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http://www.rad.upenn.edu/sbia/braid/braid_web/index.html

Large-scale archive of normalized digital spatial and functional data with an analytical query mechanism. One of its many applications is the elucidation of brain structure-function relationships. BRAID stores spatially defined data from digital brain images which have been mapped into normalized Cartesian coordinates, allowing image data from large populations of patients to be combined and compared. The database also contains neurological data from each patient and a query mechanism that can perform statistical structure-function correlations. The project is developing database technology for the manipulation and analysis of 3-dimensional brain images derived from MRI, PET, CT, etc. BRAID is based on the PostgreSQL server, an object/relational DBMS, which allows a standard relational DBMS to be augmented with application-specific datatypes and operators. The BRAID project is adding operations and datatypes to support querying, manipulation and analysis of 3D medical images, including: * Image Datatypes: BRAID supports a family of 3D image datatypes, each having an abstract type and an implementation type. Abstract types include boolean (for regions of interest), integer, float, vector (for representing morphological changes), tensor (for representing derivatives and standard deviations of vector images) and color. Implementation types at present include line-segment format and voxel array. * Image Operators: BRAID supports addition of images, multiplication (which is interpreted as intersection for boolean images), coercion of an image''s abstract or implementation type to another value, and determination of volumes of regions of interest. * Statistical Operators: A chi-squared test has been added to SQL as an aggregate operator on pairs of boolean values. * Web Interface: A general-purpose Web gateway allows the results of queries that return computed images to be displayed. You can download the BRAID source code 2.0. This version is developed under postgreSQL 7.3.4., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BRAID (RRID:SCR_008702) Copy   

•   Source: SciCrunch Registry

http://www.ini.uzh.ch/~amw/seco/cx3d/

INI has developed a novel simulation tool, CX3D, for modeling the development of large realistic neural networks such as the neocortex, in a physical 3D space. The development of neural tissue is a complex organizing process, in which it is difficult to grasp how the various localized interactions between dividing cells leads relentlessly to global network organization. Simulation is a useful tool for exploring such complex processes because it permits rigorous analysis of observed global behavior in terms of the mechanistic axioms declared in the simulated model. In CX3D, as in biology, neurons arise by the replication and migration of precursors, which mature into cells able to extend axons and dendrites. Individual neurons are discretized into spherical soma and cylindrical neurite elements that have appropriate mechanical properties. The growth functions of each neuron are encapsulated in set of pre-defined modules that are automatically distributed across its segments during growth. The extracellular space is also discretized, and allows for the diffusion of extracellular signaling molecules, as well as the physical interactions of the many developing neurons. CX3D is a powerful tool for understanding neural development. Sponsors: CX3D has been developed with the support of the SECO EU Project (EU grant 216593). Keywords: Neuinformatics, Cortex, 3D, 3 Dimentional, Neocortex, Physicis, Neural, Tissue, Simulation, Neuron, Structure, Biology, Axon, Dentrite, Soma, Neurite, Development,

Proper citation: Institute for Neuroinformatics: Cortex 3D (RRID:SCR_008704) Copy   

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

Jackal is a collection of programs designed for the modeling and analysis of protein structures. Its core program is a versatile homology modeling package. It contains twelve individual programs, each with their own function.

Proper citation: Jackal (RRID:SCR_008665) Copy   

•   Source: SciCrunch Registry

http://www.orcid.org/

Non-profit organization dedicated to solving the author/contributor name ambiguity problem in scholarly communications by creating a central registry of unique identifiers for individual researchers and an open and transparent linking mechanism between ORCID and other current author ID schemes. These identifiers, and the relationships among them, can be linked to the researcher''s output to enhance the scientific discovery process and to improve the efficiency of research funding and collaboration within the research community. The ideal solution is to establish a registry that is adopted and embraced as the de facto standard by the whole of the community. A resolution to the systemic name ambiguity problem, by means of assigning unique identifiers linkable to an individual''s research output, will enhance the scientific discovery process and improve the efficiency of funding and collaboration. The organization brings together the leaders of the most influential universities, funding organizations, societies, publishers and corporations from around the globe and is managed by a fourteen member Board of Directors. A disambiguated set of authors will allow new services and benefits to be built for the research community by all stakeholders in scholarly communication: from commercial actors to non-profit organizations, from governments to universities.

Proper citation: ORCID - Open Researcher and Contributor ID (RRID:SCR_008700) Copy   

•   Source: SciCrunch Registry

https://simtk.org/home/lapack

This project is the SimTK Core implementation of the extremely reliable, high speed linear algebra package LAPACK and the underlying BLAS library on which LAPACK is built. It uses ATLAS to generate hand tuned BLAS kernels for a variety of hardware platforms, including multiprocessors, using a variety of operating systems including Windows, Mac, and Red Hat Linux. These platforms are pre-built and make the binaries available as a single shared library which can be conveniently used by any program. This means that users who are not experts in high performance scientific computation can nonetheless use the fastest linear algebra methods available for their machines.

Proper citation: LAPACK linear algebra library (RRID:SCR_008661) Copy   

•   Source: SciCrunch Registry

http://portal.ncibi.org/gateway/gin.html

GIN-IE is a high precision system for extracting protein/gene interactions, interaction cue words, and directionality from the literature. Syntax-aware inferences about the roles of the entities are made by using the syntactic and dependency parse tree structures of the sentences. Negation and speculation are frequently occurring language phenomena that modify the factuality of the information contained in text. GIN-IE detects and distinguishes interactions that are extracted from negated or speculative sentences. GIN-IE has been integrated with the NCIBI PubMed daily update and processing pipeline. The extracted interactions are accessible through MimiWeb.

Proper citation: Gene Interaction Extraction from the Literature (RRID:SCR_008660) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://www.ingenuity.com/products/pathways_analysis.html

A web-based software application that enables users to analyze, integrate, and understand data derived from gene expression, microRNA, and SNP microarrays, metabolomics, proteomics, and RNA-Seq experiments, and small-scale experiments that generate gene and chemical lists. Users can search for targeted information on genes, proteins, chemicals, and drugs, and build interactive models of experimental systems. IPA allows exploration of molecular, chemical, gene, protein and miRNA interactions, creation of custom molecular pathways, and the ability to view and modify metabolic, signaling, and toxicological canonical pathways. In addition to the networks and pathways that can be created, IPA can provide multiple layering of additional information, such as drugs, disease genes, expression data, cellular functions and processes, or a researchers own genes or chemicals of interest.

Proper citation: Ingenuity Pathway Analysis (RRID:SCR_008653) Copy   

•   Source: SciCrunch Registry

http://www.mmv.org/

MMV, a not-for-profit public-private partnership, was established as a foundation in Switzerland in 1999. Our mission is to reduce the burden of malaria in disease-endemic countries by discovering, developing and facilitating delivery of new, effective and affordable antimalarial drugs. Our vision is a world in which these innovative medicines will cure and protect the vulnerable and under-served populations at risk of malaria, and help to ultimately eradicate this terrible disease. Sponsors/Donors: -Bill and Melinda Gates Foundation -CRIMALDDI -ExxonMobil -Irish Aid -National Institutes of Health -Netherlands Ministry of Foreign Affairs -Rockefeller Foundation (former donor) -Secretaria de Estado de Cooperacin Internacional (Spanish Agency for International Cooperation) -Swiss Agency for Development and Cooperation -UK Department for International Development -USAID -Wellcome Trust -World Bank -World Health Organization

Proper citation: Medicines for Maleria Venture (RRID:SCR_008603) Copy   

•   Source: SciCrunch Registry

http://www.alzfdn.org/index.htm

Non profit organization and informational portal directed towards patients and families. AFA is an umbrella orgnization uniting over 1600 member organizations to collaborate on education, resources, best practices and advocacy. AFA provides several grant opportunities for AFA's nonprofit member organizations and to individuals in need.

Proper citation: Alzheimer's Foundation of America (RRID:SCR_008724) Copy   

•   Source: SciCrunch Registry

http://www.zoomify.com/

Zoomify makes high-quality images zoom-and-pan for fast, interactive viewing on the web. Zoomify''s image viewing solutions use just HTML, JPEGs, and Flash - no large downloads, no special installs, and no server-side setup is required. And Zoomify''s innovative features provided added value including support for slideshows, hotspots, annotation, side-by-side comparison, and much more. Zoomifys products meet the high-quality, high-resolution imaging needs of creative professionals and image-centric applications. Zoomify is revolutionizing digital imaging in medicine and the sciences, image archiving and museum exhibits, defense and security, education, entertainment, and more.

Proper citation: Zoomify (RRID:SCR_008601) Copy   

•   Source: SciCrunch Registry

http://rgd.mcw.edu/rgdCuration/?module=portal&func=show&name=nuro

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Portal that provides researchers with easy access to data on rat genes, QTLs, strain models, biological processes and pathways related to neurological diseases. This resource also includes dynamic data analysis tools.

Proper citation: Rat Genome Database: Neurological Disease Portal (RRID:SCR_008685) Copy   

•   Source: SciCrunch Registry

http://www.magellanbioscience.com/

Founded in 1997 with the mission to provide a new source of microbial extracts for drug discovery, agrochemical, enzyme, and specialty chemical research. Discovery company pursuing untapped sources of chemical diversity and identifying lead candidates derived from microorganisms for development of new chemical entities.

Proper citation: Magellan Bioscience Group (RRID:SCR_008715) Copy   

•   Source: SciCrunch Registry

http://brainu.org/

A neuroscience training program for Minnesota students and teachers. It provides teachers with three years of neuroscience training, materials, and staff support to bring brain science to their students. In these professional workshops, participants receive updates on the latest in neuroscience research -- discussion is complemented with hands-on activities and lab work. Teachers also receive curriculum materials to aid them in using neuroscience topics in support of Minnesota Intermediate and Middle Level standards. The program was expanded in 2008 to include high school teachers.

Proper citation: BrainU: The Neuroscience Teacher Institute (RRID:SCR_008677) Copy   

•   Source: SciCrunch Registry

http://homes.esat.kuleuven.be/~bioiuser/eXtasy/

A pipeline for ranking nonsynonymous single nucleotide variants given a specific phenotype.

Proper citation: eXtasy (RRID:SCR_008671) Copy   

•   Source: SciCrunch Registry

https://matplotlib.org

Python 2D plotting library which produces publication quality figures in variety of hardcopy formats and interactive environments across platforms. Used in python scripts, web application servers, and six graphical user interface toolkits. Used to generate plots, histograms, power spectra, bar charts, error charts, scatter plots.

Proper citation: Matplotlib (RRID:SCR_008624) Copy   

•   Source: SciCrunch Registry

http://www.rosettabiosoftware.com

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. Following completion of the acquisition of Rosetta Biosoftware assets from Merck & Co., Inc. by Microsoft Corp. on June 26, 2009, Merck & Co., Inc. selected Ceiba Solutions, Inc (http://www.ceibasolutions.com) as the provider of product support for Rosetta Resolver, Elucidator and Syllego customers. Ceiba Solutions is a software and IT services company helping customers streamline and extend business processes through composite software development, application integration, and managed application services. Ceiba currently serves Life Science industry customers with outsourced managed services for R&D applications, as well as business software and integrated business processes. Ceiba Solutions is an active member of the Massachusetts Biotechnology Council and the BayBio Council. Ceiba Solutions has assumed complete responsibility for software maintenance and support associated with Rosetta Biosoftware product Licensees who are eligible for continued Technical Support and Software Upgrade Protection, and will retain that responsibility throughout the remainder of the 24 month Desupport Period.

Proper citation: Rosetta Biosoftware (RRID:SCR_008587) Copy   

•   Source: SciCrunch Registry

http://people.scs.carleton.ca/~dehne/projects/clustalxp/

This portal runs on a processor cluster and allows Biochemists to use our parallel implementation of Clustal W together with our parallel implementation of Minimum Vertex Cover.

Proper citation: An Extended and Parallel version of Clustal (RRID:SCR_008620) Copy   

•   Source: SciCrunch Registry

http://www.well.ox.ac.uk/bioinformatics-statistical-genetics

Bioinformatics, statistical genetics, functional genomics, databases and scientific computing support and services for The Wellcome Trust Centre for Human Genetics to support the disease gene cloning projects within the centre and to maintain independent research in development of methods, algorithms and software for mapping multifactorial trait loci. The group has current research foci in the areas of sequence alignment statistics, comparative genomics, ancestral haplotype construction, LIMS database development, QTL linkage and association methods, variability in patterns of linkage disequilibrium and multivariate modelling of quantitative traits.

Proper citation: Bioinformatics and Statistical Genetics (RRID:SCR_008589) Copy   

•   Source: SciCrunch Registry

http://thedecisiontree.com/blog/?p=278

In many respects, this book will be an extension of many of the preoccupations Ive pursued here at Epidemix. Those handful of you who follow my magazine writing will no doubt recognize the theme as well. The premise is that we are at a new phase of health and medical care, where more decisions are being made by individuals on their own behalf, rather than by physicians, and that, furthermore, these decisions are being informed by new tools based on statistics, data, and predictions. This is a good thing it will let us, the general public, live better, happier, and even longer lives. But it will require us to be stewards of our health in ways we may not be prepared for. We will act on the basis of risk factors and predictive scores, rather than on conventional wisdom and doctors recommendations. We will act in collaboration with others, drawing on collective experience with health and disease, rather than in the isolation and ignorance that can come with privacy concerns. And we will act early, well before symptoms appear, opting to tap the science of genomics and proteomics in order to mitigate our risks down the road. Together, these tools will create a new opportunity and a new responsibility for people to act to make health decisions well before they become patients. This can be characterized as a decision tree, a series of informed choices we will make to minimize uncertainty and optimize our outcomes. Indeed, we will use decision trees to navigate most of our health decisions, sometimes in overt ways new decision support tools will both inform us and guide us, and theyll be steeped in statistics, predicition, and the power of collective experience.

Proper citation: The Decision Tree (RRID:SCR_008622) Copy   

•   Source: SciCrunch Registry

http://bg.upf.edu/condel/home

A method to assess the outcome of nonsynonymous SNVs using a consensus deleteriousness score that combines various tools (e.g. SIFT, Polyphen2, MutationAssessor).

Proper citation: Condel (RRID:SCR_008584) Copy   

•   Source: SciCrunch Registry