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http://www.moldiscovery.com/software/vsplus/
Software package for molecular descriptors, ADME prediction and membrane permeability prediction. These can then be used with provided chemometric tools to build statistical models.
Proper citation: VolSurf (RRID:SCR_014911) Copy
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.bio-rad.com/en-us/sku/soft-om-sw-opticon-monitor-software
Software which controls all operations in the experimental setup, data acquisition and monitoring, and data analysis stages of the Bio-Rad Opticon 2 system. In the experimental setup stage, setup and programming operations are accessed from the Master File window. The master file consists of a plate file, which specifies the parameters of the plate, and a protocol file, which specifies the experimental conditions. After a plate and a protocol setup have been created or selected, a run can be initiated, which begins the data acquisition and monitoring stage. Data collection can be monitored during the run by viewing a plot of fluorescence intensity vs. cycle number. In the data analysis stage, data can be analyzed using the Quantitation, Melting Curve, and/or Analysis windows. The window used depends on the type of data being collected.
Proper citation: Opticon Monitor Software (RRID:SCR_014241) Copy
A GDS and OASIS file viewer editor that has file overlay and file creation capabilities. It features include: layer grouping, flexible rulers, image overlay, partial editing functions, and external library support.
Proper citation: KLayout (RRID:SCR_014644) 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://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
http://CRAN.R-project.org/package=RVAideMemoire
Software package that contains miscellaneous functions useful in biostatistics, such as univariate and multivariate testing procedures with a special emphasis on permutation tests. Many functions shorten existing procedures and implement plotting functions that can be used with a variety of methods and packages.
Proper citation: R package: RVAideMemoire (RRID:SCR_015657) Copy
http://www.salk.edu/science/core-facilities/media-preparation-core/
Core facility that provides media, plates, and commonly used buffers for molecular biology applications and culturing mammalian cells, C. elegans, yeast, and bacteria. The Media Preparation Core Facility is equipped with 3 automatic plate pourers supported by 2 programmable media kettles capable of producing up to 9 liters of agar or nutrient media per run under gentle and reproducible conditions. Plates are available in 6 cm or 10 cm formats.
Proper citation: Salk Institute Media Preparation Core Facility (MPRP) (RRID:SCR_014844) Copy
http://www.ccp4.ac.uk/html/pointless.html
Pointless scores all the possible Laue groups consistent with the crystal class, which is based on cell dimension restraints, by matching potential symmetry equivalent reflections. For chiral systems, the Laue group uniquely implies the point group then checks sets of reflections which may be systematically absent to suggest a possible spacegroup. There is also a check for lattice centering, i.e., a check for whole classes of reflections having essentially zero intensity, including a check for obverse/inverse twinning in rhombohedral systems. Pointless is also capable of converting XDS, Scalepack, SHELX or SAINT formats to MTZ.
Proper citation: Pointless (RRID:SCR_014218) Copy
http://www.sbpdiscovery.org/technology/sr/Pages/LaJolla_StemCells.aspx
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The former functions of this facility are split into two separate operations. The first is the generation and characterization of induced Pluripotent Stem Cells (iPSCs) is now being performed on a collaborative basis for both internal and external investigators with the Snyder lab. The second is a shared laboratory dedicated to the culture and analysis of stem cells that is available to SBP investigators.
Proper citation: Sanford Burnham Prebys Medical Discovery Institute Stem Cell Core (RRID:SCR_014856) 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://www.sbpdiscovery.org/technology/sr/Pages/LaJolla_TumorAnalysis.aspx
Facility that provides analysis of animal models of human cancer and other diseases. It provides investigators access to a wide variety of human cancer cell lines for xenograft studies, some primary human xenograft models and additional transgenic mouse solid tumors and leukemia models. The core also offers serial passaging of tumors and derivation of 2D and 3D cultures from xenograft tumors, including patient-derived xenograft (PDX) models. These short-term cell cultures established from PDXs enable in vitro analysis including high throughput screening with compounds or RNAi for functional characterization.
Proper citation: Sanford Burnham Prebys Medical Discovery Institute Tumor Analysis (RRID:SCR_014858) 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/missy139/PreSurgMapp
A MATLAB toolbox for processing the functional areas of the brain using multi-modal fMRI data for pre-surgical mapping. It is composed of three types of individual-level ICA analyses for user use. Traditional ICA (task) can be used for task fMRI. Either Traditional ICA (rest) or ICA with DICI (rest) can be used for rs-fMRI. Traditional ICA (rest) is designed for users who already have a hypothesis of the pattern of the target component and want to have manually set components by themselves. ICA with DICI (rest) is completely automatic, given that the user provides a template (provided). The software utilizes an automatic component identification method that is based on the discriminatory-index. All the components from multiple ICA runs with multiple component settings are ranked and compiled.
Proper citation: PreSurgMapp (RRID:SCR_014427) Copy
https://github.com/jyeatman/AFQ
A framework for generating Tract Profiles of tissue properties for major fiber tracts in healthy and diseased brains. Online documentation can be found at: https://github.com/yeatmanlab/AFQ/wiki. AFQ has been tested for MATLAB r2009b through MATLAB r2014b. It requires functions from the MATLAB stats toolbox, vistasoft and SPM.
Proper citation: AFQ: Automated Fiber Quatification (RRID:SCR_014546) 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
An open-source cheminformatics and machine-learning toolkit that is useable from Java or Python. It includes a collection of standard cheminformatics functionality for molecule I/O, substructure searching, chemical reactions, coordinate generation (2D or 3D), fingerprinting, etc., as well as a high-performance database cartridge for working with molecules using the PostgreSQL database. Documentation is available on the main website.
Proper citation: RDKit: Open-Source Cheminformatics Software (RRID:SCR_014274) Copy
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