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http://www.med.upenn.edu/cndr/index.shtml

A research institution which conducts clinical research to understand brain dysfunction and degeneration in Alzheimer's disease (AD), Parkinson's disease (PD), Frontotemporal disease (FTD), Amyotrophic Lateral Sclerosis (ALS or Lou Gehrig's disease), and other age-related neurodegenerative disorders. This organization also houses a general training program that has a focus on drug discovery. This program teaches trainees in etiology, pathogenesis, and diagnosis and treatment of Alzheimer's disease, Parkinson's disease, frontotemporal dementias, motor neuron disease and related disorders. This program also trains Ph.D and M.D/Ph.D students, as well scientists, physicians, and veterinarians who have already completed their advanced degree and are looking for a postdoctoral research fellowship. The program is designed to give a solid background in basic and translational neuroscience, and related disciplines.

Proper citation: University of Pennsylvania Center for Neurodegenerative Disease Research (RRID:SCR_008798) Copy   

•   Source: SciCrunch Registry

http://www.raetschlab.org/suppl/qpalma

An alignment tool targeted to align spliced reads produced by Next Generation sequencing platforms such as Illumina Solexa or 454.

Proper citation: QPALMA (RRID:SCR_008791) Copy   

•   Source: SciCrunch Registry

http://www.muschealth.com/multimedia/Podcasts/index.aspx?type=main

The MUSChealth.com Podcast Library, featuring podcasts on a variety of topics related to your health and our services here at MUSC. These medical podcasts are hosted by MUSC faculty, physicians and special guests and are produced and directed by Linda Austin, M.D. Current topics include: * Academics and Education * Aging, Geriatrics and Caregiving * Alcohol and Drug Dependency * Allergies and Asthma * Ashley River Tower * Bones, Joints, Muscles and Spine * Cancer * Children''s Health * Cosmetic Surgery * Dental * Dermatology/Skin Problems * Diabetes, Endocrinology and Metabolism * Digestive Health * ENT: Ear, Nose and Throat * Executive Health * Eye Health * General Health and Wellness * Heart and Vascular Health * Hospice * Kohl''s Take a Minute for Kids * Lungs and Breathing * Men''s Health * Mental Health * MUSC News and Events * Neurological Health * Organ Transplant * Osteoporosis * Pregnancy - Week by Week * Pregnancy and Childbirth * Radiology * Research and Clinical Trials * SC Health, Leadership and Policy * Sports Medicine * Stroke * Urology * Weight Loss Surgery Follow-up * Weight Management * Women''s Health

Proper citation: MUSC Health Podcast Library (RRID:SCR_008827) Copy   

•   Source: SciCrunch Registry

http://r-forge.r-project.org/projects/sequgio/

An algorithm to estimate isoforms expression from RNA-seq data based on a model that doesn''t assume uniform distribution of count within transcripts.

Proper citation: Sequgio (RRID:SCR_008867) Copy   

•   Source: SciCrunch Registry

http://www.cbtrus.org/

Voluntary, non-profit organization dedicated to collecting and disseminating statistical data. Resource for gathering and disseminating epidemiologic data on all primary benign and malignant brain and other CNS tumors.

Proper citation: Central Brain Tumor Registry of the United States (RRID:SCR_008748) Copy   

•   Source: SciCrunch Registry

http://www.cbioc.org

A tool for extraction and collaboration for data curation related to biology. CBioC runs as a web browser extension and allows unobtrusive use of the system during the regular course of research in PubMed. It can also be accessed directly (without having to install a plug-in). Automated text extraction is used as a starting point to bootstrap the database, but then it is up to biologists improve upon the extracted data, ironing out inconsistencies by subsequent edits on a massive scale. * After install, it loads when you visit PubMed. * Gets interactions from PubMed abstracts. * Allows you to vote and modify extracted data. * Also shows data from BIND, DIP, MINT, GRID, IntAct.

Proper citation: CBioC (RRID:SCR_008863) Copy   

•   Source: SciCrunch Registry

http://meme.nbcr.net/meme/cgi-bin/gomo.cgi

Gene Ontology for Motifs (GOMO) is an alignment- and threshold-free comparative genomics approach for assigning functional roles to DNA regulatory motifs from DNA sequence. The algorithm detects associations between a user-specified DNA regulatory motif (expressed as a position weight matrix; PWM) and Gene Ontology terms. The original method for predicting the roles of transcription factors (TFs starts with a PWM motif describing the DNA-binding affinity of the TF. GOMO uses the PWM to score the promoter region of each gene in the genome for its likelihood to be bound by the TF. The resulting ''''affinity'''' scores are then used to test each term in the Gene Ontology for association with high-scoring genes. The algorithm was subsequently extended to leverage conserved signals using multiple, related species in a comparative approach, which greatly improves the resulting annotations. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: GOMO - Gene Ontology for Motifs (RRID:SCR_008864) Copy   

•   Source: SciCrunch Registry

http://vortex.cs.wayne.edu/projects.htm#OE2GO

Onto-Express is a web-based tool in the Onto-Tools suite that performs automated function profiling for a list of differentially expressed genes. However, Onto-Express does not support functional profiling for the organisms that do not have annotations in public domain, or use of custom (i.e. user-defined) ontologies. This limitation is also true for most of the other existing tools for functional profiling, which means that researchers working with uncommon organisms and/or new annotations or ontologies may be forced to construct such profiles manually. Onto-Express To Go (OE2GO) is a new tool added to the Onto-Tools ensemble to address these issues. OE2GO is built on top of OE to leverage its existing functionality. In OE2GO, the users now have an option to use either the Onto-Tools database as a source of functional annotations or provide their own annotations in a separate file. Currently, OE2GO supports annotation file in the Gene Ontology format. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: Onto-Express To Go (OE2GO) (RRID:SCR_008854) Copy   

•   Source: SciCrunch Registry

http://www.ucl.ac.uk/tapb/

We aim to facilitate the pathway for access, storage, use and transfer of human organs, cells and tissue between clinical centers within UCL Partners, academic groups in UCL, other universities, hospitals, medical researcher and biotechnology companies, to enhance the ability for researchers to access the materials they need. Alongside this, researchers will be able to exchange information and access guides on regulatory, ethics and practical issues concerning access, transfer and use of this type of material. These guides will be video and documents format, based on talks at organized events given by experts in the relevant fields. All of this information will be accessible on a website that seeks to link groups within UCL and attract attention from the wider world through social media and expansion of existing contacts. Our vision is to develop a centralized human tissue provision and utilization service for academic and commercial researchers UCL has the highest concentration of biomedical researchers in Europe. As part of this, UCL has numerous licensed biobanks and is associated with many research intensive hospitals in North London. The role of a biobank is to prepare and hold human tissue samples in for use by medical researchers to help delivery new treatments. Hospitals can also provide human tissue for research by utilizing waste human tissue taken as part of surgery or diagnostic procedures, but is normally incinerated. The researchers using the human tissue could be working within academic laboratories in UK universities and institutions or as part of commercial companies. Researchers currently cannot easily access human tissue to meet the demands of their research, often due to the long ethical, regulatory and contractual processes. However, with the enormous UCL biobanking and research Hospital resources, UCL could be a leading academic institution in providing human tissue for medical research within the UK and internationally. Our vision is to develop a centralized human tissue provision and utilization service for academic and commercial researchers. This relies on creating an overarching infrastructure, to consolidate information on disparate human tissue resources around UCL, and (where possible) gain centralized ethical and regulatory and contractual approval for use of the tissue. Funding the infrastructure will rely on a cost recovery model for a per sample basis. As a result the time needed to obtain tissue for research will be dramatically reduced, whilst providing a simple costing model for obtaining human tissue. This will make human tissue procurement much more efficient for end users.

Proper citation: Tissue Access for Patient Benefit (RRID:SCR_008853) Copy   

•   Source: SciCrunch Registry

http://www.openmicroscopy.org/site

Open tools to support data management for biological light microscopy produced by a multi-site collaborative effort among academic laboratories and a number of commercial entities. Designed to interact with existing commercial software, all OME formats and software are free, and all OME source code is available under the GNU General public license or through commercial license from Glencoe Software. OME is developed as a joint project between research-active laboratories at the Dundee, NIA Baltimore, and Harvard Medical School and LOCI. In addition, OME has active collaborations with many imaging and informatics groups. While many other applications could use OME''s architecture and design, their specific implementation is focused on biological and biomedical imaging. Those interested in applying OME''s technology to other applications should contact the developers. OME work is divided into several different standards and software projects: * Bio-Formats: A Java-based library for reading and writing over 90 microscopy file formats. * OMERO Software: The Java-based OMERO software project, which currently includes tools for storing, visualizing, managing, and annotating microscopic images and metadata. * OME-XML & OME-TIFF: The OME-XML and OME-TIFF file format specifications, which are open file formats for sharing microscope image data. * OME Server: This was the original OME server project which has now ended and is a legacy product. It implements image-based analysis of cellular dynamics and image-based screening of cellular localization or phenotypes, and included a fully developed version of the 2003 version of OME-XML Schema language.

Proper citation: OME - Open Microscopy Environment (RRID:SCR_008849) Copy   

•   Source: SciCrunch Registry

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

A suite of tools for efficient management of neuroimaging project data. Specifically, DFBIdb was designed to allow users to quickly perform routine management tasks of sorting, archiving, exploring, exporting and organising raw data. DFBIdb was implemented as a collection of Python scripts that maintain a project-based, centralised database that is based on the XCEDE 2 data model. Project data is imported from a filesystem hierarchy of raw files, which is an often-used convention of imaging devices, using a single script that catalogues meta-data into a modified XCEDE 2 data model. During the import process data are reversibly anonymised, archived and compressed. The import script was designed to support multiple file formats and features an extensible framework that can be adapted to novel file formats. Graphical user interfaces are provided for data exploration. DFBIdb includes facilities to export, convert and organise customisable subsets of project data according to user-specified criteria.

Proper citation: DFBIdb (RRID:SCR_009456) Copy   

•   Source: SciCrunch Registry

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

Software to: view dicom files and assemble them into 3D volumes. View and convert between Analyze, Nifti, and Interfile. Classify and organize dicoms and 3D volumes using metadata. Search and report on a collection of scans.

Proper citation: DIAMOND (RRID:SCR_009457) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=gma

Software package to perform Granger mediation analysis for time series. Includes single level GMA model and two-level GMA model, for time series with hierarchically nested structure.

Proper citation: GMA (RRID:SCR_009212) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/cbs-tools/

A fully automated processing pipeline for cortical analysis of structural MR images at a resolution of up to 400������m, including skull stripping, whole brain segmentation, cortical extraction, surface inflation and mapping, as well as dedicated tools for profile estimation across the cortical thickness. The tools are released as a set of plug-ins for the MIPAV software package and the JIST pipeline environment. They are therefore cross-platform and compatible with a wide variety of file formats.

Proper citation: CBS High-Res Brain Processing Tools (RRID:SCR_009452) Copy   

•   Source: SciCrunch Registry

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

An open-source C++-based application that allows automatic as well as user-interactive segmentation of the Corpus Callosum. Via a Qt-based graphical user interface, CCSeg also performs semi-automatic segmentation.

Proper citation: CCSeg - Corpus Callosum Segmentation (RRID:SCR_009453) Copy   

•   Source: SciCrunch Registry

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

A collection of tools for MRI T1 brain image segmentation in the Windows environment. It helps construct a complete pipeline with necessary preprocessing and postprocessing procedures besides brainparser, the core program of our fast brain segmentation. The execution of the whole pipeline can be completed in 2 hours with good segmentation results. Execution requires: FSL

Proper citation: BrainSolution (RRID:SCR_009447) Copy   

•   Source: SciCrunch Registry

http://www.mmpc.org

Center mission is to advance medical and biological research by providing the scientific community with standardized, high quality metabolic and physiologic phenotyping services for mouse models of diabetes, diabetic complications, obesity and related disorders.

Proper citation: National Mouse Metabolic Phenotyping Centers (RRID:SCR_008997) Copy   

•   Source: SciCrunch Registry

http://www.biomatik.com/

An Antibody supplier, Core facility

Proper citation: Biomatik (RRID:SCR_008944) Copy   

•   Source: SciCrunch Registry

https://www.beckmancoulter.com/

An Organization portal, Material service resource, Antibody supplier, Instrument supplier

Proper citation: Beckman Coulter (RRID:SCR_008940) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE, documented on November 05, 2013. It has been superseeded by the CALATK, available here http://www.calatk.org c++ libraries and applications for performing fluid registration based operations on 2D and 3D images. The registration method is based on the large displacement diffeomorphic mapping (LDDM) registration method and implements discretized fluid registration. This registration method is then applied to time series analysis, cross-sectional atlas building, and longitudinal atlas building. The individual tool components are: * LDDM: Fluid registration between two images. * TimeSeries: Time series analysis of longitudinal data for a single subject. * AtlasBuilder: Cross-sectional atlas building for a population of images. * LongitudinalAtlasBuilder: Longitudinal atlas building for a population of subjects, each with a longitudinal data set. * FRATUtils: A collection of utility functions for working with volumes and time series files

Proper citation: Fluid Registration and Atlas Toolkit (RRID:SCR_009478) Copy   

•   Source: SciCrunch Registry