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http://decgpu.sourceforge.net/homepage.htm
Software tool as parallel and distributed error correction algorithm for high-throughput short reads using CUDA and MPI parallel programming models.
Proper citation: DecGPU (RRID:SCR_000585) Copy
https://cme.h-its.org/exelixis/web/software/sweed/
Software tool for likelihood based detection of selective sweeps in thousands of genomes. Software parallel and checkpointable tool that implements composite likelihood ratio test for detecting selective sweeps.
Proper citation: sweed (RRID:SCR_024357) Copy
https://github.com/magnusmanske/snpomatic
Short read mapping software. Read mapping tool offering variety of analytical output functions, with emphasis on genotyping,
Proper citation: snpomatic (RRID:SCR_024348) Copy
https://www.certara.com/software/phoenix-pkpd/
Software to automate repetitive analysis steps and is widely considered the industry standard for NCA, TK, and PK/PD modeling. Used as non-compartmental analysis (NCA), pharmacokinetic/pharmacodynamic (PK/PD), and toxicokinetic (TK) modeling tool.
Proper citation: WinNonlin (RRID:SCR_024504) Copy
http://www.paintshoppro.com/en/products/paintshop-pro/standard/
Photo-editing software including editing features, fast brushes, creative tools and color selection that will help turn snapshots into beautiful, gallery-worthy images.
Proper citation: PaintShop Pro (RRID:SCR_000338) Copy
https://github.com/harvardinformatics/NGmerge
Software tool for merging paired-end reads via novel empirically derived models of sequencing errors. Used for merging paired-end reads and removing adapters. Corrects errors and ambiguous bases and assigns quality scores for merged bases that accurately reflect the error rates.
Proper citation: NGmerge (RRID:SCR_024483) Copy
Software tool to assist in recovery and prevention of Repetitive Strain Injury. Monitors keyboard and mouse usage and using this information, it frequently alerts you to take microbreaks, rest breaks and restricts you to your daily computer usage.
Proper citation: Workrave (RRID:SCR_024364) Copy
http://xmedcon.sourceforge.net/
Open source software toolkit for medical image conversion.
Proper citation: XMedCon (RRID:SCR_024366) Copy
http://www.ks.uiuc.edu/Research/vmd/
Software tool as molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.
Proper citation: VMD (RRID:SCR_024368) Copy
Local Run Manager DNA Amplicon analysis module aligns amplicon reads against reference specified in the manifest file. Variants are called for the targeted regions.
Proper citation: DNA Amplicon (RRID:SCR_024481) Copy
Organization and funder of polycystic kidney disease research to find treatments. The organization also raises awareness for the disease through education, advocacy and support.
Proper citation: PKD Foundation (RRID:SCR_000209) Copy
The BioCurrents Research Center (BRC) is an integrated technology resource of the NIH:NCRR. The activities of the Center focus on molecular physiology as it relates to the cell function and disease. Our particular interest is how the dynamics of cell responses are reflected in the chemical profiles of microdomains surrounding single living cells. In order to measure complex cellular boundary layers, the BRC has specialized in the development of extremely sensitive signal acquisition and processing methods along with miniaturized electrochemical sensor designs. The technique is non-invasive and termed self-referencing. Since its establishment in 1996, the BRC has directed its technological research and development to the design and application of ultra-microelectrodes (tip diameters of less than 10m) tailored for the detection of specific chemicals. These have been successfully applied to the boundary layer profiles of many different cell types, with thematic strength in diabetes research, reproductive health and development (see collaborative profiles). More recently, it is changing its focus to technical developments, enhancing the integrative approach to cell function. To understand a cell as a dynamic and integrated whole, BRC must be able to examine responses from different domains as near to real time and as synchronously as possible. To this end, it is developing imaging capabilities to work in parallel with electrochemistry and conventional electrophysiological techniques. Imaging includes a spinning disc confocal, as well as a low light/luminescent imager designed and built within the BRC. The technologies developed or under development are in high demand within the biomedical community. Over 40 investigators work with the Center each year in a collaborative or service capacity. Over 80 of our visitor pool is NIH funded, representing approximately 25 NIH divisions and institutes. As part of our training and dissemination program we host occasional workshops at major national and international meetings, train a significant number of new investigators each year and host graduate students undertaking portions of their thesis dissertation using our technologies. In dissemination we advise on, and install, electrochemical systems in off campus research endeavors, both academic and industrial.
Proper citation: BioCurrents Research Center (RRID:SCR_002020) Copy
A commercial software laboratory notebook.
Proper citation: hivebench (RRID:SCR_000915) Copy
https://www.acrobat.com/formscentral/en/
Service to create PDF and web forms.
Proper citation: Adobe FormsCentral (RRID:SCR_001729) Copy
Biomedical technology research center that develops, tests and applies technology aimed toward completely automating the processes involved in solving macromolecular structures using cryo-electron microscopy. The goal is to establish a resource that will serve both as a center for high-throughput molecular microscopy as well as for transferring this technique to the research community. Current Core Technology Research and Development is focused on 4 areas: improving grid substrates and specimen preparation; further automation and optimization of image acquisition; development of an integrated single particle analysis and processing pipeline; and the development of automated high throughput EM screening. NRAMM welcomes applications of both collaborative and service projects.
Proper citation: National Resource for Automated Molecular Microscopy (RRID:SCR_001448) Copy
Biomedical technology research center that develops methods, both experimental and theoretical, of modern electron spin resonance (ESR) for biomedical applications. Center technologies are applicable to the determination of the structure and complex dynamics of proteins. Principal areas of expertise: * Pulsed Fourier Transform and Two Dimensional ESR * High Frequency-High Field (HFHF) ESR * High Resolution ESR Microscopy * Theory and Computational Methods for Modern ESR Activities include: * making resources available to the biomedical community, * publishing results, * running workshops on the new methodologies, * addressing the need to bring these new technologies to other laboratories.
Proper citation: National Biomedical Center for Advanced ESR Technology (RRID:SCR_001444) Copy
Biomedical technology research center that produces open-source software tools for biomedical image-based modeling, biomedical simulation and estimation, and the visualization of biomedical data. The Center works closely with software users and collaborators in a range of scientific domains to produce user-optimized tools and provides advice, technical support, workshops, and education to enhance user success. Biological projects and collaborations drive their development efforts, all with a single unifying vision: to develop the role of image-based modeling and analysis in biomedical science and clinical practice. The CIBC has a strong, ongoing emphasis on software simulation of bioelectric fields, with clinically oriented collaborations in cardiac defibrillation and the diagnosis/treatment of epilepsy. In addition, the CIBC has expanded in recent years to include applications of statistical shape analysis and three-dimensional visualization to mouse genetics and neuroimaging and applications of image and geometry processing to cell biology.
Proper citation: Center for Integrative Biomedical Computing (RRID:SCR_001961) Copy
http://www.dnastar.com/t-genvision.aspx
A genomic visualization application to support easy generation of publication quality graphics and maps. It produces high quality images of annotated genomes but it can also be customized to accentuate specific areas of interest, such as comparing gene functionality, illustrating gene expression levels, and visualizing the coverage in an assembled contig.
Proper citation: GenVision (RRID:SCR_001166) Copy
Biomedical technology research center focusing on the structure and function of supramolecular systems in the living cell as well as on the development of new algorithms and efficient computing tools for physical biology. They bring the most advanced molecular modeling, bioinformatics, and computational technologies to bear on questions of biomedical relevance. They extend, refine and deliver these technologies in response to experimental progress and emerging needs of the wide biomedical research community. They magnify the impact of their work through direct collaboration with experimental researchers, the distribution of cutting-edge and user-friendly software, and via extensive training, service, and dissemination efforts. The multidisciplinary team is engaged in the modeling of large macromolecular systems in realistic environments, and has produced ground-breaking insights into biomolecular processes coupled with mechanical force, bioelectronic processes in metabolism and vision, and with the function and mechanism of membrane proteins. They are committed and work towards further advancement of * Molecular modeling tools which can integrate structural information with bioinformatics databases and molecular dynamics simulations, and which can be used by a wide audience; * High performance molecular visualization and simulation software, capable of modeling biomolecules in realistic environments of 100,000,000 atoms or more; * Conceptual and methodological foundations of molecular modeling in the fields of quantum biology, mechanobiology, and interactive modeling; * Biomedical science through collaborations between theoretical and experimental researchers; * Support of the entire research process and training through a web-enabled collaborative environment; and * Service, training, and dissemination by leveraging web-based molecular graphics and integrated modeling technologies.
Proper citation: NIH Center for Macromolecular Modeling and Bioinformatics (RRID:SCR_001435) Copy
http://wyss.harvard.edu/viewpage/594/
A core facility with access to imaging equipment and analysis software such as wide-field light microscopy, Total Internal Reflection Fluorescence microscopy (TIRF), confocal microscopy, Atomic Force Microscopy (AFM), Transmission Electron Microscopy (TEM), small animal imaging, spectroscopy, and flow cytometry.
Proper citation: Wyss Institute Imaging Core (RRID:SCR_000898) Copy
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