Tools   Select Another Resource Report Type

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.nikon.com/products/microscope-solutions/support/download/software/confocal/c1_freevw_v390.htm

Software for browsing the image data acquired by Nikon C1 and a Nikon C1si system.

Proper citation: EZ-C1 FreeViewer (RRID:SCR_014277) Copy   

•   Source: SciCrunch Registry

http://www.rdkit.org/

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   

•   Source: SciCrunch Registry

https://imdevsoftware.wordpress.com/imdev/

A software application of RExcel that integrates R into Excel as an embedded additon for omics tasks and analysis. It can be used specifically for tasks concerning multivariate data visualization, exploration, and analysis. imDev has interactive modules for dimensional reduction, prediction, feature selection, analysis of correlation, and generation of networked structures, all of which provide an integrated environment for systems level analysis of multivariate data.

Proper citation: imDEV (RRID:SCR_014674) Copy   

•   Source: SciCrunch Registry

http://www.avisoft.com/soundanalysis.htm

Sound analysis software used to process and analyze animal acoustic communications. Its features include digital filtering, real-time spectrogram display, and advanced metadata management. Avisoft SASLabPro is designed to accommodate large numbers of sound files and includes organizational features, including labeling options for single point data and time section labels.

Proper citation: Avisoft SASLabPro (RRID:SCR_014438) Copy   

•   Source: SciCrunch Registry

http://prospector.ucsf.edu

A package of over twenty mass spectrometry-based tools primarily geared toward proteomic data analysis and database mining. It can be run from the command line, but is primarily used through a web browser, and there is a public website that allows anyone to use the software without local installation. Tandem mass spectrometry analysis tools are used for database searching and identification of peptides, including post-translationally modified peptides and cross-linked peptides. Support for isotope and label-free quantification from this type of data is provided. MS-Viewer software allows sharing and displaying of annotated spectra from many different tandem mass spectrometry data analysis packages. Other tools include software for analyzing peptide mass fingerprinting data (MS-Fit); prediction of theoretical fragmentation of peptides (MS-Product); theoretical chemical or enzymatic digestion of proteins (MS-Digest); and theoretical modeling of the isotope distribution of any chemical, including peptides (MS-Isotope). Searches using amino acid sequence can be used to identify homologous peptides in a database (MS-Pattern); the use of the combination of amino acid sequence and masses can be used for homologous peptide and protein identification using MS-Homology. Tandem mass spectrometry peak list files can be filtered for the presence of certain peaks or neutral losses using MS-Filter. Given a list of proteins, MS-Bridge can report all potential cross-linked peptide combinations of a specified mass. Given a precursor peptide mass and information about known amino acid presence, absence, or modifications, MS-Comp can report all amino acid combinations that could lead to the observed mass.

Proper citation: Protein Prospector (RRID:SCR_014558) Copy   

•   Source: SciCrunch Registry

http://www.acdlabs.com/resources/freeware/nmr_proc/

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 27, 2016. A software package that provides 1D and 2D NMR tools as well as processing and interpretation for all other major analytical techniques (LC/MS, IR, Raman, and more) in one package. It also has support for structure verification and multiplet reports.

Proper citation: ACD/ NMR Processor (RRID:SCR_014679) Copy   

•   Source: SciCrunch Registry

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

Structure from motion algorithms repository. Common interface for various sfm algorithms.

Proper citation: SFMProject (RRID:SCR_014166) Copy   

•   Source: SciCrunch Registry

http://www.canvasgfx.com/en/products/canvas-15

Illustration and communication software for engineers and technical graphics professionals that combines the ability to make 3D images while also applying filters and duatone images. The software has minimum precision levels and object illustration and image editing tools to keep data accurate throughout the authoring process. Users can accelerate and streamline the technical illustration workflow from initial import and design to final presentation, facilitate collaboration, and improve the overall productivity. Tutorials and technical documents are available on the website.

Proper citation: Canvas X (RRID:SCR_014288) Copy   

•   Source: SciCrunch Registry

http://www.yerkes.emory.edu/about/news/neuropharmacology_neurologic_diseases/Transgenic_Huntingtons_Disease_Monkey_Resource_Available.html

Center for resources to facilitate basic and preclinical applications of the transgenic Huntington's disease (HD) monkey model to advance scientific knowledge and the discovery of a cure for HD. Their resources include longitudinal biomaterials and MRI data, postmortem biomaterials, and research proposal assistance.

Proper citation: Transgenic Huntington's Disease Monkey Resources (RRID:SCR_014560) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://neurophysics.ucsd.edu/software.php

Matlab-based routines for the detection and clustering of putative single units from a multi-unit time series, along with quality metrics. This sofwtare was developed by the David Kleinfeld Laboratory at UC San Diego.

Proper citation: UltraMegaSort 2000 (RRID:SCR_015857) Copy   

•   Source: SciCrunch Registry

https://www.omicron-laser.de/english/lasers/diode-lasers/phoxx-lasers/phoxx-diode-laser.html

Software application for PhoxX® Diode Laser to support Omicron products. It is related to uManager open source microscopy software for control of microscopes.

Proper citation: PhoxX Controller (RRID:SCR_016309) Copy   

•   Source: SciCrunch Registry