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http://www.dnabaser.com/download/chromatogram-explorer/

A Windows Explorer clone dedicated to DNA sequence analysis and manipulation. View, edit, and convert chromatograms. Trim low quality ends automatically. The Lite version of Chromatogram Explorer is freeware.

Proper citation: DNA Chromatogram Explorer (RRID:SCR_005585) Copy   

•   Source: SciCrunch Registry

http://depts.washington.edu/yeastrc/

Biomedical technology research center that (1) exploits the budding yeast Saccharomyces cerevisiae to develop novel technologies for investigating and characterizing protein function and protein structure (2) facilitates research and extension of new technologies through collaboration, and (3) actively disseminates data and technology to the research community. Through collaboration, the YRC freely provides resources and expertise in six core technology areas: Protein Tandem Mass Spectrometry, Protein Sequence-Function Relationships, Quantitative Phenotyping, Protein Structure Prediction and Design, Fluorescence Microscopy, Computational Biology.

Proper citation: Yeast Resource Center (RRID:SCR_007942) Copy   

•   Source: SciCrunch Registry

http://nac.spl.harvard.edu/

Biomedical Technology Resource Center that develops image processing and analysis techniques for basic and clinical neurosciences. The NAC research approach emphasizes both specific core technologies and collaborative application projects. The core activity of the center is the development of algorithms and techniques for postprocessing of imaging data. New segmentation techniques aid identification of brain structures and disease. Registration methods are used for relating image data to specific patient anatomy or one set of images to another. Visualization tools allow the display of complex anatomical and quantitative information. High-performance computing hardware and associated software techniques further accelerate algorithms and methods. Digital anatomy atlases are developed for the support of both interactive and algorithmic computational tools. Although the emphasis of the NAC is on the dissemination of concepts and techniques, specific elements of the core software technologies have been made available to outside researchers or the community at large. The NAC's core technologies serve the following major collaborative projects: Alzheimer's disease and the aging brain, morphometric measures in schizophrenia and schizotypal disorder, quantitative analysis of multiple sclerosis, and interactive image-based planning and guidance in neurosurgery. One or more NAC researchers have been designated as responsible for each of the core technologies and the collaborative projects.

Proper citation: Neuroimage Analysis Center (RRID:SCR_008998) Copy   

•   Source: SciCrunch Registry

http://proteomics.ucsd.edu/

Biomedical technology research center that focuses on the computational bottlenecks that impair the interpretation of data, bringing modern algorithmic approaches to mass spectrometry and building a new generation of reliable, open-access software tools to support both new mass spectrometry instrumentation and emerging applications.

Proper citation: Center for Computational Mass Spectrometry (RRID:SCR_008161) Copy   

•   Source: SciCrunch Registry

http://msr.dom.wustl.edu/

Biomedical technology research center that develops mass spectrometry-based tools for the study of proteins, lipids and metaboilites. These include biomarker identification, stable isotope mass spectrometry and the analysis of intact proteins. Our goals are: * to conduct basic research in the science of mass spectrometry * to establish collaborative research projects with scientists at WU and at other institutions * to provide a service in mass spectrometry * to educate and train students in mass spectrometry * to disseminate results of our research and descriptions of the subject of mass spectrometry

Proper citation: NIH / NCRR Mass Spectrometry Resource Washington University in St. Louis (RRID:SCR_009009) Copy   

•   Source: SciCrunch Registry

http://glycotech.ccrc.uga.edu/

Biomedical technology research center that develops technologies to increase understanding of the molecular basis of the involvement of carbohydrates in protein-carbohydrate interactions in disease and to develop more powerful technologies necessary to achieve this goal. Complex carbohydrates play an important role in many biomedically important processes, including inflammatory response, hormone action, malignancy, viral and bacterial infections and cell differentiation. The resource combines complimentary technologies: synthetic chemistry, nuclear magnetic resonance, mass spectrometry, computational biology, protein expression and cell-based assays. As new technologies are developed, application to these processes will be pursued through collaborative and service projects.

Proper citation: Resource for Integrated Glycotechnology (RRID:SCR_009008) Copy   

•   Source: SciCrunch Registry

http://cell.ccrc.uga.edu/world/glycomics/glycomics.php

Biomedical technology research center that develops and implements new technologies to investigate the glycome of cells, including glycoproteomics and glycoconjugate analysis, transcript analysis and bioinformatics. It develops the tools and technology to analyze in detail the glycoprotein and glycolipid expression of mouse embryonic stem cells and the cells into which they differentiate. The technology developed in the Center will allow an understanding of how glycosylation is controlled during differentiation and will allow the development of tools to promote the use of stem cells to treat human disease. In addition, the technology developed will be applicable to the study of other cell types, including cancer cells that are progressing to a more invasive phenotype. The technology developed will also allow others in the scientific community to participate in glycomics research through dissemination of the new methods developed and through the analytical services provided by the resource to other scientists requesting assistance in glycomic analyses.

Proper citation: Integrated Technology Resource for Biomedical Glycomics (RRID:SCR_009003) Copy   

•   Source: SciCrunch Registry

http://www-ssrl.slac.stanford.edu/content/science/ssrl-smb-program

Biomedical technology research center that operates as a integrated center with three primary areas (or cores) of technological research and development and scientific focus: macromolecular crystallography (MC), X-ray absorption spectroscopy (XAS) and small-angle X-ray scattering/diffraction (SAXS) . Central to the core technological developments in all three areas is the development and utilization of improved detectors and instrumentation, especially to be able to take maximum advantage of the high brightness of SSRL?s third-generation synchrotron X-ray storage ring (SPEAR3). A primary focus is the use of enhanced computing and data management tools to provide more user-friendly, real-time and on-line instrumentation control, including full remote access for crystallography, data reduction and analysis.

Proper citation: SSRL Structural Molecular Biology (RRID:SCR_009000) Copy   

•   Source: SciCrunch Registry

https://github.com/luo-xiaolong/GSC

Software tool for lossless compression of VCF files, designed to efficiently store and manage VCF files in compressed format. It accepts VCF/BCF files as input and utilizes advanced compression techniques to significantly reduce storage requirements while ensuring fast query capabilities.

Proper citation: Genotype Sparse Compression (RRID:SCR_025071) Copy   

•   Source: SciCrunch Registry

https://numba.readthedocs.io/en/stable/index.html

Open source JIT compiler that translates subset of Python and NumPy code into fast machine code. Can compile large subset of numerically-focused Python, including many NumPy functions. Has support for automatic parallelization of loops, generation of GPU-accelerated code, and creation of ufuncs and C callbacks.

Proper citation: Numba (RRID:SCR_025056) Copy   

•   Source: SciCrunch Registry

http://www.ldbase.org

NIH funded collaboration between researchers and librarians to build behavioral project oriented data repository containing decades of knowledge from educational and developmental sciences on individuals across the full range of abilities.

Proper citation: LDbase (RRID:SCR_025052) Copy   

•   Source: SciCrunch Registry

https://readysetpotato.com/

Software tool that helps users write experimental protocols.

Proper citation: Ready Set Potato (RRID:SCR_025289) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/us/en/home/industrial/spectroscopy-elemental-isotope-analysis/molecular-spectroscopy/uv-vis-spectrophotometry/instruments/nanodrop/software.html

Operating software for Thermo Scientific NanoDrop 1000 Spectrophotometer. Free NanoDrop operating software to update your instrument.

Proper citation: Thermo Scientific NanoDrop 1000 Software (RRID:SCR_025282) Copy   

•   Source: SciCrunch Registry

https://www.beckman.com/centrifuges/high-speed/avanti-j-30i

Refrigerated centrifuge that generates centrifugal forces required for wide variety of applications. Together with Beckman Coulter rotors are designed for use in this centrifuge. Centrifuge is microprocessor controlled, providing interactive operation.

Proper citation: Beckman Coulter: Avanti J-30I High-Speed Centrifuge (RRID:SCR_025297) Copy   

•   Source: SciCrunch Registry

https://www.bruker.com/en/products-and-solutions/preclinical-imaging/paravision-360.html

Software for preclinical imaging integrated with Bruker MRI spectrometers. Used with Bruker MRI, PET/MR, and PET/CT instruments. Enables easy and high throughput imaging. All images, protocols, and subjects are in one location with inherent co-registration, image fusion, data processing, and analysis.

Proper citation: ParaVision 360 (RRID:SCR_025295) Copy   

•   Source: SciCrunch Registry

https://shop.sartorius.com/ca/p/incucyte-ai-cell-health-analysis-software-module/BA-04871#

Software for analysis to determine live versus dead cells – no fluorescent dyes needed.

Proper citation: Incucyte Cell-By-Cell Analysis Software Module (RRID:SCR_025367) Copy   

•   Source: SciCrunch Registry

https://dokumate.com/knowledgebase/docid/

DokuMate helps standardize and reuse documents, simplifies and speeds-up editing, and automates many tedious tasks. A docId” is one of the “magic” Content Control tag names. A docId is an alphanumerical ID (e.g., “R01-01-C00”, “R01-11-100”, “R01-11-410”, “R01-30-100”) that uniquely identifies and sorts documents (e.g., Schedule C, Exhibit 1, Attachment 4.1, Appendix 1) within a larger set of documents, e.g., all documents belonging to (a) a specific RFP or (b) the set of contracts between a first party and a second party.

Proper citation: DokuMate (RRID:SCR_025402) Copy   

•   Source: SciCrunch Registry

http://www.okazolab.com

Software for designing and running advanced behavioral experiments and neuroscientific studies.

Proper citation: EventIDE (RRID:SCR_025412) Copy   

•   Source: SciCrunch Registry

https://www.yworks.com/products/yed

Software desktop application as general purpose diagramming program with multi-document interface. Cross-platform Java application to generate high-quality diagrams. Runs on Windows, Linux, Mac OS, and other platforms that support Java Virtual Machine.

Proper citation: yEd (RRID:SCR_025325) Copy   

•   Source: SciCrunch Registry

https://nwbinspector.readthedocs.io/en/dev/

Software Python-based package designed to asses quality of Neurodata Without Borders files and based on compliance with Best Practice. Meant as companion to PyNWB validator, which checks for strict schema compliance. Attempts to apply some commonsense rules and heuristics to find data components of file that pass validation, but are probably incorrect, or suboptimal, or deviate from best practices. In other words, while PyNWB validator focuses on compliance of structure of file with the schema, the inspector focuses on compliance of actual data with best practices. Meant as data review aid. It does not catch all best practice violations, and any warnings it does produce should be checked by knowledgeable reviewer.

Proper citation: NWB Inspector (RRID:SCR_025465) Copy   

•   Source: SciCrunch Registry