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http://harvard.eagle-i.net/i/0000012e-58c7-d44f-55da-381e80000000

Core to provide gene expression data analysis service. Activities range from the provision of services to fully collaborative grant funded investigations.

Proper citation: Harvard Partners HealthCare Center for Personalized Genetic Medicine Bioinformatics Core Facility (RRID:SCR_000882) Copy   

•   Source: SciCrunch Registry

http://www.scienceexchange.com/facilities/macquarie-university

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23,2023. Set of facilities based out of Macquarie University in New South Wales. Some facilities provide services such as proteome analysis or resources of various academic departments like engineering, biological sciences, and geography.

Proper citation: Macquarie University Labs and Facilities (RRID:SCR_000944) Copy   

•   Source: SciCrunch Registry

https://phenogen.org

Website for analyzing microarray data. Software toolbox for storing, analyzing and integrating microarray data and related genotype and phenotype data. The site is particularly suited for combining QTL and microarray data to search for candidate genes contributing to complex traits. In addition, the site allows, if desired by the investigators, sharing of the data. Investigators can conduct in-silico microarray experiments using their own and/or shared data. There are five major sections of the site: Genome/Transcriptome Data Browser, Microarray Analysis Tools, Gene List Analysis Tools, QTL Tools, and Downloads. The genome/transcriptome data browser combines a genome browser with all the microarray, RNA-Seq, and Genomic Sequencing data. This provides an effective platform to view all of this data side by side. Source code is available on GitHub.

Proper citation: PhenoGen Informatics (RRID:SCR_001613) Copy   

•   Source: SciCrunch Registry

http://ilyinlab.org/friend/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Friend is a bioinformatics application designed for simultaneous analysis and visualization of multiple structures and sequences of proteins and/or DNA/RNA. The application provides basic functionalities such as: structure visualization with different rendering and coloring, sequence alignment, and simple phylogeny analysis, along with a number of extended features to perform more complex analyses of sequence structure relationships, including: structural alignment of proteins, investigation of specific interaction motifs, studies of protein-protein and protein-DNA interactions, and protein super-families. Friend is also useful for the functional annotation of proteins, protein modeling, and protein folding studies. Friend provides three levels of usage; 1) an extensive GUI for a scientist with no programming experience, 2) a command line interface for scripting for a scientist with some programming experience, and 3) the ability to extend Friend with user written libraries for an experienced programmer. The application is linked and communicates with local and remote sequence and structure databases.

Proper citation: An Integrated Multiple Structure Visualization and Multiple Sequence Alignment Application (RRID:SCR_001646) Copy   

•   Source: SciCrunch Registry

http://www.farsight-toolkit.org/wiki/FARSIGHT_Toolkit

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. A collection of software modules for image data handling, pre-processing, segmentation, inspection, editing, post-processing, and secondary analysis. These modules can be scripted to accomplish a variety of automated image analysis tasks. All of the modules are written in accordance with software practices of the Insight Toolkit Community. Importantly, all modules are accessible through the Python scripting language which allows users to create scripts to accomplish sophisticated associative image analysis tasks over multi-dimensional microscopy image data. This language works on most computing platforms, providing a high degree of platform independence. Another important design principle is the use of standardized XML file formats for data interchange between modules.

Proper citation: Farsight Toolkit (RRID:SCR_001728) Copy   

•   Source: SciCrunch Registry

http://surfer.nmr.mgh.harvard.edu/

Open source software suite for processing and analyzing human brain MRI images. Used for reconstruction of brain cortical surface from structural MRI data, and overlay of functional MRI data onto reconstructed surface. Contains automatic structural imaging stream for processing cross sectional and longitudinal data. Provides anatomical analysis tools, including: representation of cortical surface between white and gray matter, representation of the pial surface, segmentation of white matter from rest of brain, skull stripping, B1 bias field correction, nonlinear registration of cortical surface of individual with stereotaxic atlas, labeling of regions of cortical surface, statistical analysis of group morphometry differences, and labeling of subcortical brain structures.Operating System: Linux, macOS.

Proper citation: FreeSurfer (RRID:SCR_001847) Copy   

•   Source: SciCrunch Registry

http://dial.mc.duke.edu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. The Duke Image Analysis Laboratory (DIAL) is committed to providing comprehensive imaging support in research studies and clinical trials to various agencies. The capabilities of the lab include protocol development, site training and certification, and image archival and analysis for a variety of modalities including magnetic resonance imaging, magnetic resonance spectroscopy, computed tomography and nuclear medicine. DIAL uses the latest technologies to analyze Magnetic Resonance Imaging (MRI) data sets of the brain. Currently the lab is engaged in measurement of the hippocampus, amygdala, caudate, ventricular system, and other brain regional volumes. Each of these techniques have undergone a rigorous validation process. The measurements of brain structures provide a useful means of non-invasively testing for changes in the brain of the patient. Changes over time in the brain can be detected, and evaluated with respect to the treatment that the patient is receiving. Magnetic Resonance Spectroscopy (MRS) allows DIAL to obtain an accurate profile of the chemical content of the brain. This sensitive technique can detect small changes in the metabolic state of the brain; changes that vary in response to administration of therapeutic agents. The ability to detect these subtle shifts in brain chemistry allows DIAL to identify changes in the brain with more sensitivity than allowed by image analysis. In this respect, NMR spectroscopy can provide early detection of changes in the brain, and serves to compliment the data obtained from image analysis. Additionally, DIAL also contains SQUID (Scalable Query Utility and Image Database). It is an image management system developed to facilitate image management in research and clinical trials: SQUID offers secure, redundant image storage and organizational functions for sorting and searching digital images for a variety of modalities including MRI, MRS, CAT Scan, X-Ray and Nuclear Medicine. SQUID can access images directly from DUMC scanners. Data can also be loaded via DICOM CDs, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Duke University Medical Center: Duke Image Analysis Laboratory (RRID:SCR_001716) Copy   

•   Source: SciCrunch Registry

http://www.nesys.uio.no/Atlas3D/

A multi-platform visualization tool which allows import and visualization of 3-D atlas structures in combination with tomographic and histological image data. The tool allows visualization and analysis of the reconstructed atlas framework, surface modeling and rotation of selected structures, user-defined slicing at any chosen angle, and import of data produced by the user for merging with the atlas framework. Tomographic image data in NIfTI (Neuroimaging Informatics Technology Initiative) file format, VRML and PNG files can be imported and visualized within the atlas framework. XYZ coordinate lists are also supported. Atlases that are available with the tool include mouse brain structures (3-D reconstructed from The Mouse Brain in Stereotaxic Coordinates by Paxinos and Franklin (2001)) and rat brain structures (3-D reconstructed from The Rat Brain in Stereotaxic Coordinates by Paxinos and Watson (2005)). Experimental data can be imported in Atlas3D and warped to atlas space, using manual linear registration, with the possibility to scale, rotate, and position the imported data. This facilitates assignment of location and comparative analysis of signal location in tomographic images.

Proper citation: Atlas3D (RRID:SCR_001808) Copy   

•   Source: SciCrunch Registry

http://icahn.mssm.edu/research/resources/shared-resource-facilities/in-vivo-molecular-imaging

The In-Vivo Molecular Imaging Laboratory (IMIL) is a MSSM shared resource facility serving the research community of Mount Sinai with equipment and imaging expertise. State-of-the-art bioluminescent as well as fluorescent imaging modalities are supported for in-vivo monitoring of cellular and genetic activity. Investigators are provided with cutting edge imaging technologies as well as analysis techniques. The long-term goal is to establish a comprehensive SRF for in-vivo molecular imaging using micro-MRI, micro-PET and other modalities. IMIL houses a Xenogen IVIS-200 Series imaging system with the integrated fluorescent imaging options. Simultaneous dual reporter in-vivo imaging is possible with bioluminescence and fluorescence probes. The imaging chamber has a gas anesthesia manifold that can accommodate up to 5 mice for simultaneously image acquisition. Selectable field of views allow in-plane (X,Y) imaging resolutions of up to 60-microm. Integrated spectra filters allow for the determination of signal source depth (Z). IMIL will provide data acquisition services as well as analysis. IMIL has a dedicated imaging technologist for data acquisition. Investigators will bring their prepared animal to the lab and an IMIL imaging technologist will assist in sedating the animals and acquire imaging data. Typical imaging sessions last about an hour. Certified users who are trained in the use of the software will be able to perform their own analysis at the console. Usage of the imaging device is charged by the hour ($100/hour). Structural Imaging The IVIS-200 has the built-in capability of obtaining an image of the surface topography of the animal for 2D and 3D localization. If additional true 3D imaging data is required, micro MRI is available through the Imaging Science Laboratories (ISL). Image Analysis The IVIS-200 has an integrated image acquisition and analysis software (Living Image Software 2.50). Comprehensive data quantification is possible with this software. Raw data as well as analyzed results can be electronically transferred to the investigators. Support is also available for additional image analysis such as intermodality coregistration, 3D rendering, and group statistics. Additional software packages include MedX, SPM, Brainvoyager, Analyze, and in-house developed software.

Proper citation: Mount Sinai School of Medicine: In-Vivo Molecular Imaging Laboratory (RRID:SCR_001785) Copy   

•   Source: SciCrunch Registry

http://meme-suite.org/

Suite of motif-based sequence analysis tools to discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences; search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN; compare a motif to all motifs in a database of motifs; associate motifs with Gene Ontology terms via their putative target genes, and analyze motif enrichment using SpaMo or CentriMo. Source code, binaries and a web server are freely available for noncommercial use.

Proper citation: MEME Suite - Motif-based sequence analysis tools (RRID:SCR_001783) Copy   

•   Source: SciCrunch Registry

http://www.nesys.uio.no/Micro3D/

The Micro3D 2004 is a software for 3-D reconstruction, visualization, and analysis of neuronal populations and brain regions. Micro3D generates geometric models from line and point coded data sets, representing labeled objects such as cell bodies or axonal plexuses, and boundaries of brain regions in serial sections. Data are typically imported from image-combining computerized microscopy systems, such as Neurolucida (MicroBrightField, Colchester, VT). The models may be rotated and zoomed in real-time. Surfaces are re-synthesized on the basis of stacks of contour lines. Clipping is used for defining section-independent subdivisions of the model. Flattening of sheets of points in curved layers (e.g., neurons in a cortical lamina) facilitates inspection of complicated distribution patterns. Micro3D computes color-coded density maps, and allows production of mpeg videos. Micro3D 2004 runs on LINUX PCs equipped with Open Inventor. It performs operations similar to the Silicon Graphics based version that has been used in more than 25 investigations and in various species, ranging from insects to monkeys, at the LM- and EM-level. Sponsors:Micro 3D was developed with support from The Research Council of Norway and The Oslo Research Park / FORNY.

Proper citation: Neural Systems and Graphics Computing Laboratory: Micro3D Software (RRID:SCR_001811) Copy   

•   Source: SciCrunch Registry

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

Software package for brain image manipulation and analysis, focusing on fMRI and lesion analysis. VoxBo can be used independently or in conjunction with other packages. It provides GLM-based statistical tools, an architecture for interoperability with other tools (they encourage users to incorporate SPM and FSL into their processing pipelines), an automation system, a system for parallel distributed computing, numerous stand-alone tools, decent wiki-based documentation, and lots more.

Proper citation: VoxBo (RRID:SCR_002166) Copy   

•   Source: SciCrunch Registry

http://www.mevislab.de/index.php?id=6

Modular framework for the development of image processing algorithms and visualization and interaction methods, with a special focus on medical imaging. It includes advanced medical imaging modules for segmentation, registration, volumetry, and quantitative morphological and functional analysis. The platform allows fast integration and testing of new algorithms and the development of application prototypes that can be used in clinical environments. In MeVisLab, individual image processing, visualization and interaction modules can be combined to complex image processing networks using a graphical programming approach. The algorithms can easily be integrated using a modular, platform-independent C++ class library. An abstract, hierarchical definition language allows the design of efficient graphical user interfaces, hiding the complexity of the underlying module network to the end user. JavaScript components can be added to implement dynamic functionality on both the network and the user interface level. MeVisLab is based on the Qt application framework, the OpenInventor 3D visualization toolkit and OpenGL. Several clinical prototypes have been realized on the basis of MeVisLab, including software assistants for neuro-imaging, dynamic image analysis, surgery planning, and vessel analysis. Feature Overview: :- Basic image processing algorithms and advanced medical imaging modules :- Full featured, flexible 2D/3D visualization and interaction tools :- High performance for large datasets :- Modular, expandable C++ image processing library :- Graphical programming of complex, hierarchical module networks :- Object-oriented GUI definition and scripting :- Full scripting functionality using Python and JavaScript :- DICOM support and PACS integration :- Intuitive user interface :- Integrated movie and screenshot generation for demonstration purposes :- Generic integration of the Insight Toolkit (ITK) and the Visualization Toolkit (VTK) :- Cross-platform support for Windows, Linux, and MacOS X :- Available for 64-bit operating systems

Proper citation: Medical Image Processing and Visualization (RRID:SCR_002055) Copy   

•   Source: SciCrunch Registry

http://microarrays.curie.fr/publications/U900-RPPA_PLT/Normacurve/

Analysis methodology that allows simultaneous quantification and normalization of reverse phase protein array (RPPA) data.

Proper citation: NormaCurve (RRID:SCR_001995) Copy   

•   Source: SciCrunch Registry

https://tracedrawer.com/product/tracedrawer/

Software for evaluating, comparing and presenting real-time interaction data. Used for quantification of kinetics and affinity through curve fitting, with large number of binding models to choose from. Can extract experimental information from measurement, requiring minimal user input.

Proper citation: TraceDrawer (RRID:SCR_025782) Copy   

•   Source: SciCrunch Registry

http://www.megx.net

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Set of databases and tools that handle genomic and metagenomic sequences in their environmental contexts.Includes geographic information system to systematically store and analyse marine genomic and metagenomic data in conjunction with contextual information; environmental genome browser with fast search functionalities; database with precomputed analyses for selected complete genomes; database and tool to classify metagenomic fragments based on oligonucleotide signatures.

Proper citation: MeGX (RRID:SCR_000738) Copy   

•   Source: SciCrunch Registry

http://franklin.imgen.bcm.tmc.edu/

The mission of the Baylor College of Medicine - Shaw Laboratory is to apply methods of statistics and bioinformatics to the analysis of large scale genomic data. Our vision is data integration to reveal the underlying connections between genes and processes in order to cure disease and improve healthcare.

Proper citation: Baylor College of Medicine - Shaw Laboratory (RRID:SCR_000604) Copy   

•   Source: SciCrunch Registry

http://www.genmapp.org/

GenMAPP is a free computer application designed to visualize gene expression and other genomic data on maps representing biological pathways and groupings of genes. Integrated with GenMAPP are programs to perform a global analysis of gene expression or genomic data in the context of hundreds of pathway MAPPs and thousands of Gene Ontology Terms (MAPPFinder), import lists of genes/proteins to build new MAPPs (MAPPBuilder), and export archives of MAPPs and expression/genomic data to the web. The main features underlying GenMAPP are: *Draw pathways with easy to use graphics tools *Color genes on MAPP files based on user-imported genomic data *Query data against MAPPs and the GeneOntology Enhanced features include the simultaneous view of multiple color sets, expanded species-specific gene databases and custom database options.

Proper citation: Gene Map Annotator and Pathway Profiler (RRID:SCR_005094) Copy   

•   Source: SciCrunch Registry

http://primegens.org/

A Web-based Tool for High-throughput Primer and Probe Design. The program has its different utilities available on its web server. A standalone version is also available. Algorithms: * SSPD - Sequence Specific Primer Design: to design primers for each of the specific sequences given by the user in the query input file against any alternate potential hybridization with any of the sequences given in the database input file. * PSPD - Probe Specific Primer Design: to design primers it selects the gene-specific fragments (probes) to design primer pairs for their PCR amplification. * FSPD Fragment Specific Primer Design: primer design algorithm used when there is a very long query sequence for which multiple primers are required for its amplification. * Check Binding Specificity * Probe Design Only: Probe design algorithm could be used to find sequence-specific probes, which doesn''t show any blast hit against database. Such probe design has been used for targeted sequencing like agilent sure-select technology with next-generation sequencing.

Proper citation: PRIMEGENS (RRID:SCR_005474) Copy   

•   Source: SciCrunch Registry

http://bowtie-bio.sourceforge.net/index.shtml

Software ultrafast memory efficient tool for aligning sequencing reads. Bowtie is short read aligner.

Proper citation: Bowtie (RRID:SCR_005476) Copy   

•   Source: SciCrunch Registry