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Software used to simulate tumor progression in various stages of growth in order to study the process' dynamics. The input can be fitness landscape, mutation rate, and cell division time. The output is growth dynamics and other relevant statistics, such as expected tumor detection time and expected appearance time of surviving mutants. The tool is implemented in Java and runs on all operating systems which run a Java Virtual Machine (JVM) of version 1.7 or above.
Proper citation: Tool for Tumor Progression (RRID:SCR_014700) Copy
A consortium of leading national Australian universities which collects and preserves digital research data and makes these data available for secondary analysis. The consortium provides a data catalogue comprised of seven sub-archives: Social Science, HIstorical, Indigenous, Longitudinal, Qualitative, Crime and Justice, and International. All users can browse and search the catalogue, view study and variable documentation, and download related material. Registered users can also analyze and visualize most data online and users who have completed the relevant undertaking form(s) can download entire studies or subsets of variables. Deposited data are processed, reviewed, and published for research use.
Proper citation: Australian Data Archive (RRID:SCR_014706) Copy
Computing platform for biomolecular NMR available to not-for-profit or government users. It consists of a virtual machine (VM) provisioned with dozens of widely-used NMR software packages, and is available as a cloud-based Platform-as-a-Service (PaaS) or as a downloadable VM for local execution.
Proper citation: NMRbox (RRID:SCR_014827) Copy
https://www.ebi.ac.uk/efo/webulous/
Server used to create spreadsheets with ontology based data validations. Webulous can process populated templates and transform them into OWL/RDF using design patterns expressed in OPPL. It also has an add-on with Google spreadsheets which supports loading templates from a Webulous server and allows users to submit populated spreadsheets back to the Webulous server for transformation into OWL.
Proper citation: Webulous (RRID:SCR_014825) Copy
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/hclust.html
R documentation for hierarchical cluster analysis on a set of dissimilarities for n objects. Each object is assigned to its own cluster, which an algorithm proceeds through iteratively. Two of the most similar clusters are joined at each stage until there is a single cluster. Distances between clusters are recomputed at each stage by the Lance–Williams dissimilarity update formula according to the particular clustering method being used. Clustering methods include: Ward's minimum variance method, complete linkage method, and single linkage method.
Proper citation: Hierarchical Clustering (RRID:SCR_014673) Copy
https://github.com/jakejh/zeitzeiger
R package for regularized supervised learning on high-dimensional data from an oscillatory system. Zeitzeiger can quantify rhythmic behavior, make accurate predictions, identify major patterns and important features, and detect when the oscillator is perturbed.
Proper citation: Zeitzeiger (RRID:SCR_014791) Copy
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/prcomp.html
R documentation for a function that performs a principal components analysis on a given data matrix and returns the results as an object of class prcomp.
Proper citation: Principal Components Analysis (RRID:SCR_014676) Copy
Mobile software application for behavioral social science experiments on an online platform. It can be used on computers, tablets, and smartphones. It is hardware independent, does not require online connectivity to perform a test, and has the option of interfacing with outside sensors, such as heart rate or weighting scales.
Proper citation: Xperiment (RRID:SCR_014712) Copy
https://imdevsoftware.wordpress.com/software/
A software suite for data wrangling, creating interactive data visualization, performing statistical analyses, cluster analyses, exploratory data analysis and visualization (such as principal component analysis), predictive modeling and biochemical pathway analysis.
Proper citation: DeviumWeb (RRID:SCR_014683) Copy
Imaging center dedicated to fostering research in the social, behavioral, biological, engineering, and materials sciences where imaging methodologies play a central role. The SLEIC provides the Penn State research community with instrumentation, technological and substantive expertise, educational opportunities, and financial support for conducting magnetic resonance imaging (MRI) and electrophysiology (EEG, ERP) experiments.
Proper citation: Pennsylvania State University SLEIC (RRID:SCR_014922) Copy
http://www.sailing.cs.cmu.edu/main/?page_id=511
Automatic software program for profiling spatial gene expression patterns from Fly embryo ISH images. It utilizes image-based genome-scale profiling of whole-body mRNA patterns.
Proper citation: SPEX2 (RRID:SCR_014923) Copy
Collection of databases with standalone databases, which gives opportunity for customers to integrate the data into their internal tools and databases, as well as online databases, that are available to the customers from a dedicated website where an individual can query and export the data in the selected format. The standalone database topics include medicinal chemistry, drugs and target class based compounds. The online databases are comprised of three major compilations: GVK BIO Online Structure Activity Relation Database (GOSTAR), GVK BIO Biomarker Database (GOBIOM), and Clinical Trial Outcome Database (CTOD).
Proper citation: GVKBIO databases (RRID:SCR_014893) Copy
https://dogma.ccbb.utexas.edu/
Web-based annotation tool for plant chloroplasts and animal mitochondrial genomes. DOGMA allows the use of BLAST searches against a custom database, and conservation of basepairing in the secondary structure of animal mitochondrial tRNAs to identify and annotate genes.
Proper citation: DOGMA (RRID:SCR_015060) Copy
https://diabetes.med.umich.edu/partners/michigan-diabetes-research-center-mdrc
Multidisciplinary unit of the University of Michigan funded by the National Institute of Diabetes and Digestive and Kidney Diseases/National Institute of Health. Promotes new discoveries and enhance scientific progress through the support of basic and clinical research related to diabetes, its complications, and related disorders. Creates environment that supports innovative research; attracts and retains early stage investigators and investigators new to diabetes research; provides core services that leverage funding and unique expertise; fosters interdisciplinary collaborations; raises awareness and interest in fundamental and clinical diabetes research at their institutions, as well as locally, regionally, and nationally.
Proper citation: Michigan Diabetes Research Center (RRID:SCR_015112) Copy
http://www.compudrug.com/toxalert
Software tool for high-throughput toxicity prediction; it assists in the early and quick identification of toxic drug candidates. ToxAlert provides probability percentages for different toxicity endpoints such as oncogenicity, mutagenicity, teratogenicity, neurotoxicity or cell toxicity.
Proper citation: ToxAlert (RRID:SCR_014907) Copy
http://bioinformatics.psb.ugent.be/orcae/
Online genome annotation tool for validating and correcting gene annotations. OrcAE is community-driven and can be edited by account-holders in the research community.
Proper citation: Online Resource for Community Annotation of Eukaryotes (RRID:SCR_014989) Copy
https://www.thermofisher.com/order/catalog/product/IQLAAEGAAPFADBMBCX
Mass spectrometer that combines quadrupole, ion trap, and Orbitrap mass analysis.
Proper citation: LTQ-Orbitrap Fusion Tribrid Mass Spectrometer (RRID:SCR_014992) Copy
Statistical software for ROC curve analysis. MedCalc performs several statistical tests such as method comparison, method evaluation, reference intervals, and meta-analysis.
Proper citation: MedCalc (RRID:SCR_015044) Copy
https://www.nikoninstruments.com/en_EU/Products/Upright-Microscopes/Research/Eclipse-FN1
Fixed-stage microscope for electrophysiological research. Features include open design, noise reduction, 16x objective lens, and water dipping objective with depth induced aberration correction.
Proper citation: Nikon: Eclipse FN1 Microscope (RRID:SCR_014995) Copy
https://www.agilent.com/cs/library/datasheets/Public/5991-2541EN.pdf
Hardware system which automates RNA, DNA, and protein sample QC, including sample loading, separation, and imaging.
Proper citation: Agilent: 2200 TapeStation Instrument (RRID:SCR_014994) Copy
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