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http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=1

International society dedicated to advancing understanding of anatomical and functional organization of human brain using neuroimaging. Primary function of society is to provide educational forums for exchange of up-to-the-minute and groundbreaking research across neuroimaging methods and applications. OHBM achieves this through its member led committees and Annual Meeting that is held in different locations throughout the world.

Proper citation: Organization for Human Brain Mapping (RRID:SCR_001978) Copy   

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http://www.neuralgate.org/download/NeuralAct

Software to visualize electrocorticographic (ECoG) and possibly also other kinds of neural activity (EEG / EMG/ DOT) on a 3D model of the cortical surface. The tool has been used to produce cortical activation images and image sequences in several recent studies using ECoG. The tool is written in matlab. The package is thoroughly documented and includes a demo.

Proper citation: NeuralAct (RRID:SCR_002066) Copy   

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https://cran.r-project.org/src/contrib/Archive/PurBayes/

An MCMC-based algorithm that uses next-generation sequencing data to estimate tumor purity and clonality for paired tumor-normal data.

Proper citation: PurBayes (RRID:SCR_002068) Copy   

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http://adrc.ucsd.edu/

The UCSD ADRC conducts a wide variety of research studies dedicated to understanding the causes, clinical features, and treatments for Alzheimer's disease and related memory disorders. The goal of the center is to discover ways to prevent and eradicate the disease. The Center aims to maintain research subjects, clinical resources, and clinical data to support ongoing and proposed research and to assist in the development of new clinical and interdisciplinary research. An Alzheimer's brain bank with well characterized cases, including Mild Cognitive Impairment and Lewy Body disease, is maintained at the Center.

Proper citation: Shiley-Marcos Alzheimer's Disease Research Center (RRID:SCR_001928) Copy   

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http://www.doe-mbi.ucla.edu/

The UCLA-DOE Institute for Genomics and Proteomics carries out research in bioenergy, structural biology, genomics and proteomics, consistent with the research mission of the United States Department of Energy. Major interests of the 12 Principal Investigators and 9 Associate Members include systems approaches to organisms, structural biology, bioinformatics, and bioenergetic systems. The Institute sponsors 5 Core Technology Centers, for X-ray and NMR structural determination, bioinformatics and computation, protein expression and purification, and biochemical instrumentation. Services offered by this Institute: - Databases: * DIP (The Database of Interacting Proteins): The DIPTM database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. * ProLinks Database of Functional Linkages: The Prolinks database is a collection of inference methods used to predict functional linkages between proteins. These methods include the Phylogenetic Profile method which uses the presence and absence of proteins across multiple genomes to detect functional linkages; the Gene Cluster method, which uses genome proximity to predict functional linkage; Rosetta Stone, which uses a gene fusion event in a second organism to infer functional relatedness; and the Gene Neighbor method, which uses both gene proximity and phylogenetic distribution to infer linkage. - Data-to-Structure Servers: * SAVEs Structure Verification Server * Merohedral Twinning Test Server * SER Surface Entropy Reduction Server * VERIFY3D Structure Verification Server * ERRAT Structure Verification Server - Structure-to-Function Servers: * ProKnow Protein Functionator * Hot Patch Functional Site Locator

Proper citation: University of California at Los Angeles - Department of Energy Institute for Genomics and Proteomics (RRID:SCR_001921) Copy   

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http://www.mevislab.de/index.php?id=6

Modular framework for the development of image processing algorithms and visualization and interaction methods, with a special focus on medical imaging. It includes advanced medical imaging modules for segmentation, registration, volumetry, and quantitative morphological and functional analysis. The platform allows fast integration and testing of new algorithms and the development of application prototypes that can be used in clinical environments. In MeVisLab, individual image processing, visualization and interaction modules can be combined to complex image processing networks using a graphical programming approach. The algorithms can easily be integrated using a modular, platform-independent C++ class library. An abstract, hierarchical definition language allows the design of efficient graphical user interfaces, hiding the complexity of the underlying module network to the end user. JavaScript components can be added to implement dynamic functionality on both the network and the user interface level. MeVisLab is based on the Qt application framework, the OpenInventor 3D visualization toolkit and OpenGL. Several clinical prototypes have been realized on the basis of MeVisLab, including software assistants for neuro-imaging, dynamic image analysis, surgery planning, and vessel analysis. Feature Overview: :- Basic image processing algorithms and advanced medical imaging modules :- Full featured, flexible 2D/3D visualization and interaction tools :- High performance for large datasets :- Modular, expandable C++ image processing library :- Graphical programming of complex, hierarchical module networks :- Object-oriented GUI definition and scripting :- Full scripting functionality using Python and JavaScript :- DICOM support and PACS integration :- Intuitive user interface :- Integrated movie and screenshot generation for demonstration purposes :- Generic integration of the Insight Toolkit (ITK) and the Visualization Toolkit (VTK) :- Cross-platform support for Windows, Linux, and MacOS X :- Available for 64-bit operating systems

Proper citation: Medical Image Processing and Visualization (RRID:SCR_002055) Copy   

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https://netbio.bgu.ac.il/tissuenet3/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on 7/15/13. The Nation's one-stop resource for information about substance abuse prevention and addiction treatment offering more than 500 items to the public, many of which are free of charge. They distribute the latest studies and surveys, guides, videocassettes, and other types of information and materials on substance abuse from various agencies, such as the U.S. Departments of Education and Labor, the Center for Substance Abuse Prevention, the Center for Substance Abuse Treatment, the National Institute on Alcohol Abuse and Alcoholism, and the National Institute on Drug Abuse. They staff both English- and Spanish-speaking information specialists who are skilled at recommending appropriate publications, posters, and videocassettes; conducting customized searches; providing grant and funding information; and referring people to appropriate organizations. They are available 24 hours a day, 7 days a week to take your calls at 1-800-729-6686. NCADI services include: * an information services staff (English, Spanish, TDD capability) equipped to respond to the public's alcohol, tobacco, and drug (ATD) inquiries; * the distribution of free or low-cost ATD materials, including fact sheets, brochures, pamphlets, monographs, posters, and video tapes from an inventory of over 1,000 items; * a repertoire of culturally-diverse prevention, intervention, and treatment resources tailored for use by parents, teachers, youth, communities and prevention/treatment professionals; * customized searches in the form of annotated bibliographies from alcohol and drug data bases; * access to the Prevention Materials database (PMD) including over 8,000 prevention-related materials and the Treatment Resources Database, available to the public in electronic form; * rapid dissemination of Federal grant announcements for ATD prevention, treatment, and research funding opportunities.

Proper citation: SAMHSAs National Clearinghouse for Alcohol and Drug Information (RRID:SCR_002053) Copy   

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https://med.stanford.edu/sfgf.html

Stanford Genomics formerly Stanford Functional Genomics Facility provides services for high throughput sequencing, single cell assays, gene expression and genotyping studies utilizing microarray and real time PCR, and related services. High throughput sequencing (Illumina HiSeq 4000, NextSeq 500, MiSeq and MiniSeq), microarray gene expression and genotyping services (Affymetrix, Agilent and Illumina). Provides 24/7 access to instruments, equipment and software utilized within genomics field.

Proper citation: Stanford Genomics Service Center Core Facility (RRID:SCR_002050) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/tbrowse/

Software providing a HTML5/javascript based browser for visualizing RNA-seq results in the familiar track layout of common genome browser. But given the quantitative nature of RNA-seq data, in addition to visualizing sequence coverage, the browser quantitates transcript abundance across regions of interest. The HTML5 functionality is made of use to render all the tracks using the canvas drawing element. This greatly reduces the load on servers and allows for rich interactive graphics without the need for third-party plugins. Furthermore, this framework completely segregates data from visualization, making development much easier. The browser is designed to run on all modern browsers: Firefox, Safari, Chrome, Opera and Internet Explorer (though not recommended).

Proper citation: tbrowse (RRID:SCR_001918) Copy   

•   Source: SciCrunch Registry

https://dataverse.org/

Project portal for publishing, citing, sharing and discovering research data. Software, protocols, and community connections for creating research data repositories that automate professional archival practices, guarantee long term preservation, and enable researchers to share, retain control of, and receive web visibility and formal academic citations for their data contributions. Researchers, data authors, publishers, data distributors, and affiliated institutions all receive appropriate credit. Hosts multiple dataverses. Each dataverse contains studies or collections of studies, and each study contains cataloging information that describes the data plus the actual data files and complementary files. Data related to social sciences, health, medicine, humanities or other sciences with an emphasis in human behavior are uploaded to the IQSS Dataverse Network (Harvard). You can create your own dataverse for free and start adding studies for your data files and complementary material (documents, software, etc). You may install your own Dataverse Network for your University or organization.

Proper citation: Dataverse Network Project (RRID:SCR_001997) Copy   

•   Source: SciCrunch Registry

http://microarrays.curie.fr/publications/U900-RPPA_PLT/Normacurve/

Analysis methodology that allows simultaneous quantification and normalization of reverse phase protein array (RPPA) data.

Proper citation: NormaCurve (RRID:SCR_001995) Copy   

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http://www.math.pitt.edu/~bard/xpp/xpp.html

XPPAUT is a tool for solving differential equations, difference equations, delay equations, functional equations, boundary value problems, and stochastic equations. It evolved from a chapter written by John Rinzel and me on the qualitative theory of nerve membranes and eventually became a commercial product for MSDOS computers called PHASEPLANE. It is now available as a program running under X11 and Windows. The code brings together a number of useful algorithms and is extremely portable. All the graphics and interface are written completely in Xlib which explains the somewhat idiosyncratic and primitive widgets interface. XPP contains the code for the popular bifurcation program, AUTO . Thus, you can switch back and forth between XPP and AUTO, using the values of one program in the other and vice-versa. I have put a ``friendly'' face on AUTO as well. You do not need to know much about it to play around with it. XPP has the capabilities for handling up to 590 differential equations. There are over a dozen solvers including several for stiff systems, a solver for integral equations and a symplectic solver. Up to 10 graphics windows can be visible at once and a variety of color combinations is supported. PostScript output is supported as well as GIF and animator GIF movies Post processing is easy and includes the ability to make histograms, FFTs and applying functions to columns of your data. Equilibria and linear stability as well as one-dimensional invariant sets can be computed. Nullclines and flow fields aid in the qualitative understanding of two-dimensional models. Poincare maps and equations on cylinders and tori are also supported. Some useful averaging theory tricks and various methods for dealing with coupled oscillators are included primarily because that is what I do for a living. Equations with Dirac delta functions are allowable. I have added an animation package that allows you to create animated versions of your simulations, such as a little pendulum moving back and forth or lamprey swimming. See toys! for examples. There is a curve-fitter based on the Marquardt-Levenberg algorithm which lets you fit data points to the solutions to dynamical systems. It is possible to automatically generate "movies'' of three-dimensional views of attractors or parametric changes in the attractor as some parameters vary. Dynamically link to external subroutines XPP has been successfully compiled on a SPARC II under OpenLook, a SPARC 1.5 running generic X, a NeXT running X11R4, a DEC 5000, a PC using Linux or Windows, and SGI and an HP 730. It also runs under Win95/NT/98 if you have an X-Server. I cannot vouch for other platforms but it has been compiled on the IBM RS6000. Building XPP requires only the standard C compiler, and Xlib. Look at the any README files that come with the distribution for solutions to common compilation problems.

Proper citation: XPP-Aut: X-Windows Phase Plane plus Auto (RRID:SCR_001996) Copy   

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https://github.com/xflouris/gapmis

A software tool for pairwise sequence alignment with a single gap.

Proper citation: GapMis (RRID:SCR_001999) Copy   

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http://gara.bio.uci.edu

THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 24, 2017. Database of images depicting the spatial distribution of 2-deoxyglucose uptake evoked in the glomerular layer of the rat olfactory bulb in response to a wide range of defined odorant stimuli. A number of different display and comparison tools are provided allowing patterns to be viewed from different perspectives, and descriptions of the methods and interpretations of these data are provided. Some of the more advanced tools require you to download software.

Proper citation: Glomerular Activity Response Archive (RRID:SCR_002089) Copy   

•   Source: SciCrunch Registry

http://figshare.com/articles/Tool_for_rapid_annotation_of_microbial_SNPs_TRAMS_a_simple_program_for_rapid_annotation_of_genomic_variation_in_prokaryotes_/782261

A software program for functional annotation of genomic single nucleotide polymorphisms (SNPs) which is available to download as a single file executable for WINDOWS users with limited computational experience and as a Python script for Mac OS and Linux users. It needs only a tab delimited text file containing SNP locations, reference nucleotide and SNPs in different strains along with a reference genome sequence in standard GenBank or EMBL format. It annotates SNPs as synonymous, non-synonymous or nonsense. Non-synonymous SNPs in start and stop codons are separated as non-start and non-stop SNPs, respectively. SNPs in overlapping features are annotated separately for each feature and multiple nucleotide polymorphisms (MNPs) within a codon are combined prior to annotation. A workflow has also been developed for use in Galaxy to map short reads to a reference genome and extract and annotate the SNPs.

Proper citation: TRAMS (RRID:SCR_002003) Copy   

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http://drpowell.github.io/vennt/

A web-tool to generate dynamic Venn diagrams for differential gene expression.

Proper citation: Vennt (RRID:SCR_002083) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/TEQC.html

An R/Bioconductor package for quality assessment of target enrichment experiments. This package provides functionalities for assessing and visualizing the quality of the target enrichment process, like specificity and sensitivity of the capture, per-target read coverage and so on.

Proper citation: TEQC (RRID:SCR_001943) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/flowViz.html

Software that provides visualization tools for flow cytometry data.

Proper citation: flowViz (RRID:SCR_002075) Copy   

•   Source: SciCrunch Registry

http://www.cellsignal.com/

Privately held company that develops and produces antibodies, ELISA kits, ChIP kits, proteomic kits, and other related reagents used to study cell signaling pathways that impact human health.

Proper citation: Cell Signaling Technology (RRID:SCR_002071) Copy   

•   Source: SciCrunch Registry

http://ncmir.ucsd.edu/downloads/jinx.shtm

Jinx was developed to aid in the 3D reconstruction of tomographic datasets acquired with one of the various electron microscopes available at the resource. Tomographic datasets consist of a series of 2D images from which objects of interest are segmented out for the 3D reconstruction. Jinx offers the user a graphical interface to step through each image of the series and facilities to manually trace out objects of interest. It relies on JadeDisplay to support the display of large images with graphical overlays and the JAI libraries for histogram functionality and other types of image manipulations. Jinx is currently under active development and future releases will offer semi-automated segmentation algorithms based on fuzzy logic, level set, and watershed algorithm. This software is free; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or any later version. See the GNU General Public License for more details. For a copy of the GNU General Public License, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA. Sponsors: Jinx presented here was produced at the National Center for Microscopy and Imaging Research at San Diego, which is supported by the National Institutes of Health (NIH) through a National Center for Research Resources program grant P41 RR04050. open source license, GNU general public license

Proper citation: National Center for Microscopy and Imaging Research: Jinx (RRID:SCR_001939) Copy   

•   Source: SciCrunch Registry