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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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GeneWindow Resource Report Resource Website 1+ mentions |
GeneWindow (RRID:SCR_008183) | software resource, data processing software, software application, data analysis software | Software tool for pre- and post-genetic bioinformatics and analytical work, developed and used at the Core Genotyping Facility (CGF) at the National Cancer Institute. While Genewindow is implemented for the human genome and integrated with the CGF laboratory data, it stands as a useful tool to assist investigators in the selection of variants for study in vitro, or in novel genetic association studies. The Genewindow application and source code is publicly available for use in other genomes, and can be integrated with the analysis, storage, and archiving of data generated in any laboratory setting. This can assist laboratories in the choice and tracking of information related to genetic annotations, including variations and genomic positions. Features of GeneWindow include: -Intuitive representation of genomic variation using advanced web-based graphics (SVG) -Search by HUGO gene symbol, dbSNP ID, internal CGF polymorphism ID, or chromosome coordinates -Gene-centric display (only when a gene of interest is in view) oriented 5 to 3 regardless of the reference strand and adjacent genes -Two views, a Locus Overview, which varies in size depending on the gene or genomic region being viewed and, below it, a Sequence View displaying 2000 base pairs within the overview -Navigate the genome by clicking along the gene in the Locus Overview to change the Sequence View, expand or contract the genomic interval, or shift the view in the 5 or 3 direction (relative to the current gene) -Lists of available genomic features -Search for sequence matches in the Locus Overview -Genomic features are represented by shape, color and opacity with contextual information visible when the user moves over or clicks on a feature -Administrators can insert newly-discovered polymorphisms into the Genewindow database by entering annotations directly through the GUI -Integration with a Laboratory Information Management System (LIMS) or other databases is possible | gene, genetic, analysis, annotation, archive, bioinformatic, cancer, genome, genomic, genotype, genotyping, human, human genome databases, maps, polymorphism, position, variation, data set |
is listed by: 3DVC has parent organization: National Cancer Institute |
nif-0000-21173 | SCR_008183 | GeneWindow | 2026-08-03 09:33:55 | 1 | |||||||||
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LIMMA Resource Report Resource Website 10000+ mentions |
LIMMA (RRID:SCR_010943) | LIMMA | software resource, data processing software, software application, data analysis software | Software package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression. | analysis, gene, expression, microarray, data, linear, model, bio.tools |
is used by: Glimma is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: GEO2R is related to: Bioconductor |
Free, Available for download, Freely available | biotools:limma, OMICS_00769 | https://omictools.com/limma-tool, https://bio.tools/limma, https://sources.debian.org/src/r-bioc-limma/ | SCR_010943 | Linear Models for Microarray Data | 2026-08-03 09:34:36 | 24583 | ||||||
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pClamp Resource Report Resource Website 5000+ mentions |
pClamp (RRID:SCR_011323) | data acquisition software, software application, data processing software, data analysis software, software resource | Software suite for electrophysiology data acquisition and analysis by Molecular Devices. Used for the control and recording of voltage clamp, current clamp, and patch clamp experiments. The software suite consists of Clampex 11 Software for data acquisition, AxoScope 11 Software for background recording, Clampfit 11 Software for data analysis, and optional Clampfit Advanced Analysis Module for sophisticated and streamlined analysis. | electrophysiology, data, acquisition, analysis, Molecular Device, voltage, clamp, | is listed by: SoftCite | Commercially available | rid_000085 | https://www.moleculardevices.com/products/axon-patch-clamp-system/acquisition-and-analysis-software/pclamp-software-suite#gref | SCR_011323 | patch clamp, Axon™pCLAMP™ 10 Electrophysiology Data Acquisition and Analysis Software, patch CLAMP, pCLAMP 11, pCLAMP 10, patch Clamp | 2026-08-03 09:34:51 | 9678 | |||||||
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HOMER Resource Report Resource Website 5000+ mentions |
HOMER (RRID:SCR_010881) | HOMER | sequence analysis software, software application, data processing software, data analysis software, software resource | Software tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++. | motif, discovery, next, generation, sequencing, analysis, genomic, data |
is listed by: OMICtools is related to: findMotif.pl has parent organization: University of California at San Diego; California; USA |
NURSA consortium grant ; NIH HC088093; NIDDK DK063491; NCI CA52599; NIGMS P50 GM081892; Foundation Leducq Transatlantic Network Grant |
PMID:20513432 | OMICS_00483 | http://biowhat.ucsd.edu/homer/index.html | SCR_010881 | HOMER, Hypergeometric Optimization of Motif EnRichment, Homer, Homer v4.5 | 2026-08-03 09:34:49 | 5370 | |||||
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Neuroimaging in Python Resource Report Resource Website 10+ mentions |
Neuroimaging in Python (RRID:SCR_013141) | NIPY, | software development tool, portal, community building portal, software development environment, software application, data or information resource, software resource | Community site to make brain imaging research easier that aims to build software that is clearly written, clearly explained, a good fit for the underlying ideas, and a natural home for collaboration. | brain, imaging, neuroimaging, analysis, python, fmri, fmri analysis, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Python Programming Language has parent organization: SourceForge has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; is parent organization of: Dipy is parent organization of: NiLearn is parent organization of: NIPY is parent organization of: NiBabel is parent organization of: Nipype is parent organization of: Nitime |
NIMH 5R01MH081909-02; NIBIB 1R03EB008673-01 |
PMID:21897815 | Revised BSD license | nlx_149365 | http://www.nitrc.org/projects/nipy-community http://www.nitrc.org/projects/nipype | SCR_013141 | NIPY Community | 2026-08-03 09:35:09 | 24 | ||||
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TopHat Resource Report Resource Website 5000+ mentions Rating or validation data |
TopHat (RRID:SCR_013035) | sequence analysis software, image analysis software, software application, data processing software, data analysis software, alignment software, software resource | Software tool for fast and high throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies. Fast splice junction mapper for RNA-Seq reads. Aligns RNA-Seq reads to mammalian-sized genomes using ultra high-throughput short read aligner Bowtie, and then analyzes mapping results to identify splice junctions between exons.TopHat2 is accurate alignment of transcriptomes in presence of insertions, deletions and gene fusions. | align, RNA-Seq, read, cDNA, sequencing, transcriptomics, fast, splice, junction, mapper, exon, analysis, bio.tools |
uses: Bowtie is used by: CIRCexplorer is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: HISAT2 has parent organization: University of Maryland; Maryland; USA has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: Johns Hopkins University; Maryland; USA has parent organization: University of Washington; Seattle; USA works with: GeneScissors |
NHGRI R01 HG006102; NHGRI R01 HG006677 |
PMID:23618408 PMID:19289445 DOI:10.1093/bioinformatics/btp120 |
Free, Available for download, Freely available | biotools:tophat, OMICS_01257 | https://github.com/infphilo/tophat, https://bio.tools/tophat, https://sources.debian.org/src/tophat/ | http://tophat.cbcb.umd.edu/ | SCR_013035 | tophat, TopHat1, Tophat2 | 2026-08-03 09:35:08 | 9575 | ||||
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affy Resource Report Resource Website 1000+ mentions |
affy (RRID:SCR_012835) | Affy | software resource, data processing software, software application, data analysis software | Software R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. Used to process probe level data and for exploratory oligonucleotide array analysis. | analysis, oligonucleotide, array, Affymetrix, process, probe, data, function, bio.tools |
is listed by: OMICtools is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: affydata is related to: R Project for Statistical Computing is related to: OMICtools |
Danish Biotechnology Instrument Center | PMID:14960456 | Free, Available for download, Freely available | BioTools:affy, OMICS_00740, biotools:affy | https://bio.tools/affy, https://sources.debian.org/src/r-bioc-affy/ | SCR_012835 | Affymetrix, analysis of Affymetrix GeneChip data at the probe level, analysis of Affymetrix GeneChip data | 2026-08-03 09:35:05 | 2996 | ||||
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edgeR Resource Report Resource Website 10000+ mentions |
edgeR (RRID:SCR_012802) | edgeR | software resource, data processing software, software application, data analysis software | Bioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication. | empirical, analysis, digital, gene, expression, data, R, RNA-seq data, bio.tools |
is used by: Glimma is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: SARTools is related to: Bioconductor works with: tximport |
NHMRC 406657; Independent Research Institutes Infrastructure Support Scheme 361646; Victorian State Government OIS grant ; Melbourne International Research Scholarship ; Harris and IBS Honours scholarships |
PMID:19910308 DOI:10.1093/bioinformatics/btp616 |
Free, Available for download, Freely available | OMICS_01308, biotools:edger | https://bio.tools/edger, https://sources.debian.org/src/r-bioc-edger/ | SCR_012802 | edgeR, empirical analysis of digital gene expression data in R, Empirical analysis of Digital Gene Expression data in R | 2026-08-03 09:35:15 | 21899 | ||||
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PlasmoDB Resource Report Resource Website 1000+ mentions |
PlasmoDB (RRID:SCR_013331) | data repository, production service resource, data analysis service, web service, service resource, database, storage service resource, analysis service resource, data access protocol, data or information resource, software resource | Functional genomic database for malaria parasites. Database for Plasmodium spp. Provides resource for data analysis and visualization in gene-by-gene or genome-wide scale. PlasmoDB 5.5 contains annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution data. Data can be queried by selecting from query grid or drop down menus. Results can be combined with each other on query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis.Key community database for malaria researchers, intersecting many types of laboratory and computational data, aggregated by gene. | Functional, genomic, database, malaria, parasite, data, analysis, visualization, gene, genome, annotation, transcription, proteomics, protein, evolution, FASEB list |
uses: SynView is related to: GeneDB Pfalciparum has parent organization: Eukaryotic Pathogen Database Resources has parent organization: Pennsylvania State University has parent organization: University of Georgia; Georgia; USA |
malaria | NIAID | PMID:18957442 | nif-0000-03314, SCR_017665, r3d100011569 | SCR_013331 | PlasmoDB, Plasmodium Genomics Resource, PlasmoDB 5.5, Plasmodium genome-resource | 2026-08-03 09:35:13 | 1239 | ||||||
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MeGX Resource Report Resource Website 1+ mentions |
MeGX (RRID:SCR_000738) | web service, database, data access protocol, data or information resource, software resource | 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. | functioning of marine ecosystems, marine bacterial, archaeal, phage, metagenome, marine microbe, megdb, analysis |
is listed by: 3DVC has parent organization: Max Planck Institute for Marine Microbiology; Bremen; Germany |
PMID:16381894 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03109, nif-0000-21260, SCR_008204, r3d100011324 | https://doi.org/10.17616/R3B05S | SCR_000738 | Marine Ecological GenomiX, megx: marine ecological genomics, Megx.net | 2026-08-03 09:31:08 | 2 | ||||||
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Baylor College of Medicine - Shaw Laboratory Resource Report Resource Website 1+ mentions |
Baylor College of Medicine - Shaw Laboratory (RRID:SCR_000604) | BCM - Shaw Laboratory, BCM Shaw Laboratory, BCM Shaw Lab | organization portal, data or information resource, laboratory portal, portal | 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. | statistics, bioinformatics, analysis, genomic, gene, biological process | has parent organization: Baylor University; Texas; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149156 | SCR_000604 | 2026-08-03 09:31:06 | 1 | ||||||||
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Harvard Partners HealthCare Center for Personalized Genetic Medicine Bioinformatics Core Facility Resource Report Resource Website |
Harvard Partners HealthCare Center for Personalized Genetic Medicine Bioinformatics Core Facility (RRID:SCR_000882) | production service resource, access service resource, analysis service resource, service resource, core facility | Core to provide gene expression data analysis service. Activities range from the provision of services to fully collaborative grant funded investigations. | affymetrix, array, PCPGM, gene, expression, data, analysis, service |
is listed by: Eagle I has parent organization: Harvard University; Cambridge; United States |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156324 | http://www.partners.org/researchcores/trash/bioinformatics_HPCGG.html | SCR_000882 | PCPGM, bioinformatics, The Partners HealthCare Center for Personalized Genetic Medicine | 2026-08-03 09:31:11 | 0 | |||||||
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Macquarie University Labs and Facilities Resource Report Resource Website |
Macquarie University Labs and Facilities (RRID:SCR_000944) | topical portal, data or information resource, portal | 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. | proteome, analysis, research, university, biological science, engineering, geography |
is listed by: ScienceExchange is related to: MQ Australian Proteome Analysis Facility is related to: MQ Animal Behaviour Laboratory is related to: MQ Ramaciotti Centre for Gene Function Analysis is related to: MQ BioFocus Research Centre is related to: MQ ARC Centre of Excellence for Engineered Quantum Systems is related to: Macquarie University MQ Research Centre in Quantum Science and Technology is related to: MQ Research Centre for Astronomy Astrophysics and Astrophotnics has parent organization: Macquarie University; Sydney; Australia |
THIS RESOURCE IS NO LONGER IN SERVICE | SciEx_9680 | https://www.mq.edu.au/ | SCR_000944 | Macquarie University Labs Facilities | 2026-08-03 09:31:11 | 0 | |||||||
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PhenoGen Informatics Resource Report Resource Website 10+ mentions |
PhenoGen Informatics (RRID:SCR_001613) | PhenoGen | data repository, production service resource, data analysis service, data or information resource, source code, storage service resource, analysis service resource, data access protocol, service resource, software resource, application programming interface, data set | 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. | genome, transcription, microarray, gene, quantitative trait loci, analysis, complex trait, genotype, phenotype, high-throughput, rna-seq, snp, genomic marker, region, data sharing, normalize, statistics, gene list, pathway, expression value, expression, correlation, exon, annotation, promoter, homolog, brain, heart, liver, adipose, candidate gene, genetics, transcriptome, eqtl, genome browser, inbred panel |
is related to: MONARCH Initiative has parent organization: University of Colorado Denver; Colorado; USA |
NIAAA R24 AA013162; NIAAA R01 AA13162; NIAAA U01 AA013524 |
PMID:17760997 | Free, Freely available | rid_000093, nlx_153879, r3d100011596 | https://github.com/TabakoffLab/PhenogenCloud, https://doi.org/10.17616/R3WS7F | http://phenogen.ucdenver.edu, http://phenogen.uchsc.edu | SCR_001613 | PhenoGen Informatics - The site for quantitative genetics of the transcriptome. | 2026-08-03 09:31:25 | 22 | |||
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Farsight Toolkit Resource Report Resource Website 1+ mentions |
Farsight Toolkit (RRID:SCR_001728) | FARSIGHT | image processing software, software toolkit, software application, data processing software, image analysis software, software resource | 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. | editing, 2d, 3d, algorithm, analysis, bio-format, computational, data, graphical, inspection, metadata, microscopy, morphological, morphology, pixel, processing, segmentation, taxonomy, image | has parent organization: University of Houston; Texas; USA | NIBIB R01-EB005157; NSF EEC-9986821; NIBIB R01EB005157 |
PMID:24808857 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10227 | SCR_001728 | FARSIGHTWiki | 2026-08-03 09:31:32 | 2 | |||||
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FreeSurfer Resource Report Resource Website 10000+ mentions |
FreeSurfer (RRID:SCR_001847) | FreeSurfer | software application, data processing software, image analysis software, software resource, data visualization software | 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. | processing, analysis, human, brain, MRI, image, reconstruction, cortical, surface, fMRI, data |
is used by: Wisconsin Cortical Thickness Analysis (CTA) Toolbox is used by: freesurfR is used by: Automatic Analysis is used by: NHP Freesurfer is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: Debian is listed by: SoftCite is related to: PySurfer is related to: RFT FDR is related to: FMRLAB is related to: TRACULA is related to: BASH4RfMRI has parent organization: Harvard University; Cambridge; United States has plug in: JOSA works with: NIAG Addiction Data |
NCRR U24 RR021382; NINDS R01 NS052585; NCRR RR014075 |
PMID:22248573 | Free, Available for download, Freely available | nif-0000-00304 | https://sources.debian.org/src/freesurfer/, http://www.nitrc.org/projects/freesurfer, http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall | SCR_001847 | 2026-08-03 09:31:36 | 11817 | |||||
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Duke University Medical Center: Duke Image Analysis Laboratory Resource Report Resource Website 10+ mentions |
Duke University Medical Center: Duke Image Analysis Laboratory (RRID:SCR_001716) | topical portal, data or information resource, database, portal | 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. | academic, amygdala, analysis, biotechnology, brain, cat scan, caudate, chemical, clinical, computed, development, digital, hippocampus, imaging, lab, laboratory, magnetic resonance imaging, magnetic resonance spectroscopy, medical, medicine, metabolic, mri, mrs, nmr, nuclear, nuclear medicine, pharmaceutical, research, spectroscopy, structure, technology, therapeutic, tomography, treatment, trial, ventricular, ventricular system, volume, x-ray, FASEB list | has parent organization: Duke University; North Carolina; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10213 | SCR_001716 | DMC DIAL | 2026-08-03 09:31:25 | 33 | ||||||||
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Atlas3D Resource Report Resource Website 10+ mentions |
Atlas3D (RRID:SCR_001808) | software application, data processing software, atlas, data or information resource, software resource, data visualization software | 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. | analysis, brain, histological, mouse, rat, slicing, structure, 3d, tomographic, visualization, neuroimaging, image, magnetic resonance, visualization |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Oslo; Oslo; Norway |
Research Council of Norway ; NIH ; NIBIB R01-EB00790; NCRR U24-RR021382 |
Free, Freely available | nif-0000-10373 | http://www.nitrc.org/projects/incf_atlas3d | SCR_001808 | Neural Systems and Graphics Computing Laboratory: Atlas3D Software, NeSys Atlas3D | 2026-08-03 09:31:34 | 17 | ||||||
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An Integrated Multiple Structure Visualization and Multiple Sequence Alignment Application Resource Report Resource Website |
An Integrated Multiple Structure Visualization and Multiple Sequence Alignment Application (RRID:SCR_001646) | software application, data processing software, data analysis software, rendering software, software resource, data visualization software | 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. | alignment, analysis, bioinformatics, database, dna, interaction, motif, phylogeny, protein, rna, scientist, sequence, structure, super-family, visualization, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Northeastern University; Massachusetts; USA |
PMID:16076889 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:friend, nif-0000-10149 | https://bio.tools/friend | SCR_001646 | FRIEND | 2026-08-03 09:31:26 | 0 | ||||||
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Mount Sinai School of Medicine: In-Vivo Molecular Imaging Laboratory Resource Report Resource Website |
Mount Sinai School of Medicine: In-Vivo Molecular Imaging Laboratory (RRID:SCR_001785) | data computation service, production service resource, analysis service resource, material analysis service, biomaterial analysis service, service resource | 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. | equipment, fluorescence, fluorescent, genetic, 2d, 3d, analysis, bioluminescence, bioluminescent, cellular, imaging, intermodality coregistration, in-vivo, localization, mice, micro-mri, micro-pet, molecular, probe, software, spectra, technology, xenogen ivis-200 series | has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA | Free, Freely available | nif-0000-10299 | http://www.mssm.edu/research/resources/molecular_imaging/ | SCR_001785 | MSSM IMIL | 2026-08-03 09:31:26 | 0 |
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