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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14, 2026. Software tools which can perform Stochastic Tractography and related analysis on DWMRI data. Stochastic Tractography applies a Bayesian approach towards the estimation of nerve fiber tracts from DWMRI images.

Proper citation: Stochastic Tractography System (RRID:SCR_002594) Copy   

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http://liquidpub.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 08, 2014. Project proposing a "liquid" format for science papers that consists of a set of research objects, connected by links. The immediate targets are the scientific research communities including publishers that, in a liquid world, will need to develop novel services and business models. Results and additional reading material (case studies, surveys, and the like) will be made available. The project also is creating an open source development effort and a platform to manage liquid publications and their evaluation. Their current main effort is developing the Liquid Journal and Liquid Conference use cases.

Proper citation: Liquid Publications: Scientific Publications meet the Web (RRID:SCR_002471) Copy   

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

Software package representing Spatial Statistical Parametric Mapping that includes two tools presently: MAGEE and FADTTS. MAGEE represents the Multiscale Adaptive Generalized Estimating Equation. It was developed specifically for analyzing multivariate neuroimaging data in 3-dimensional volume (or on 2-dimensional surface) from longitudinal neuroimaging studies. FADTTS represents Functional Analysis of Diffusion Tensor Tract Statistics. The aim of this tool is to implement a functional analysis pipeline, for delineating the structure of the variability of multiple diffusion properties along major white matter fiber bundles and their association with a set of covariates of interest, in various diffusion tensor imaging studies.

Proper citation: Spatial Statistical Parametric Mapping (RRID:SCR_002592) Copy   

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http://mialab.mrn.org/software/eegift/index.html

Implements multiple algorithms for independent component analysis and blind source separation of group (and single subject) EEG data. This MATLAB toolbox is compatible with MATLAB 6.5 and higher.

Proper citation: Group ICA Of EEG Toolbox (RRID:SCR_002478) Copy   

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http://brainproducts.com/productdetails.php?id=17

Software to manage the daily work of analyzing various neurophysiological data. Features include a history tree, automated analysis, various data format readers, and more.

Proper citation: BrainVision Analyzer (RRID:SCR_002356) Copy   

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http://commons.esipfed.org/datamanagementshortcourse

ESIP Federation training courses to improve the understanding of scientific data management among scientists, emerging scientists, and data professionals. The ESIP Federation, in cooperation with NOAA, seeks to share the community's knowledge with scientists who increasingly need to be better data managers, as well as to support workforce development for new data management professionals.

Proper citation: ESIP Data Management Short Course for Scientists (RRID:SCR_002597) Copy   

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

A brain imaging classification tool, which can help researchers to discriminate patients from normal controls. The M3 includes three steps: feature selection, maximum uncertainty linear discriminant analysis (MLDA)-based classification and multi-classifier. A leave-one-out cross-validation (LOOCV) is further used to estimate the performance of the M3. Finally, the most discriminative features are identified.

Proper citation: M3 (RRID:SCR_002475) Copy   

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http://fged.org/projects/miame/

Standard specification for the Minimum Information About a Microarray Experiment that is needed to enable the interpretation of the results of the experiment unambiguously and potentially to reproduce the experiment.

Proper citation: MIAME (RRID:SCR_002349) Copy   

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http://www.Ablynx.com

A biopharmaceutical company engaged in the discovery and development of Nanobodies, a novel class of antibody-derived therapeutic proteins based on single-domain antibody fragments, for a range of serious life-threatening human diseases including inflammation, hematology, oncology and pulmonary disease.

Proper citation: Ablynx (RRID:SCR_002940) Copy   

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http://perso.telecom-paristech.fr/~cardoso/guidesepsou.html

Blind Source Separation and Independent Component Analysis (ICA) algorithms including: An efficient batch algorithm: JADE and Adaptive algorithms: relative gradient algorithms. Associated papers / documentation are included as well as thoughts on Multi-dimensional independent component analysis. * An efficient batch algorithm: JADE - For off-line ICA, an algorithm has been developed based on the (joint) diagonalization of cumulant matrices. "Good" statistical performance is achieved by involving all the cumulants of order 2 and 4 while a fast optimization is obtained by the device of joint diagonalization. JADE has been successfully applied to the processing of real data sets, such as found in mobile telephony and in airport radar as well as to bio-medical signals (ECG, EEG, multi-electrode neural recordings). The strongest point of JADE for applications of ICA is that it works off-the-shelf (no parameter tuning). They advocate using the code provided as a plug-in replacement for PCA (whenever one is willing to investigate if such a replacement is appropriate). The weakest point of the current implementation is that the number of sources (but not of sensors) is limited in practice (by the available memory) to something like 40 or 50 depending on your computer. The JADE algorithm was originally developed to process complex signals, motivated by applications to digital communications. Another implementation is now available which is tuned to process more efficiently real-valued signals. * Adaptive algorithms: relative gradient algorithms - For adaptive source separation, they have developed a class of equivariant algorithms. This means that their performance is independent of the mixing matrix. They are obtained as stochastic relative gradient algorithms. * Multi-dimensional independent component analysis - Performing ICA on ECG signals with the JADE algorithm, it was realized that an interesting extension of the notion of independent component analysis would be to consider an analysis into linear components that would be "as independent as possible" as in ICA, but would be "livin" in subspaces of dimension greater than 1. This could be called "MICA" for Multi-dimensional Independent Component Analysis.

Proper citation: Blind Source Separation and Independent Component Analysis (RRID:SCR_002812) Copy   

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http://www.ataxia.org/

Membership supported, nonprofit organization established dedicated to improving the lives of persons affected by ataxia through support, education, and research. The Foundation's primary purpose is to support promising ataxia research and to provide vital programs and services for ataxia families. The Foundation first began direct funding of ataxia research through the NAF Research Seed-Money Program. Since that time, the Foundation has established additional research programs which have included programs such as the NAF Young Investigator Award, the NAF Fellowship Award and other research initiatives. NAF research programs continue to fund promising ataxia research studies throughout the world. The Foundation supports research in dominant ataxia (including SCAs), recessive ataxia (including Friedreich's) and sporadic ataxia. The Foundation has developed an extensive library of NAF brochures, fact sheets, books, and videos on ataxia. Also available to its members is the Foundation's quarterly news publication, Generations. This 48 page ataxia news magazine provides the latest information on ataxia research, articles on living with ataxia, personal accounts from ataxia families throughout the United States, and much more.

Proper citation: National Ataxia Foundation (RRID:SCR_002933) Copy   

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http://microcal-origin.software.informer.com/

A complete graphing and data analysis software package that provides a suite of features catering to the needs of scientists and engineers. Main features: * Drag-and-drop import of data and images * Save import settings to a worksheet or external files for repeated use * Use saved settings to re-import files with a single click * Post-process imported data * Import Wizard with visual feedback * Handle non-standard files by programming

Proper citation: Microcal Origin (RRID:SCR_002815) Copy   

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http://www.bioconductor.org/packages/devel/bioc/html/CGHnormaliter.html

Software for normalization and centralization of array comparative genomic hybridization (aCGH) data with imbalanced aberrations. The algorithm uses an iterative procedure that effectively eliminates the influence of imbalanced copy numbers. This leads to a more reliable assessment of copy number alterations (CNAs).

Proper citation: CGHnormaliter (RRID:SCR_002936) Copy   

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http://www.loni.usc.edu/Software/MBAT

Workflow environment bringing together heterogenous, online biological image resources, a user's image data and biological atlases in a concise, unified and intuitive workspace. The MBAT viewer displays multiple images on a single virtual canvas allowing easy side-by-side comparisons and image compositing. MBAT is written in Java so it is platform independent and is highly extensible through it's plugin architecture. MBAT integrates three distinct workspaces for online search, image alignment (registration) and image display: * Search Workspace: able to submit a query to multiple databases simultaneously and online literature searches. * Registration Workspace: performs 2D landmark based registration. * Viewer Workspace: displays & composites images and image volumes using high performance graphics hardware. * Atlas Viewer: allows navigation and interrogation of volumetric atlases. * Hierarchy Editor: create logical groupings of atlas labels.

Proper citation: Mouse BIRN Atlasing Toolkit (RRID:SCR_002814) Copy   

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http://www.training.nih.gov/

Division of the Office of Intramural Research (OIR), Office of the Director (OD) which provides services to current trainees in programs in the NIH Intramural Research Program, potential applicants to training programs at the NIH, investigators and staff at the NIH, and trainees and investigators outside the NIH.

Proper citation: Office of Intramural Training and Education (RRID:SCR_002934) Copy   

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http://sourceforge.net/projects/b-o-s-s/

Batch primer selection software program designed to select PCR oligos for gap closure for assemblies containing a large number of gaps. It will select oligos for gap closure of both contig and scaffold gaps.

Proper citation: Batch Oligo Selection Script (RRID:SCR_002808) Copy   

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http://rana.lbl.gov/drosophila

A single source for sequences, assemblies, annotations and analyses of the genomes of members of the fruitfly genus Drosophlia. It is meant as resource for Drosophilists and other researchers interested in comparative analysis of these species and their genomes. There are pages for each species, as well as pages for different types of multi-species resources (e.g. alignments). If you have a public resource that will help this project, please consider making it available through this page by emailing multiple_at_fruitfly.org.

Proper citation: Assembly/Alignment/Annotation of 12 Related Drosophila Species (RRID:SCR_002921) Copy   

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http://www.brainscape.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 23, 2013. Database for resting state functional connectivity studies. Functional connectivity has shown tremendous promise in mapping the intrinsic functional topography of the brain, evaluating neuroanatomical models, and investigating neurological and psychiatric disease. Brainscape includes a repository of public and private data and an analysis engine for exploring the correlation structure of spontaneous fluctuations in the fMRI BOLD signal. (DICOM data is the image format that can be uploaded.) With Brainscape you can upload, analyze, and share your own data. You can search for, download, and analyze studies in the repository of shared data. The analysis engine works by selecting one or more studies, typing in the coordinates of a brain region of interest, and the seed-region correlation engine computes the correlation structure across the whole brain. (T1, T2 and EPI data are the scan types Brainscape can process.) You decide who can access your data. You can keep it to yourself, share with select colleagues, or share it with everyone. The Brainscape database and analysis tools are open source and freely available.

Proper citation: Brainscape (RRID:SCR_002962) Copy   

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http://www.grassfoundation.org/

The Grass Foundation is a small, not-for-profit, private foundation chartered to support research and education in neuroscience. The hallmark program of The Grass Foundation is the Grass Fellowship Program at the Marine Biological Laboratory in Woods Hole, Massachusetts. This program provides a first opportunity for neuroscientists during late stages of predoctoral training or during postdoctoral years to conduct independent research for scientific discovery on their own at the MBL each summer. While sharing the Grass Laboratory, Fellows function as an intellectual and social group within the MBL community. The number of fellowships awarded varies annually. Additional programs supported by The Grass Foundation include the Robert S. Morison Fellowship, The Grass-MBL Faculty Grant Program, the Ricardo Miledi Program for Neuroscience Training, several neuroscience courses at the MBL, and yearly funding of a few lectureships and prizes. Please see our Program Grants section for more information.

Proper citation: Grass Foundation (RRID:SCR_002960) Copy   

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http://bioportal.bioontology.org/

Open repository of biomedical ontologies that provides access via Web browsers and Web services to ontologies. It supports ontologies in OBO format, OWL, RDF, Rich Release Format (RRF), Protege frames, and LexGrid XML. Functionality includes the ability to browse, search and visualize ontologies as well as to comment on, and create mappings for ontologies. Any registered user can submit an ontology. The NCBO Annotator and NCBO Resource Index can also be accessed via BioPortal. Additional features: * Add Reviews: rate the ontology according to several criteria and describe your experience using the ontology. * Add Mappings: submit point-to-point mappings or upload bulk mappings created with external tools. Notification of new Mappings is RSS-enabled and Mappings can be browsed via BioPortal and accessed via Web services. * NCBO Annotator: Tool that tags free text with ontology terms. NCBO uses the Annotator to generate ontology annotations, creating an ontology index of these resources accessible via the NCBO Resource Index. The Annotator can be accessed through BioPortal or directly as a Web service. The annotation workflow is based on syntactic concept recognition (using the preferred name and synonyms for terms) and on a set of semantic expansion algorithms that leverage the ontology structure (e.g., is_a relations). * NCBO Resource Index: The NCBO Resource Index is a system for ontology based annotation and indexing of biomedical data; the key functionality of this system is to enable users to locate biomedical data linked via ontology terms. A set of annotations is generated automatically, using the NCBO Annotator, and presented in BioPortal. This service uses a concept recognizer (developed by the National Center for Integrative Biomedical Informatics, University of Michigan) to produce a set of annotations and expand them using ontology is_a relations. * Web services: Documentation on all Web services and example code is available at: BioPortal Web services.

Proper citation: BioPortal (RRID:SCR_002713) Copy   

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