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http://www.biomol-informatics.com/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 12, 2021. Technology based company in Madrid that offers consulting services on Bioinformatics in areas of research, diagnostics and pharmaceutical industry.

Proper citation: Biomol-Informatics (RRID:SCR_004081) 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://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://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://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://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://blog.expressionplot.com/

Software package consisting of a default back end, which prepares raw sequencing or Affymetrix microarray data, and a web-based front end, which offers a biologically centered interface to browse, visualize, and compare different data sets.

Proper citation: ExpressionPlot (RRID:SCR_001904) 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.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

http://bioconductor.org/packages/2.9/bioc/html/RamiGO.html

Software package with an R interface sending requests to AmiGO visualize, retrieving DAG GO trees, parsing GraphViz DOT format files and exporting GML files for Cytoscape. Also uses RCytoscape to interactively display AmiGO trees in Cytoscape.

Proper citation: RamiGO (RRID:SCR_006922) Copy   

•   Source: SciCrunch Registry

http://scicrunch.org

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 27, 2019.

Database for those interested in the consequences of Factor VIII genetic variation at the DNA and protein level, it provides access to data on the molecular pathology of haemophilia A. The database presents a review of the structure and function of factor VIII and the molecular genetics of haemophilia A, a real time update of the biostatistics of each parameter in the database, a molecular model of the A1, A2 and A3 domains of the factor VIII protein (based on the crystal structure of caeruloplasmin) and a bulletin board for discussion of issues in the molecular biology of factor VIII. The database is completely updated with easy submission of point mutations, deletions and insertions via e-mail of custom-designed forms. A methods section devoted to mutation detection is available, highlighting issues such as choice of technique and PCR primer sequences. The FVIII structure section now includes a download of a FVIII A domain homology model in Protein Data Bank format and a multiple alignment of the FVIII amino-acid sequences from four species (human, murine, porcine and canine) in addition to the virtual reality simulations, secondary structural data and FVIII animation already available. Finally, to aid navigation across this site, a clickable roadmap of the main features provides easy access to the page desired. Their intention is that continued development and updating of the site shall provide workers in the fields of molecular and structural biology with a one-stop resource site to facilitate FVIII research and education. To submit your mutants to the Haemophilia A Mutation Database email the details. (Refer to Submission Guidelines)

Proper citation: HAMSTeRS - The Haemophilia A Mutation Structure Test and Resource Site (RRID:SCR_006883) Copy   

•   Source: SciCrunch Registry

http://geneontology.org/docs/tools-overview/

Collection of tools developed by GO Consortium and by third parties. Tools are listed by category or alphabetically and continue to be improved and expanded.

Proper citation: Gene Ontology Tools (RRID:SCR_006941) Copy   

•   Source: SciCrunch Registry

http://www.bmu.psychiatry.cam.ac.uk/software/

Suite of programs developed for fMRI analysis in a Virtual Pipeline Laboratory facilitates combining program modules from different software packages into processing pipelines to create analysis solutions which are not possible with a single software package alone. Current pipelines include fMRI analysis, statistical testing based on randomization methods and fractal spectral analysis. Pipelines are continually being added. The software is mostly written in C. This fMRI analysis package supports batch processing and comprises the following general functions at the first level of individual image analysis: movement correction (interpolation and regression), time series modeling, data resampling in the wavelet domain, hypothesis testing at voxel and cluster levels. Additionally, there is code for second level analysis - group and factorial or ANOVA mapping - after co-registration of voxel statistic maps from individual images in a standard space. The main point of difference from other fMRI analysis packages is the emphasis throughout on the use of data resampling (permutation or randomization) as a basis for inference on individual, group and factorial test statistics at voxel and cluster levels of resolution.

Proper citation: Cambridge Brain Activation (RRID:SCR_007109) Copy   

•   Source: SciCrunch Registry

http://weizhong-lab.ucsd.edu/cd-hit/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software program for clustering biological sequences with many applications in various fields such as making non-redundant databases, finding duplicates, identifying protein families, filtering sequence errors and improving sequence assembly etc. It is very fast and can handle extremely large databases. CD-HIT helps to significantly reduce the computational and manual efforts in many sequence analysis tasks and aids in understanding the data structure and correct the bias within a dataset. The CD-HIT package has CD-HIT, CD-HIT-2D, CD-HIT-EST, CD-HIT-EST-2D, CD-HIT-454, CD-HIT-PARA, PSI-CD-HIT, CD-HIT-OTU and over a dozen scripts. * CD-HIT (CD-HIT-EST) clusters similar proteins (DNAs) into clusters that meet a user-defined similarity threshold. * CD-HIT-2D (CD-HIT-EST-2D) compares 2 datasets and identifies the sequences in db2 that are similar to db1 above a threshold. * CD-HIT-454 identifies natural and artificial duplicates from pyrosequencing reads. * CD-HIT-OTU cluster rRNA tags into OTUs The usage of other programs and scripts can be found in CD-HIT user''s guide. CD-HIT was originally developed by Dr. Weizhong Li at Dr. Adam Godzik''s Lab at the Burnham Institute (now Sanford-Burnham Medical Research Institute)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CD-HIT (RRID:SCR_007105) Copy   

•   Source: SciCrunch Registry

https://bams1.org/

Knowledge management system designed to handle neurobiological information at different levels of organization of vertebrate nervous system. Database and repository for information about neural circuitry, storing and analyzing data concerned with nomenclature, taxonomy, axonal connections, and neuronal cell types. Handles data and metadata collated from original literature, or inserted by scientists that is associated to four levels of organization of vertebrate nervous system. Data about expressed molecules, neuron types and classes, brain regions, and networks of brain regions.

Proper citation: Brain Architecture Management System (RRID:SCR_007251) Copy   

•   Source: SciCrunch Registry

http://apid.dep.usal.es

APID Interactomes (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). The interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier.

Proper citation: Agile Protein Interactomes DataServer (RRID:SCR_008871) Copy   

•   Source: SciCrunch Registry