to bolster research on the effects of HIV infection on human brain by providing high-quality, well-characterized tissue samples from patients who died with HIV, and for whom comprehensive neuromedical and neuropsychiatric data were gathered antemortem. Researchers can request tissues from patients who have been characterized by: * degree of neurobehavioral impairment * neurological and other clinical diagnoses * history of drug use * antiretroviral treatments * blood and CSF viral load * neuropathological diagnosis The NNTC encourages external researchers to submit tissue requests for ancillary studies. The Specimen Query Tool is a web-based utility that allows researchers to quickly sort and identify appropriate NNTC specimens to support their research projects. The results generated by the tool reflect the inventory at a previous time. Actual availability at the local repositories may vary as specimens are added or distributed to other investigators.

Proper citation: National NeuroAIDS Tissue Consortium (RRID:SCR_007323) Copy   

•   Source: SciCrunch Registry

http://seurat.r-forge.r-project.org/

Software tool which provides interactive visualization capability for the integrated analysis of high-dimensional gene expression data. Visual analytics for the integrated analysis of microarray data.

Proper citation: SEURAT (RRID:SCR_007322) Copy   

•   Source: SciCrunch Registry

http://www.nih.gov/science/models/

Information about national and international activities and major resources that are being developed to facilitate biomedical research using animal models Mammalian Models: * Mouse * Rat Non-Mammalian Models * S. cerevisiae (budding yeast) * S.pombe (Fission Yeast) * Neurospora (filamentous fungus) * D. discoideum (social amoebae) * C. elegans (round worm) * Daphnia * D. melanogaster (fruit fly) * D. rerio (zebrafish) * Xenopus (frog) * Gallus (chicken) Other Model Organisms: * Arabidopsis

Proper citation: Model Organisms for Biomedical Research (RRID:SCR_007282) Copy   

•   Source: SciCrunch Registry

http://www.nervenet.org

Portal to neurogenetic resources: the mouse brain library, digital atlases of the mouse brain, extensive brain microarray data in WebQTL, and internet access to microscopes and stereology tools.Mouse Brain Library. Mouse Brain Library is an expanding collection of high-resolution histological images, atlases, MRIs, and databases on brain structure of more than 120 different lines of mice. Nervenet also includes several useful genetics and gene mapping databases to download (SNP databases, Map Manager databases, and the Portable Dictionary of the Mouse Genome). The publications section includes revised, expanded, and annotated papers, tutorials, and reviews on neurogenetics, gene mapping, complex trait analysis, stereology, and the control of neuron number.

Proper citation: Neurogenetics Online (RRID:SCR_007280) Copy   

•   Source: SciCrunch Registry

http://www.cerefy.com/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 19, 2015. Commercial brain atlases distributed by Theime Medical Publishers. It supports a complete electronic version of the Talairach Atlas, as well as gyral-level description of the human brain and atlases for cerebral vasculature, cranial nerves and a probabilistic functional atlas. In addition, this tool permits the incorporation of user image data, both structural and functional, into the viewer for direct co-visualization with the atlas. This CD-ROM provides numerous tools for the analysis of functional images: It contains the fully color-coded and labeled Talairach-Tournoux brain atlas in the axial, coronal and sagittal orientations, along with Brodmann''s areas and gyri in the axial orientation. -Allows anatomical and functional images to be loaded and registered. -Enables interactive placement of the Talairach landmarks in 3D Space. -Provides automatic data-to-atlas warping based on the Talairaich proportional grid system transformation. In addition, real-time interactive warping for fine tuning is available. -Allows the user to place marks on the activation loci in the warped functional images, display these marks with the atlas, and edit them simultaneously on the axial, cornal and sagittal orientations. Mark placement is assisted by a grey-value thresholding feature. -Provides simultaneous display of the atlas, anatomical image and functional image withing one interactively blended image. Atlas-data blending and anatomical-functional image blending are controlled independently. -Labels the data by means of the atlas. The atlas can be flipped left/right so that Brodmann''s areas areas and gyri can be labeled on both hemispheres. -Provides additional functions such as friendly navigation, simultaneous display of axial, coronal and sagittal atlas plates, cross-referenced display, image and atlas sequencing, readout of the Talairach coordinates and intensities, save, print, help.

Proper citation: Brain Atlas for Functional Imaging (RRID:SCR_007356) Copy   

•   Source: SciCrunch Registry

http://www.cmc.ca/

CMC Microsystems enables and supports the creation and application of micro- and nano-system knowledge by providing a national infrastructure for excellence in research and a path to commercialization of related devices, components and systems. CMC Microsystems provides the tools, technologies and services that make microsystems research and development possible in universities across Canada. CMC delivers innovative and cost-effective services to a growing community of microsystems researchers that connect 43 universities and one college across Canada, and presently involves over 3,100 faculty and graduate students. A 4th Pillar organization stimulating synergistic collaboration among universities, companies and government agencies, CMC is a pioneer in developing creative solutions including Canada-wide Internet-based access to advanced microsystems testing facilities-at a fraction of the cost of conventional methods. Over the last five years, CMC delivered a value of 342 million to Canadian universities. Throughout the last 25 years CMC has successfully demonstrated the ability to specify, acquire and distribute all the necessary tools and technologies to design, make and test microsystems devices, components and systems and in the last five years has significantly expanded its skill base and partnerships. CMC has also developed a series of key relationships with suppliers which have enabled smooth and uninterrupted access to the latest tools and technologies. The governance structure is widely viewed as one of the soundest among organizations of this type and the management team of five people has a total experience of well over 100 years in the microsystems field.

Proper citation: Canadian Microelectronics Corporation Microsystems (RRID:SCR_007234) Copy   

•   Source: SciCrunch Registry

http://isda.ncsa.uiuc.edu/NARA/csrAbout.html

Conversion Software Registry (CSR) has been designed for collecting information about software packages that are capable of file format conversions. The work is motivated by a community need for finding file format conversions inaccessible via current search engines and by the specific need to support systems that could actually perform conversions, such as the NCSA Polyglot. In addition, the value of CSR is in complementing the existing file format registries and introducing software quality information obtained by content-based comparisons of files before and after conversions. The contribution of this work is in the CSR data model design that includes file format extension based conversion, as well as software scripts, software quality measures and test file specific information for evaluating software quality. The CSR system serves as the source of information and a test bed for the system that can execute the conversions automatically by using the third party software, for example, NCSA Polyglot. The CSR system is a database with a web-based interface that provides services related to a) finding a conversion path between formats b) uploading information about the 3rd party software packages and file extensions, c) uploading files for testing, and finally d) uploading scripts in operating system (OS) specific scripting languages (Windows AutoHotKey, AppleScript and Perl) for automated conversions according to the idea of imposed code reuse used by NCSA Polyglot. In order to provide file format conversion services, CSR have included the following components into CSR related to software capable of conversions: input and output file formats (extensions), scripts operating on the software, validated files to be used for information loss measurements, as well as quantitative measures of the information loss for conversions. The CSR focuses: on software and finding the format conversion paths described by a number of software packages and unique input and output formats. The formats themselves are represented by extensions. While not always unique, extensions are often the only accessible information when the 3rd party software is installed (often listed under the File/Open menu in most packages). The CSR also contains information about the software, operating system, software interface and scripts to execute the software. The scripts are important for the automating conversions with the 3rd party software and can be implemented using AutoHotkey scripts (Windows), AppleScript (Mac) or one of a variety of scripting languages for Unix. The information loss due to file format conversions is measured externally by different techniques within the NCSA object-to-object comparison framework called Versus. The comparison is relevant to the software domain, for example for 3D applications surface area or spin images are used and the loss (0-100 range with 100 representing no loss) for a particular software-conversion pair is stored in the database. The information loss also represents edge weights to Input/Output (I/O) Graph, a simple workflow used for finding the shortest conversion path. The CSR is written as a web service. It consists of three main components: Query, Add, Edit. In the Query mode users can a) view list of all software packages with their conversion options, b) select subsets of software in the I/O-Graph, c) search the database by conversions, software, extensions, MIME and PUID. The I/O-Graph contains all information about installed applications and the conversions they allow. The JAVA applet front end is part of the CSR web visualization interface. Section Add allows users to add new software packages with their conversion capabilities and upload the software scripts to automate them. The last section, Edit is designed for adding detailed information about the software, extensions and for uploading the test files. CSR requires users to login for adding and editing. The web fields are auto completed to help search. Sponsors: This research was partially supported by a National Archive and Records Administration (NARA) supplement to NSF PACI cooperative agreement CA #SCI-9619019. Keywords: Software, Registry, Information, Conversion, Database, Tool

Proper citation: Conversion Software Registry (RRID:SCR_007236) Copy   

•   Source: SciCrunch Registry

http://www.brainvisa.info/

BrainVISA is a modular an customizable software platform built to host heterogeneous tools dedicated to neuroimaging research. Many toolboxes have already been developed for BrainVISA (T1 MRI, sulcal identification and morphometry, cortical surface analysis, diffusion imaging and tractography, fMRI, nuclear imaging, EEG and MEG, TMS, histology and autoradiography, etc.). Anatomist is a software for interactive visualization of multimodal data and for manipulation of structured 3D objects. It allows to build scenes that merge or combine images, meshes, regions of interest, fibers, textures, color palettes, referential changes, etc. A user can interact in 3D and in real time with the objects of an Anatomist scene: change point of view, select objects, add/suppress objects, change colors, draw regions of interests, do manual registration, etc. BrainVISA main features are: * Harmonization of communications between different software. For instance, BrainVISA toolboxes are using home-made software but also third-party software such as FreeSurfer, FSL, SPM, nipy, R-project, Matlab, etc. * Ontology-based data organization allowing database sharing and automation of mass of data analysis. * Fusion and interactive visualization of multimodal data (using Anatomist software). * Automatic generation of graphical user interfaces. * Workflow monitoring and data quality checking. * Full customization possible. * Runs on Linux, Mac and Windows. * Programming Language: C++, Python * Supported Data Format: ANALYZE, DICOM, GIfTI, MINC, NIfTI-1, Other Format

Proper citation: BrainVISA / Anatomist (RRID:SCR_007354) Copy   

•   Source: SciCrunch Registry

http://www.fei.com/software/amira-3d-for-life-sciences/

Software tool for visualizing, manipulating, and understanding data from tomography, microscopy, MRI and other imaging processes.Used to import and export options, to processes 3D image filtering and DTI based fiber tracking to visualization, volume and surface rendering, author tools for virtual reality navigation, video generation, and more.

Proper citation: Advanced 3D Visualization and Volume Modeling (RRID:SCR_007353) Copy   

•   Source: SciCrunch Registry

https://cgc.umn.edu

Center that acquires, maintains, and distributes genetic stocks and information about stocks of the small free-living nematode Caenorhabditis elegans for use by investigators initiating or continuing research on this genetic model organism. A searchable strain database, general information about C. elegans, and links to key Web sites of use to scientists, including WormBase, WormAtlas, and WormBook are available.

Proper citation: Caenorhabditis Genetics Center (RRID:SCR_007341) Copy   

•   Source: SciCrunch Registry

http://fmri.wfubmc.edu/software/PickAtlas

A software toolbox that provides a method for generating Region of Interest (ROI) masks based on the Talairach Daemon database. The atlases include Brodmann area, Lobar, Hemisphere, Anatomic Label (gyral anatomy), and Tissue type. The atlases have been extended to the vertex in MNI space, and corrected for the precentral gyrus anomaly. Additional atlases (including non-human atlases) can be added without difficulty., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: WFU PickAtlas (RRID:SCR_007378) Copy   

•   Source: SciCrunch Registry

http://booly.ucsd.edu

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A database tool that allows for any combination of the Boolean operations union/disjunction (OR), intersection/conjunction (AND), and subtraction/negation (NOT) to be performed on multiple datasets. Booly brings the power of biological data integration to the researcher by helping researchers analyze and integrate their data. Booly offers a simple contribution model, where users can simply cut and paste spreadsheet data to create new datasets that could thereafter be stored, shared, and compared. Users may also take advantage of publically available datasets created by other members such as Gene Ontology datasets and species-species BLAST datasets.

Proper citation: Booly: A Resource for Biological Data Integration (RRID:SCR_007373) Copy   

•   Source: SciCrunch Registry