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Research Resources

Use the NIA Research Resources database to find NIA-supported scientific resources, datasets, informatics resources, and more. Search by keyword, resource type, or NIA Division or IRP. 

Informatics

ANOVA

NIA Array Analysis tool is a free on-line software for statistical analysis of gene expression data (microarrays or RNA-seq). The tool uses ANOVA to evaluate the statistical significance (p-value and FDR) of differential gene expression on log-scale. Results are visualized using log-ratio plots and scatter-plots. Principal Component Analysis (PCA) is used to identify major patterns of variability in gene expression, and then clusters of genes correlated with each PC are delineated. Additional tools include finding genes whose expression matches a given pattern, plotting the dendrogram for individual replications, the error function (SD vs. expression level), and displaying the correlation matrix. Input data is uploaded as tab-delimited text together with annotation file for microarray platform.

To learn more about ANOVA and download the tool for use, click here.


MitoAnalyzer

mitoAnalyzer is a software package that provides a general approach for the analysis of mitochondrial DNA (mtDNA) in next-generation sequencing studies, using whole-genome sequencing data. It has two components:

  • mitoCaller -- an algorithm designed specifically to identify mtDNA variants (i.e., homoplasmies and heteroplasmies)
  • mitoCaller incorporates sequencing error rates at each base in a likelihood calculation and allows allele fractions at a variant site to differ among individuals. It relies on a genotype likelihood calculation, described below: 
  • Genotype Likelihood Calculation:Genotype Likelihood Calculation
  • mitoCalc and fastMitoCalc -- programs to estimate mtDNA copy number in a cell directly from sequencing data
  • mitoCalc and fastMitoCalc estimate mtDNA copy number based on the observed ratios of sequence coverages between mtDNA and autosomal DNA.
  • The most recent update, fastMitoCalc is a program that can estimate mtDNA copy number highly accurately but is more than 100 times faster than mitoCalc.
  • fastMitoCalc can rapidly analyze hundreds of thousands of genomes, thereby facilitating association studies of mtDNA copy number with quantitative traits or nuclear variants.

Click here for more information, including download and use instructions for MitoAnalyzer


Pancreas++

Pancreas++ is a novel algorithm that facilitates the fully-automated, non-biased, and highly reproducible investigation of islet area and alpha- and beta-cell quantity, as well as position within the islet for either single or large batches of fluorescent images. The algorithm uses active contour models to quantify images accurately and quickly, resulting in an output of an easy-to-read tabular format. Pancreas++ can distinguish between relevant pixels and noise, process multiple islets within the same image, and function without the aid of user interaction. Read more about Pancreas++


Plurigon

Plurigon is a data visualization and classification tool for the integration of high-dimensionality visualization algorithms with a user-friendly, interactive graphical interface. Plurigon processes a series of floating-point numbers into a deformable 3D object with a visible topography using spiral spacing, convex hulls, and laplacian smoothing of polygonal meshes. Plurigon contains an easy-to-use keyboard layout for axial drawing, zooming, rotating, importing, and exporting. Read more about Plurigon and download the tool.


Textrous!

Textrous! is a web-based framework for the extraction of biomedical semantic meaning from a given input gene set of arbitrary length. Textrous! employs natural language processing techniques, including latent semantic indexing , sentence splitting, word tokenization, parts-of-speech tagging, and noun-phrase chunking, to mine MEDLINE abstracts, PubMed Central articles, articles from the Online Mendelian Inheritance in Man, and Mammalian Phenotype annotation obtained from Jackson Laboratories.


VennPlex

VennPlex is a novel Venn diagram generating tool that can separate factors between two to four input datasets. VennPlex has been designed to separate data which possesses a sortable denominator (e.g. official Gene Symbol) with an associated variable numerator (e.g. z-ratio value). VennPlex can separate denominators between sets and also demonstrate the differences in the numerator values for denominators common to multiple set intersections that possess distinct numerical values. Read more about VennPlex and download the file


VENNTURE

VENNTURE is a novel Venn diagram-generating tool that can accommodate the input of up to 6 distinct data sets from an Excel spreadsheet. VENNTURE allows Venn diagram set image generation with additional intersection data representation viewing modes. The Venn segment contents can either be viewed in the VENNTURE Venn diagram image itself or they can be exported to an annotated Excel spreadsheet.

This software is available for download and is contained in a Winzip file along with the NIH Software Transfer Agreement and a PDF formatted copy of the journal article. Download the VENNTURE ZIP file. Please cite the following paper when employing this tool in publications or other forms of media:

Martin B, Chadwick W, Yi T, Park SS, Lu D, Ni B, Gadkaree S, Farhang K, Becker KG, Maudsley S.  VENNTURE–A Novel Venn Diagram Investigational Tool for Multiple Pharmacological Dataset Analysis.  PLoS ONE 10.1371/journal.pone.0036911


WND-CHARM

WND-CHARM is an acronym that stands for "Weighted Neighbor Distance using Compound Hierarchy of Algorithms Representing Morphology.  "WND-CHARM is a multi-purpose image classifier that can be applied to a wide variety of image classification tasks without modifications or fine-tuning, and yet provides classification accuracy comparable to state-of-the-art task-specific image classifiers. WND-CHARM can extract up to ~3,000 generic image descriptors (features) including polynomial decompositions, high contrast features, pixel statistics, and textures. These features are derived from the raw image, transforms of the image, and compound transforms of the image (transforms of transforms). The features are filtered and weighted depending on their effectiveness in discriminating between a set of predefined image classes (the training set). These features are then used to classify test images based on their similarity to the training classes. This classifier was tested on a wide variety of imaging problems including biological and medical image classification using several imaging modalities, face recognition, and other pattern recognition tasks.

To learn more about, and download WND-CHARM for use, click here.


Clinical Research Resources

Short Physical Performance Battery (SPPB)

The Short Physical Performance Battery (SPPB) is an objective assessment tool for evaluating lower extremity functioning in older persons. It was developed by the National Institute on Aging and is available for use without permission or royalty fees. This site will allow you to download the contents of a training CD that includes comprehensive instructions on the administration of the battery, safety tips, a scoring sheet and background information on publications that support the methodology. These files may be used on your computer or written to a CD. A cover for the CD case is also available for downloading and printing.

Download the Short Physical Performance Battery (SPPB) tool here.


Biophysics Resources

XYT Event Detector

XYT Event Detector detects and analyses time-dependent increases in intensity of a fluorescent indicator recorded by high-speed 2D cameras.  Specifically, the program was developed and tuned to detect Local Calcium Releases in cardiac pacemaker cells. It works with stacks of tif images of Ca signals measured in living cells. The consecutive images in the stack represent the intensity of local Ca dynamics measured with a fixed sampling rate by a high-speed camera and a fluorescent Ca indicator. When pacemaker cells generate a cardiac impulse, the action potential induces a global Ca increase in cytoplasmic Ca (dubbed AP-induced Ca transient). The program identifies and eliminates global signal shifts and transients and detects only local signals. Read more about the XYT Event Detector