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http://www.uams.edu/

Division of medical sciences at a public research university in Arkansas. It focuses on education, research, and clinical programs with a specific goal to implement translational research in care.

Proper citation: University of Arkansas for Medical Sciences; Arkansas; USA (RRID:SCR_002522) Copy   

•   Source: SciCrunch Registry

http://www.opendoar.org/

A quality-controlled directory of academic open access repositories that provides a simple repository list, and lets you search for repositories or search repository contents. Additionally, tools and support to both repository administrators and service providers in sharing best practice and improving the quality of the repository infrastructure are provided. The current directory lists repositories and allows breakdown and selection by a variety of criteria which can also be viewed as statistical charts. The underlying database has been designed from the ground up to include in-depth information on each repository that can be used for search, analysis, or underpinning services like text-mining.

Proper citation: OpenDOAR (RRID:SCR_002641) Copy   

•   Source: SciCrunch Registry

http://jcb-dataviewer.rupress.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A web-based, multi-dimensional image data-viewing application for original microscopy image datasets associated with articles published in The Journal of Cell Biology, a peer-reviewed journal published by The Rockefeller University Press. The JCB DataViewer can host multidimensional fluorescence microscopy images, 3D tomogram data, very large (gigapixel) images, and high content imaging screens. Images are presented in an interactive viewer, and the scores from high content screens are presented in interactive graphs with data points linked to the relevant images. The JCB DataViewer uses the Bio-Formats library to read over 120 different imaging file formats and convert them to the OME-TIFF image data standard. Image data are archived by the Journal and may be freely accessed by readers using the JCB DataViewer. Download of author-provided image data and associated metadata in OME-TIFF format is also possible with author permission, allowing for independent analysis of image data irrespective of acquisition or viewing software. Although the JCB DataViewer is designed to host and facilitate sharing and analysis of original microscopy image data, authors may also upload other types of original image data as supplements to their manuscripts, including histology and electron micrographs and digital scans of gels or blots.

Proper citation: JCB DataViewer (RRID:SCR_002633) Copy   

•   Source: SciCrunch Registry

https://pdbp.ninds.nih.gov

Common data management resource and web portal to promote discovery of Parkinson's Disease diagnostic and progression biomarker candidates for early detection and measurement of disease progression. PDBP will serve as multi-faceted platform for integrating existing biomarker efforts, standardizing data collection and management across these efforts, accelerating discovery of new biomarkers, and fostering and expanding collaborative opportunities for all stakeholders.

Proper citation: Parkinson’s Disease Biomarkers Program Data Management Resource (PDBP DMR) (RRID:SCR_002517) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/tapir/

A set of command line tools allowing 2D and 3D image registration, mainly for medical imaging (although also relevant to other image registration problems).

Proper citation: TAPIR (RRID:SCR_002596) Copy   

•   Source: SciCrunch Registry

http://ckan.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A complete out-of-the-box data management software solution that makes data accessible by providing tools to streamline publishing, sharing, finding and using data. CKAN is aimed at data publishers (national and regional governments, companies and organizations) wanting to make their data open and available. It uses its internal model to store metadata about the different records, and presents it on a web interface that allows users to browse and search this metadata. It also offers a powerful API that allows third-party applications and services to be built around it. CKAN is built with Python on the backend and Javascript on the frontend, and uses the Pylons web framework and SQLAlchemy as its ORM. Its database engine is PostgreSQL and its search is powered by SOLR. It has a modular architecture that allows extensions to be developed to provide additional features such as harvesting or data upload. CKAN is currently used by governments and user groups worldwide to power both official and community data portals.

Proper citation: CKAN (RRID:SCR_002622) Copy   

•   Source: SciCrunch Registry

http://sncid.stanleyresearch.org/

A database of 1749 neuropathological markers measured in 12 different brain regions from 60 brains in the Consortium Collection from the Stanley Medical Research Institute combined with microarray data and statistical tools. Fifteen brains each are from patients diagnosed with schizophrenia, bipolar disorder, or major depression, and unaffected controls. The four groups are matched by age, sex, race, postmortem interval, pH, side of brain, and mRNA quality. A Repository of raw data is also included. Users must register for access.

Proper citation: Stanley Neuropathology Consortium Integrative Database (RRID:SCR_002749) Copy   

•   Source: SciCrunch Registry

http://rsync.samba.org/

Software that provides rapid incremental file transfer.

Proper citation: rsync (RRID:SCR_003113) Copy   

•   Source: SciCrunch Registry

http://noble.gs.washington.edu/proj/segtools/

Segtools is a Python package designed to put genomic segmentations back in the context of the genome! Using R for graphics, Segtools provides a number of modules to analyze a segmentation in various ways and help you interpret its biological relevance. Segmentations should be in BED4+ or GFF format, with the ''name'' field of each line used specifying the segment label of that line. The Segtools commands allow you to compare the properties of the segment labels with one another.

Proper citation: Segtools (RRID:SCR_004394) Copy   

•   Source: SciCrunch Registry

http://www.mdanderson.org/

The mission of The University of Texas MD Anderson Cancer Center is to eliminate cancer in Texas, the nation, and the world through outstanding programs that integrate patient care, research and prevention, and through education for undergraduate and graduate students, trainees, professionals, employees and the public. VISION: We shall be the premier cancer center in the world, based on the excellence of our people, our research-driven patient care and our science. We are Making Cancer History.

Proper citation: University of Texas MD Anderson Cancer Center (RRID:SCR_004699) Copy   

•   Source: SciCrunch Registry

https://simtk.org/home/cpodes

CPODES is a numerical integrator for solving multibody dynamics problems using coordinate projection. It is based on the CVODES integrator which is part of the DOE Sundials suite. It is a multistep integrator providing variable order Adams (up to 12th order) and BDF (up to 5th order) methods for non-stiff problems and BDF (up to 5th order) for stiff problems. It uses CVODES to advance the ODE, and then performs coordinate projection back to the constraint manifold to exactly solve the DAE. The projection is also incorporated back into the error test where it permits larger steps. Binaries of this software are bundled with other SimTK Core modules.

Proper citation: CPODES numerical integrator (RRID:SCR_000766) Copy   

•   Source: SciCrunch Registry

http://bamview.sourceforge.net/

A free interactive display of read alignments in BAM data files that can be launched with Java Web Start or downloaded. This interactive Java application for visualizing the large amounts of data stored for sequence reads which are aligned against a reference genome sequence can be used in a number of contexts including SNP calling and structural annotation. It has been integrated into Artemis so that the reads can be viewed in the context of the nucleotide sequence and genomic features. The source code is available as part of the Artemis code which can be downloaded from GitHub.

Proper citation: BamView (RRID:SCR_004207) Copy   

•   Source: SciCrunch Registry

http://www.loni.usc.edu/

Biomedical technology resource center specializing in novel approaches and tools for neuroimaging. It develops novel strategies to investigate brain structure and function in their full multidimensional complexity. There is a rapidly growing need for brain models comprehensive enough to represent brain structure and function as they change across time in large populations, in different disease states, across imaging modalities, across age and sex, and even across species. International networks of collaborators are provided with a diverse array of tools to create, analyze, visualize, and interact with models of the brain. A major focus of these collaborations is to develop four-dimensional brain models that track and analyze complex patterns of dynamically changing brain structure in development and disease, expanding investigations of brain structure-function relations to four dimensions.

Proper citation: Laboratory of Neuro Imaging (RRID:SCR_001922) Copy   

•   Source: SciCrunch Registry

http://noble.gs.washington.edu/proj/genomedata/

A format for efficient storage of multiple tracks of numeric data anchored to a genome. The format allows fast random access to hundreds of gigabytes of data, while retaining a small disk space footprint. They have also developed utilities to load data into this format. Retrieving data from this format is more than 2900 times faster than a naive approach using wiggle files. A reference implementation in Python and C components is available here under the GNU General Public License. The software has only been tested on Linux and Mac systems.

Proper citation: Genomedata (RRID:SCR_004544) Copy   

•   Source: SciCrunch Registry

http://www.bioinf.uni-leipzig.de/Software/RNAplex/

Software tool to rapidly search for short interactions between two long RNAs.

Proper citation: RNAplex (RRID:SCR_002763) Copy   

•   Source: SciCrunch Registry

https://pubmed.ncbi.nlm.nih.gov/21129402/

Source code that allows you to calculate the different measures used in Kreuz T, Chicharro D, Greschner M, Andrzejak RG (2011): Time-resolved and time-scale adaptive measures of spike train synchrony, http://www.sciencedirect.com/science/article/pii/S0165027010006564. Journal of Neuroscience Methods,195, 92-106 & Kreuz T, Chicharro D, Andrzejak RG, Haas JS, and Abarbanel HDI (2009) Measuring multiple spike train synchrony. Journal of Neuroscience Methods 183:287-299 http://www.sciencedirect.com/science/article/pii/S0165027009003616

Proper citation: Time-resolved and time-scale adaptive measures of spike train synchrony (RRID:SCR_001667) Copy   

•   Source: SciCrunch Registry

http://www.ks.uiuc.edu/Research/vmd/

A molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.

Proper citation: Visual Molecular Dynamics (RRID:SCR_001820) Copy   

•   Source: SciCrunch Registry

https://journals.aps.org/pre/abstract/10.1103/PhysRevE.80.026217

Source code that allows you to calculate the different measures used in Chicharro D, Andrzejak RG (2009): Reliable detection of directional couplings using rank statistics. Physical Review E, 80, 026217.

Proper citation: Reliable detection of directional couplings using rank statistics (RRID:SCR_001662) Copy   

•   Source: SciCrunch Registry

https://reich.hms.harvard.edu/software

XP-CLR (Chen et al. 2010) uses allele frequency differentiation at linked loci to detect selective sweeps. Source code and documentation are available.

Proper citation: XP-CLR (RRID:SCR_004961) Copy   

•   Source: SciCrunch Registry

http://alchemy.sourceforge.net/

ALCHEMY is a genotype calling algorithm for Affymetrix and Illumina products which is not based on clustering methods. Features include explicit handling of reduced heterozygosity due to inbreeding and accurate results with small sample sizes. ALCHEMY is a method for automated calling of diploid genotypes from raw intensity data produced by various high-throughput multiplexed SNP genotyping methods. It has been developed for and tested on Affymetrix GeneChip Arrays, Illumina GoldenGate, and Illumina Infinium based assays. Primary motivations for ALCHEMY''s development was the lack of available genotype calling methods which can perform well in the absence of heterozygous samples (due to panels of inbred lines being genotyped) or provide accurate calls with small sample batches. ALCHEMY differs from other genotype calling methods in that genotype inference is based on a parametric Bayesian model of the raw intensity data rather than a generalized clustering approach and the model incorporates population genetic principles such as Hardy-Weinberg equilibrium adjusted for inbreeding levels. ALCHEMY can simultaneously estimate individual sample inbreeding coefficients from the data and use them to improve statistical inference of diploid genotypes at individual SNPs. The main documentation for ALCHEMY is maintained on the sourceforge-hosted MediaWiki system. Features * Population genetic model based SNP genotype calling * Simultaneous estimation of per-sample inbreeding coefficients, allele frequencies, and genotypes * Bayesian model provides posterior probabilities of genotype correctness as quality measures * Growing number of scripts and supporting programs for validation of genotypes against control data and output reformating needs * Multithreaded program for parallel execution on multi-CPU/core systems * Non-clustering based methods can handle small sample sets for empirical optimization of sample preparation techniques and accurate calling of SNPs missing genotype classes ALCHEMY is written in C and developed on the GNU/Linux platform. It should compile on any current GNU/Linux distribution with the development packages for the GNU Scientific Library (gsl) and other development packages for standard system libraries. It may also compile and run on Mac OS X if gsl is installed.

Proper citation: ALCHEMY (RRID:SCR_005761) Copy   

•   Source: SciCrunch Registry