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https://github.com/MicrosoftGenomics/FaST-LMM

FaST-LMM (Factored Spectrally Transformed Linear Mixed Models) is a set of tools for efficiently performing genome-wide association studies (GWAS), prediction, and heritability estimation on large data sets.

Proper citation: FaST LMM (RRID:SCR_015506) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.org/ghemical/ghemical/index.html

Molecular modelling software package with 3D-visualization tools. It supports methods based on both molecular mechanics and quantum mechanics (using MOPAC7, and MPQC for QM). It contains geometry optimization (for MM and QM) and molecular dynamics (for MM) algorithms.

Proper citation: Ghemical (RRID:SCR_014899) Copy   

•   Source: SciCrunch Registry

http://www.wavefun.com/

Software program for determining molecular structure and calculating chemical properties. It has a graphical interface and accurate computational models that are compatible with the iPad, iPhone and iPod Touch. When combined with the Spartan'16 Parallel Suite, this enables the first fully-functional open-ended molecular modeling environment on popular mobile technology.

Proper citation: SPARTAN (RRID:SCR_014901) Copy   

•   Source: SciCrunch Registry

http://www.fujitsu.com/jp/group/kyushu/en/solutions/industry/lifescience/admeworks/

Software program for high-speed virtual screening intended for simultaneous evaluation of ADMET properties of compounds. ADMEWORKS Predictor employs a number of models to predict ADMET properties using models based on values of topological, geometric, physicochemical and substructure descriptors derived from the molecular structures.

Proper citation: ADMEWORKS Predictor (RRID:SCR_014905) Copy   

•   Source: SciCrunch Registry

http://www.optibrium.com/stardrop/index.php

Software toolkit for drug design and discovery, including plugins for in silico compound optimization, compound selection and integration into other databases.

Proper citation: StarDrop (RRID:SCR_014902) Copy   

•   Source: SciCrunch Registry

https://www.urmc.rochester.edu/microbiology-immunology/xenopus-laevis.aspx

A comprehensive resource specializing in the use of the amphibian Xenopus laevis (the African clawed frog) for biomedical and immunological research. Several genetically-defined inbred strains and clones are available for study. The facility also maintains and develops research tools such as transgenic animals, monoclonal antibodies, cell lines, DNA libraries, and molecular probes. XLRR includes a satellite facility devoted to study infectious diseases caused by iridovirus. Technical assistance, education, and training are also provided.

Proper citation: Xenopus laevis Research Resource for Immunobiology (XLRR) (RRID:SCR_014354) Copy   

•   Source: SciCrunch Registry

https://www.med.upenn.edu/gtp/vectorcore/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1, 2023. A full service viral vector core facility located at the University of Pennsylvania. This facility provides technological resources for investigators in their use of viral based vectors for gene transfer. The main objective of this core is to provide investigators with state-of-the-art vector technology for preclinical studies and other basic research applications, that will then increase understanding of gene function and the further development of therapeutic vectors.

Proper citation: Vector Core (RRID:SCR_014475) Copy   

•   Source: SciCrunch Registry

http://brainbox.pasteur.fr/

Web application which allows users to visualise and collaboratively segment and annotate any brain MRI dataset available online via URL. A list of brains are available for use on the main site. Segmentations are automatically saved and can be downloaded as Nifti files or triangular meshes. Users can point BrainBox to their own Nifti data, or try data catalogues created by the community.

Proper citation: BrainBox (RRID:SCR_014750) Copy   

•   Source: SciCrunch Registry

http://spina.sourceforge.net

Software tool to deliver estimated structure parameters of endocrine feedback control systems in vivo from serum or plasma hormone levels. Used for evaluation of thyroid function. Allows for calculating thyroid maximum secretory capacity (GT or SPINA-GT) and sum activity of peripheral 5'-deiodinases (GD or SPINA-GD) from levels of TSH, (F)T4 and (F)T3 that have been determined once only (SPINA Thyr). Binaries are available for Mac OS, Mac OS X, Palm OS, Garnet OS and Windows. For other operating systems, including Linux, Solaris and BSD, SPINA Thyr is available as sourcecode. Building from source requires THINK Pascal (for Mac OS Classic), winsoft PocketStudio (for Palm OS / Garnet OS) or Lazarus/Free Pascal (for Mac OS X, Windows, Linux, BSD and Solaris). Special version of calculation engine is available for modern S implementation, e.g. R.

Proper citation: SPINA Thyr (RRID:SCR_014352) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.klayout.de/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://genomespace.org

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry