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http://cran.r-project.org/src/contrib/Archive/iFad/
An R software package implementing a bayesian sparse factor model for the joint analysis of paired datasets, the gene expression and drug sensitivity profiles, measured across the same panel of samples, e.g. cell lines.
Proper citation: iFad (RRID:SCR_000271) Copy
Provides digital infrastructure capabilities for research and innovation across Queensland and Australia. Provides services, infrastructure and support for computation and data driven collaborative research and its application in industry. Members are six Queensland universities – The University of Queensland, Queensland University of Technology, Griffith University, James Cook University, CQUniversity, and the University of Southern Queensland. The University of the Sunshine Coast is an associate member. Member employees provide support and development services.
Proper citation: Queensland Cyber Infrastructure Foundation Ltd (RRID:SCR_000208) Copy
A software for genome assembly, and is specifically designed to analyze long Sanger-chemistry reads.
Proper citation: ARACHNE (RRID:SCR_000351) Copy
https://sites.google.com/site/beckerjeremie/home/nucleofinder
A software for a statistical approach for the detection of nucleosome positions in a cell population. The software identifies important features of nucleosome organization such as the spacing downstream of active promoters and the enrichment and depletion of GC/AT dinucleotides of in vitro nucleosomes.
Proper citation: NucleoFinder (RRID:SCR_000368) Copy
A commercial graphing software company that offers scientific software for statistical analyses, curve fitting and data analysis. It offers four programs: Prism, InStat, StatMate and QuickCalcs.
Proper citation: GraphPad (RRID:SCR_000306) Copy
Software environment for maintaining databases of molecular sequences and additional information, and for analyzing the sequence data, with emphasis on phylogeny reconstruction. Programs have primarily been developed for ribosomal ribonucleic acid (rRNA) sequences and, therefore, contain special tools for alignment and analysis of these structures. However, other molecular sequence data can also be handled. Protein gene sequences and predicted protein primary structures as well as protein secondary structures can be stored in the same database. ARB package is designed for graphical user interface. Program control and data display are available in a hierarchical set of windows and subwindows. Majority of operations can be controlled using mouse for moving pointer and the left mouse button for initiating and performing operations.
Proper citation: ARB project (RRID:SCR_000515) Copy
A lab organization which has bases in Munich, Germany and at Columbia University and focuses its research on protein structure and function using sequence and evolutionary information. They utilize machine learning and statistical methods to analyze genetic material and its gene products. Research goals of the lab involve using protein and DNA sequences along with evolutionary information to predict aspects of the proteins relevant to the advance of biomedical research.
Proper citation: ROSTLAB (RRID:SCR_000792) Copy
http://blog.expressionplot.com/
Software package consisting of a default back end, which prepares raw sequencing or Affymetrix microarray data, and a web-based front end, which offers a biologically centered interface to browse, visualize, and compare different data sets.
Proper citation: ExpressionPlot (RRID:SCR_001904) Copy
https://www.mangold-international.com/en/products/software/behavior-research-with-mangold-interact
Software platform for synchronized viewing and analysis of video footage and audio files in observational research by Mangold International GmbH. Qualitative and quantitative video coding software.
Proper citation: Interact (RRID:SCR_019254) Copy
https://www.leica-microsystems.com/products/microscope-software/details/product/leica-las-x-ls/
Software for image capture, processing and analysis with Leica fluorescence and confocal microscopes.
Proper citation: Leica Application Suite X (RRID:SCR_013673) Copy
http://www.cyto.purdue.edu/flowcyt/software/Winmdi.htm
Software to analyze flow cytometry listmode data files.
Proper citation: WinMDI Software (RRID:SCR_013745) Copy
http://dirt.projectbamboo.org/
Registry of digital research tools for scholarly use that makes it easy for digital humanists and others conducting digital research to find and compare resources ranging from content management systems to music OCR, statistical analysis packages to mindmapping software., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Bamboo DiRT (RRID:SCR_002556) Copy
A curated database that provides comprehensive integrated biological information for Saccharomyces cerevisiae along with search and analysis tools to explore these data. SGD allows researchers to discover functional relationships between sequence and gene products in fungi and higher organisms. The SGD also maintains the S. cerevisiae Gene Name Registry, a complete list of all gene names used in S. cerevisiae which includes a set of general guidelines to gene naming. Protein Page provides basic protein information calculated from the predicted sequence and contains links to a variety of secondary structure and tertiary structure resources. Yeast Biochemical Pathways allows users to view and search for biochemical reactions and pathways that occur in S. cerevisiae as well as map expression data onto the biochemical pathways. Literature citations are provided where available.
Proper citation: SGD (RRID:SCR_004694) Copy
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
https://edspace.american.edu/openbehavior/
Repository of open source tools for behavioral neuroscience research. OpenBehavior features hardware (tools, devices, apparatuses), as well as software for data acquisition and analysis and for the investigation of animal behavior and cognition. Dedicated to accelerating research through promotion of collaboration and open source projects.
Proper citation: OpenBehavior (RRID:SCR_015938) Copy
http://www.hunter.cuny.edu/chemistry/facilities/nmr/home
A service facility with four main spectrometers. The facility consists of four NMR instruments: a JEOL GX-400, a Varian Inova 500, a Bruker Avance 500 equipped with a 13C-1H cryoprobe, and a Bruker Avance III 600 MHz spectrometer equipped with a cryoprobe. These spectrometers are utilized by scientists from Hunter College, as well as from the entire CUNY community. The large variety of available probes allows detection of virtually any MR-active nuclide. Data analysis is performed either at the spectrometer workstation with vendor software or off-line with third party software packages.
Proper citation: Hunter NMR Spectroscopy Facility (RRID:SCR_000883) 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
http://www.adinstruments.com/products/software/modules/neuro_explorer.php
THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 19, 2018; A provider of computer-based data acquisition and analysis systems for life science. Products enable users to record and analyze life science data quickly and efficiently. ADInstruments product range is based on the PowerLab data acquisition system with LabChart software. The PowerLab system (also MacLab) is used in universities, hospitals, research institutes, pharmaceutical companies, contract research organizations and other private industry research sectors.
Proper citation: ADInstruments - Data Acquisition Systems for Life Science (RRID:SCR_001620) Copy
Biomedical technology research center that develops new algorithms, visualizations and conceptual frameworks to study biological networks at multiple levels and scales, from protein-protein and genetic interactions to cell-cell communication and vast social networks. They are developing freely available, open-source suite of software technology that broadly enables network-based visualization, analysis, and biomedical discovery for NIH-funded researchers. This software is enabling researchers to assemble large-scale biological data into models of networks and pathways and to use these networks to better understand how biological systems operate under normal conditions and how they fail in disease. The National Resource for Network Biology is organized around the following key components: Technology Research and Development, Driving Biomedical Projects, Outreach, Training and Dissemination of Tools. The NRNB supports several types of training events, including both virtual and live workshops; tutorials sessions for clinicians, biologists and bioinformaticians; presentations and demonstrations at conferences; online tutorials and webcasts; and annual symposium.
Proper citation: National Resource for Network Biology (RRID:SCR_004259) Copy
http://www.sbpdiscovery.org/technology/sr/Pages/LaJolla_GenomicsDNAAnalysis.aspx
Core facility that provides sequencing services, access to equipment and consultation on experimental design and data analysis. Available instruments include the Life Technologies Ion Torrent PGM and Ion Proton sequencers. Core also provides amplification-free analysis of RNA expression using the NanoString nCounter, and additionally provides sequencing and analysis services to investigators outside of SBP. Included in the cost of sequencing is basic bioinformatic analysis (SNP/InDel calling, transcript abundance). Lastly, the core also provides advice on experimental design, and guidance on the capabilities of next-generation sequencing.
Proper citation: Sanford Burnham Prebys Medical Discovery Institute Genomics DNA Analysis Facility (RRID:SCR_014866) Copy
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