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http://www.jcu.edu.au/

Public university in Townsville, Australia that functions as a research and teaching institution. Some well-known divisions of the university include the division of Tropical Environments and Societies, Tropical Health and Medicine, and Research and Innovation.

Proper citation: James Cook University; Townsville; Australia (RRID:SCR_001420) Copy   

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http://mugsy.sourceforge.net/

Software resource for multiple whole genome alignment. It uses Nucmer, a custom graph-based segmentation procedure, for pairwise alignment, and the Seqan:TCoffee's multiple alignment strategy.

Proper citation: Mugsy (RRID:SCR_001414) Copy   

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https://cismm.web.unc.edu/

Biomedical technology research center that develops force technologies applicable over a wide range of biological settings, from the single molecule to the tissue, with integrated systems that orchestrate facile instrument control, multimodal imaging, and analysis through visualization and modeling. The Force Microscope Technologies Core designs instruments in an area of science where there are unusual opportunities: the measurement of forces and the integration with optical microscopy. Force technologies play the obvious role of both measuring events in the sample and modifying the sample during the experiment. It is through the microscope that the force data is correlated with simultaneous 3D optical images. The force technology development includes the magnetic bead technology in the 3D Force Microscope project, Atomic Force Microscopy in the nanoManipulator project, and Control Software to drive the instrumentation. This core is focused on providing the physical capability to perform the experiments and probe structure/property correlations. The Ideal User Interfaces core makes the connection between the user and the instrument, the model building, and the data. This includes control systems that allow the user to move the bead inside the cell culture with a handheld pen and the visualization techniques to view the optical microscope data as a rendered 3D image collocated with the force data. Using data to create, change, and understand a model is the focus of the Advanced Model Fitting and Analysis core. The quantitative reduction of images to structural, shape, and velocity parameters is the goal of Image Analysis. The immediate understanding of correlations across image fields and between data sets in the challenge of Visualization. The power of combining the strength of a computer science graphics group with a microscopy technology group is most evident in the Graphics Hardware Acceleration project, which seeks to harness the speed of graphics processors for microscope data analysis and simulation. The Advanced Technology core pushes the boundaries of the Human Computer Interface through the investigation of improved techniques for the interaction of users with virtual environments, the real time lighting of virtual settings, and the enabling of multi-person collaboration. These techniques are validated and evaluated through physiological measures in virtual environments effectiveness evaluation studies.

Proper citation: Computer Integrated Systems for Microscopy and Manipulation (RRID:SCR_001413) Copy   

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http://octresearch.org/

Biomedical technology research center that pioneers and provides access to microscopic imaging instruments for biologic and clinical research. Optical coherence tomography (OCT) has evolved over the last two decades to become a standard of care for diagnostic ophthalmic imaging and is poised to make significant impact in the fields of cardiology and gastrointestinal endoscopy. Access to state-of-the-art instrumentation, however, has been limited to a relatively few research laboratories and the optimization of instruments for new biomedical applications has hindered the investigation of new opportunities. A major focus of CBORT will be to cultivate strategic research collaborations and respond to a pressing need for application-specific OCT instrumentation and hardware.

Proper citation: Center for Biomedical OCT Research (RRID:SCR_001418) Copy   

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http://www.biomemsrc.org/

Biomedical technology research center that provides biomedical investigators with novel microsystems engineering tools for biological discovery, diagnostic, prognostic, and therapeutic applications. Thrust areas of interest are the development of novel living cell-based, lab-on-a-chip type devices for sorting blood cells, for high-throughput biochemistry in small volumes, and for studying cellular behavior in controlled microenvironments.

Proper citation: BioMEMS Resource Center (RRID:SCR_001417) Copy   

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http://deweylab.biostat.wisc.edu/psginfer/

Software for inference of alternative splicing from RNA-Seq data with probabilistic splice graphs.

Proper citation: PSGInfer (RRID:SCR_000243) Copy   

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http://www.structbioinfor.org/cascleave2/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A novel tool developed using Java program for the high-throughput in silico identification of substrate cleavage sites for various caspases from the amino acid sequences of the substrates.

Proper citation: Cascleave (RRID:SCR_000197) Copy   

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

Software package that fits heterogeneous error models for analysis of microarray data

Proper citation: HEM (RRID:SCR_000194) Copy   

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http://www.aetionomy.eu/

Consortium founded to establish mechanism-based taxonomies for Alzheimer's and Parkinson's disease and other neurodegenerative disorders (NDD), with the goal of facilitating development of more effective and targeted treatments. To do this, the consortium collects and analyzes data to: * Create new ways to combine underutilized data currently available in the literature, public databases, and from private companies * Determine how to dynamically organize and structure different types of knowledge about NDD * Determine how to apply this knowledge to construct new patient group classification * Identify correlations between disease features at molecular, tissue or organ-specific, and clinical levels * Identify sub-groups of patients based on the molecular cause of their disease, as opposed to the nature and location of their symptoms * Deliver data, tools, and recommendations for the biomedical community in the treatment of NDD A mechanism-based taxonomy is hoped to advance the: # Description and organization of the indication-specific data # Linking of data to disease models, based on causal and correlative relationships The expected outcome of AETIONOMY is a new NDD taxonomy system that distinguishes mixed pathologies, allowing for new features or classes to be added into the taxonomy, all with the goal of aiding drug and biomarker discovery.

Proper citation: AETIONOMY (RRID:SCR_000232) Copy   

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http://molegro-virtual-docker.software.informer.com/

An integrated platform for predicting protein-ligand interactions, the visualization of new ideas and analyzing protein targets.

Proper citation: Molegro Virtual Docker (RRID:SCR_000190) Copy   

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http://www.zju.edu.cn/english/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A public research university with twelve main academic disciplines that include science, engineering, agriculture and medicine. The university has campuses across China in locations such as Yuquan, Zhijiang and Zhoushan. It has studies available in undergraduate, graduate and post-doctorate degrees.

Proper citation: Zhejiang University; Zhejiang; China (RRID:SCR_000224) Copy   

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http://www.paradyn.org/mrnet/

A software-based network that provides efficient multicast and reduction communications for parallel and distributed tools and systems. Some key features of this resource include scalable data aggregation, multiple concurrent data channels and high-bandwidth communication.

Proper citation: MRNet (RRID:SCR_000225) Copy   

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http://deweylab.biostat.wisc.edu/rsem/

Software package for quantifying gene and isoform abundances from single end or paired end RNA Seq data. Accurate transcript quantification from RNA Seq data with or without reference genome. Used for accurate quantification of gene and isoform expression from RNA-Seq data.

Proper citation: RSEM (RRID:SCR_000262) Copy   

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http://www.tcd.ie/

A public university, which is a part of the University of Dublin, and contains three main academic disciplines: Arts, Humanities and Social Sciences; Engineering, Mathematics and Sciences; and Health Sciences. The institution offers degrees at the undergraduate and graduate level.

Proper citation: Trinity College Dublin; Dublin; Ireland (RRID:SCR_000261) Copy   

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http://sourceforge.net/projects/ms-spectre/

Software that provides (Quantitiave) analysis of multiple ls-ms(ms) runs, using mzXML import of raw data coming from spectrometers.

Proper citation: MS-Spectre (RRID:SCR_000266) Copy   

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http://www.uca.edu.ar/index.php/home/index/es

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 10th,2023. Private medical school in Buenos Aires that offers degree programs in the medical sciences. Resource is in Spanish.

Proper citation: Pontifical Catholic University of Argentina School of Medical Sciences; Buenos Aires; Argentina (RRID:SCR_000264) Copy   

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http://tomcat.esat.kuleuven.be/MACBETH/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31, 2023. Web service for performing microarray classification. It aims at finding the best prediction among different classification methods by using randomizations of the benchmarking dataset.

Proper citation: M(at)CBETH (RRID:SCR_000265) Copy   

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https://www.gov.pl/web/science

Polish governmental agency that administers governmental activities in science and higher education. Funding is provided by the state for scientific research.

Proper citation: Polish Ministry of Science and Higher Education (RRID:SCR_000251) Copy   

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http://www.upc.edu/?set_language=en

A public research university in Spain which specializes in the fields of architecture, engineering and technology at the undergraduate, graduate and postdoctoral level. UPC focuses heavily on internationalization, this is demonstrated through their large population of international PhD and master's degree students. They are a member of the Top Industrial Managers for Europe network and several university federations, including the Conference of European Schools for Advanced Engineering Education and Research (CESAER).

Proper citation: Polytechnic University of Catalonia; Barcelona; Spain (RRID:SCR_000252) Copy   

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https://www.upv.es/

A technical university in Spain which offers degree programs in 14 different faculties, including business administration, computer science and industrial engineering at the undergraduate, graduate and postdoctoral level. The school has five different campuses.

Proper citation: Polytechnic University of Valencia; Valencia; Spain (RRID:SCR_000255) Copy   

•   Source: SciCrunch Registry