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http://www.uchicagoddrcc.org/research-cores/tissue-engineering-and-cell-models-core
Core that provides services such as a repository for intestinal cell lines, Tissue Engineering Models, experimental materials, and supplies for digestive disease research.
Proper citation: University of Chicago Digestive Diseases Research Core Center Tissue Engineering and Cell Models Core (RRID:SCR_015604) Copy
http://www.sanger.ac.uk/science/tools/alien-hunter
Software for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs). The predictions (embl format) can be automatically loaded into Artemis genome viewer.
Proper citation: Alien-hunter (RRID:SCR_015967) Copy
https://zenodo.org/record/17651
Software for interfacing with Tucker-Davis System 3 hardware. It is a Python wrapper around Tucker-Davis Technologies ActiveX library. Along with standard operations, the software can conduct type conversions between analog and digital units, handle robust errors, and has a remote procedure call server that allows multiple processes and/or programs to communicate with the hardware across the same connection.
Proper citation: TDTPy (RRID:SCR_014520) Copy
http://www.tcd.ie/IMM/trinity-biobank/index.php
The Trinity Biobank was established in 2005 to serve the needs of researchers in the area of genetic epidemiology, population genetics and pharmacogenomics. Its services are available to researchers not only in Trinity College but to other institutions at home and abroad. We provide an automated DNA extraction service purifying large volumes blood (up to 10mL whole blood) and tissue DNA for archival and other purposes. In addition it makes available purified DNA and associated GWAS data from 2000 healthy donors for research use. A key requirement for reliable downstream use of DNA is purity and strand size. The quality of DNA in blood and tissue deteriorates upon storage without purification even at -80 degrees C. We ensure rapid turnaround of biological samples through automated extraction using the Qiagen Autopure system based on optimized ''salting out'' chemistry. The purified DNA sample may then be stored safely at -20 degrees C without deterioration thus freeing up valuable -80 degree C freezer space and the associated capital and maintenance cost as well as security and lab space provision. Automated DNA extraction is particularly suitable for high-throughput sample processing called for in epidemiological studies or simply for clearing sample inventory backlogs. The Trinity Biobank distributes control DNA to researchers as part of its remit to enhance the level of research activity and to synergize molecular medicine research nationally and internationally. The buffy coat collection has been made possible with the cooperation of the Irish Blood Transfusion Service (IBTS). An important requirement to access the collection is that the use of the samples relates only to ethically-approved research and to specifically-nominated research projects. The DNA collection consists of high quality human genomic DNA. Each of the available 2,000 samples is from a single individual and each sample comes with the age and gender data of the donor. The buffy coat sample is derived from the total white cell compliment (50mL buffy coat) of a blood donation (c 400mL). We will endeavor to fulfill samples number requests based on age and gender as best as possible. This collection has also been genotyped using the Affymetrix Genome-Wide Human SNP Array 6.0, featuring 1.8 million genetic markers, including more than 906,600 single nucleotide polymorphisms (SNPs) and more than 946,000 probes for the detection of copy number variation (CNV). The DNA comes available as a 100ng/uL in 100uL of TE Buffer, ie in 10ug amounts in a separate screw-cap ampoule. The ampoules are shipped in 100-tube boxes (Sarstedt). Corresponding plasma (ACD) is also available on request. Genotype data is supplied in PLINK binary PED files format (http://pngu.mgh.harvard.edu/~purcell/plink/ ).
Proper citation: Trinity Biobank (RRID:SCR_013279) Copy
http://huttenhower.sph.harvard.edu/galaxy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Algorithm for high-dimensional biomarker discovery and explanation that identifies genes, pathways, or taxa characterizing the differences between two or more biological conditions. The algorithm identifies features that are statistically different among biological classes, then performs additional tests to assess whether these differences are consistent with respect to expected biological behavior. Statistical significance and biological relevance are emphasized., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: LEfSe (RRID:SCR_014609) Copy
Interoperability framework which supports integrative genomics analysis via access to various bioinformatics tools. Rather than performing analyses itself, GenomeSpace acts as a hub for data from supported bioinformatics tools and reformats data and results when necessary.
Proper citation: GenomeSpace (RRID:SCR_014967) Copy
https://www.thermofisher.com/order/catalog/product/4363991
Software that allows users to manually or automatically design custom primers and probes for gene quantitation and allelic discrimination (SNP) real-time PCR applications. It supports assays based on TaqMan and SYBR Green I dye chemistries.
Proper citation: Primer Express (RRID:SCR_014326) 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
https://CRAN.R-project.org/package=Boruta
Algorithm that performs feature selection. It finds relevant features by comparing original attributes' importance with importance achievable at random, estimated using their permuted copies (shadows).
Proper citation: Boruta (RRID:SCR_016234) Copy
http://www.hkl-xray.com/hkl-2000
Software package for structural determination and other functions in the field of structural biology. Its programs can perform strategy and simulation, 3-D processing, mosaicity refinement during processing, variable spot size, easy change of the space group, report generation, and other functions.
Proper citation: HKL-2000 (RRID:SCR_015547) Copy
http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software application to compute composite measures of linkage disequilibrium, their variances and covariances, and statistical tests, for all pairs of alleles from two loci when linkage phase is unkown. An extension of Weir and Cockerham (1989) to apply to multi-allelic loci. (entry from Genetic Analysis Software)
Proper citation: COMPOSITELD (RRID:SCR_013132) Copy
http://www.multichannelsystems.com/software/mc-datatool
An add-on tool used to export data retrieved with the MC_Rack program. This software is used to convert MC_Rack data files into other file formats.
Proper citation: MC DataTool (RRID:SCR_014580) Copy
https://github.com/NCBI-Hackathons/PhenVar
Software tool used to generate a list of PubMed IDs to query and generate associations between publications. It utilizes a local SQLite cache in a configurable location to keep a local copy of relevant SRIDs, PMIDs, and the Abstract sections for the PMIDs.
Proper citation: PhenVar (RRID:SCR_015515) Copy
Software for browsing the image data acquired by Nikon C1 and a Nikon C1si system.
Proper citation: EZ-C1 FreeViewer (RRID:SCR_014277) Copy
A biomaterial supply resource which collects and disseminates human heart tissue. Samples include both failing and non-failing hearts, RNA/DNA analysis, tissue staining and immunofluorescence samples.The tissue that has been flash frozen and stored at -80˚C is acquired from distinct regions of the heart such as the LV free wall, septum, and valve leaflets. Individual sample sizes are typically 100-300mg for flash frozen tissues. The DHHR also serves as a resource for assay development, target identification, and sponsored research, capable of isolating cardiomyocytes from hearts and using them for in-vitro assays such as calcium handling, enzyme activity, signalling pathways and other biochemical research activities
Proper citation: Duke Human Heart Repository (RRID:SCR_013980) Copy
A software repository which provides open source software and technology for visualization, computer vision, medical imaging, data publishing, and quality software process solutions. Kitware also provides services such as creating customized applications for clients, porting their open-source tools to specialized computing platforms, and supporting their open-source software tools with documentation, professional consulting services, and software training.
Proper citation: Kitware (RRID:SCR_013989) Copy
A software repository which provides open source software for machine learning. Software entries include information such as author, license, data format, and programming language. The ultimate goal of mloss.org is to create a comprehensive open source machine learning environment where open source machine learning software can compete with comercial closed source solutions.
Proper citation: machine learning open source software (RRID:SCR_013990) Copy
http://www.cancer.gov/researchandfunding
Federal government agency for cancer research and training established in 1937. National Cancer Program is responsibility of NCI to coordinate, conduct and support research, training, health information dissemination with respect to cause, diagnosis, prevention, and treatment of cancer, rehabilitation from cancer, and continuing care of cancer patients and families of cancer patients. Supports construction of laboratories, clinics, and related facilities necessary for cancer research through award of grants.
Proper citation: National Cancer Institute (RRID:SCR_011176) Copy
https://europepmc.org/annotations
Text mining tool from Europe PMC that allows biological terms or concepts to be highlighted for readers on full text articles. These terms and concepts are identified by text mining algorithms, which are developed by a variety of text mining groups. However, it is up to the reader to control which selection of highlighted concepts they see. Once concepts of interest have been identified within the text, they are formatted according to the W3C Web Annotation Data Model and stored in a triple store via the EMBL-EBI RDF Platform. As a reader views an article in a web browser, any annotations in the triple store associated with the article are made available in a menu alongside the article.
Proper citation: SciLite (RRID:SCR_015015) Copy
https://github.com/ChristophRau/wMICA
Weighted implementation of Maximal Information Component Analysis, a co-expression network analysis algorithm for analysis of large interconnected networks and the identification of modules of similarly-acting nodes within the larger network.
Proper citation: wMICA (RRID:SCR_015490) Copy
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