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https://github.com/compbiolabucf/PTNet

Graph based learning model for protein expression estimation by considering miRNA-mRNA interactions. Estimates protein levels by considering miRNA-mRNA interaction network, mRNA expression and miRNA expression.

Proper citation: PTNet (RRID:SCR_022975) Copy   

•   Source: SciCrunch Registry

https://github.com/protofilamentdude/Protofilament-Bending-Models

Code is written to be run with Matlab version r2020b or higher. Model accepts wave assay pulse amplitude data, and simultaneously solves and fits protofilament deflection models to deduce fundamental biophysical properties of microtubule protofilaments.

Proper citation: Protofilament Bending Models (RRID:SCR_023062) Copy   

•   Source: SciCrunch Registry

https://github.com/caraweisman/abSENSE

Software to interpret undetected homolog.Method that calculates probability that homolog of given gene would fail to be detected by homology search in given species, even if homolog were present and evolving normally.

Proper citation: abSENSE (RRID:SCR_023223) Copy   

•   Source: SciCrunch Registry

https://med.unr.edu/research/core-facilities-centers/high-spatial-temporal-resolution-imaging-core

Core provides high spatial and temporal resolution imaging methodologies and instrumentation for studying cellular structure, signaling pathways, and function in health and disease. Offers education, training and expertise in advising investigators in the use of the new technologies.

Proper citation: University of Nevada Reno School of Medicine High Spatial and Temporal Resolution Imaging Core Facility (RRID:SCR_024793) Copy   

•   Source: SciCrunch Registry

https://github.com/bioinform/somaticseq

Software accurate somatic mutation detection pipeline implementing stochastic boosting algorithm to produce somatic mutation calls for both single nucleotide variants and small insertions and deletions. NGS variant calling and classification.

Proper citation: SomaticSeq (RRID:SCR_024891) Copy   

•   Source: SciCrunch Registry

https://pephub.databio.org

Web biological metadata server to view, store, and share your sample metadata in form of Portable Encapsulated Projects. PEPhub takes advantage of PEP biological metadata standard to store, edit, and access your PEPs in one place. Components include database where PEPs are stored; API to programmatically read and write PEPs in database; web based user interface to view and manage these PEPs via front end.

Proper citation: PEPhub (RRID:SCR_024892) Copy   

•   Source: SciCrunch Registry

http://plaac.wi.mit.edu/

Web and command-line application to identify proteins with prion-like amino acid composition. Searches protein sequences to identify probable prion subsequences using hidden-Markov model algorithm.

Proper citation: PLAAC (RRID:SCR_024973) Copy   

•   Source: SciCrunch Registry

https://github.com/xinhe-lab/GSFA

Software R package that performs sparse factor analysis and differential gene expression discovery simultaneously on single cell CRISPR screening data.

Proper citation: Guided Sparse Factor Analysis (RRID:SCR_025023) Copy   

•   Source: SciCrunch Registry

https://pycontact.github.io/

Software tool for analysis of non-covalent interactions in molecular dynamics trajectories. Implemented in Python and is universally applicable to any kind of MD trajectory supported by MDAnalysis package.

Proper citation: PyContact (RRID:SCR_025066) Copy   

•   Source: SciCrunch Registry

https://www.npatlas.org

Open access knowledge base for microbial natural products discovery. Database of microbially derived natural product structures. Provides coverage of bacterial and fungal natural products to visualize chemical diversity. Includes compounds and contains referenced data for structure, compound names, source organisms, isolation references, total syntheses, and instances of structural reassignment. Interactive web portal permits searching by structure, substructure, and physical properties. Provides mechanisms for visualizing natural products chemical space and dashboards for displaying author and discovery timeline data. Atlas has been developed under FAIR principles.

Proper citation: Natural Products Atlas (RRID:SCR_025107) Copy   

•   Source: SciCrunch Registry

https://compbio.uth.edu/FusionGDB2/

Functional annotation database of human fusion genes.FusionGDB 2.0 has updates of contents such as up-to-date human fusion genes, fusion gene breakage tendency score with FusionAI deep learning model based on 20 kb DNA sequence around BP, investigation of overlapping between fusion breakpoints with human genomic features across cellular role's categories, transcribed chimeric sequence and following open reading frame analysis with coding potential based on deep learning approach with Ribo-seq read features, and rigorous investigation of protein feature retention of individual fusion partner genes in protein level.

Proper citation: FusionGDB2 (RRID:SCR_025299) Copy   

•   Source: SciCrunch Registry

https://web.uri.edu/riinbre/mic/

Core provides sequencing and bioinformatics support for INBRE and non-INBRE researchers. Provides data science services adjacent to traditional bioinformatics; access to computational and software resources for INBRE network institutions, particularly primarily undergraduate institutions; training for students and faculty in data science methods. Maintains professional network with other core and user facilities in Rhode Island and beyond to maximize resources available to our users.Utilizes novel technologies such as virtual/augmented reality for use in teaching and research.

Proper citation: Rhode Island INBRE Molecular Informatics Core Facility (RRID:SCR_017685) Copy   

•   Source: SciCrunch Registry

https://core.bioinformatics.udel.edu

CBCB Bioinformatics Data Science Core builds upon infrastructure of the Center for Bioinformatics and Computational Biology. Delaware Biotechnology Institute , Delaware Data Science Institute, and Protein Information Resource. Core helps with planning your research or analyzing your current data. Services:Consultation and Collaboration, Proposal Assistance,Training, Bioinformatics Software, Computational Hardware, Database and Web Services, Next Gen Analysis, Custom Analysis.

Proper citation: University of Delaware CBCB Bioinformatics Data Science Core Facility (RRID:SCR_017696) Copy   

•   Source: SciCrunch Registry

https://med.und.edu/imaging/index.html

Provides advanced instrumentation for researchers interested in investigating biological processes at cellular, sub cellular and molecular level.Instrumentation include Confocal Microscope Systems :Zeiss LSM-510 Meta Confocal Microscope, Olympus FV1000 MPE Basic Multiphoton Microscope;Brightfield/Fluorescence: Nikon Eclipse TE300 (inverted) Fluorescent Microscope, Nikon Eclipse 80i (upright) Fluorescent Microscope, Leica Thunder Imager; TIRF Systems:Olympus TIRF Microscope; Transmission Electron Microscopy:Hitachi 7500 TEM, RCM MTX Ultramicrotomes;Scanning Electron Microscopy:Hitachi 4700 Field Emission SEM, Denton Desk II Sputter and Turbo-sputter Coaters.Light and electron microscopic facilities, complete with ancillary support equipment, are located in close proximity to each other within suite of rooms housed in medical school.

Proper citation: University of North Dakota School of Medicine and Health Sciences Imaging Core Facility (RRID:SCR_017733) Copy   

•   Source: SciCrunch Registry

http://www.uwyo.edu/microscopy/

Core to assist researchers and students in their imaging needs of fluorescence and electron microscopy and to increase use of microscopes in science education. Consultation, training or touring facility is also available by appointment.

Proper citation: Wyoming University Jenkins Microscopy Core Facility (RRID:SCR_017758) Copy   

•   Source: SciCrunch Registry

https://www.unr.edu/proteomics

Core offers mass spectral proteomic analysis. Assists with qualitative and quantitative characterization of proteins in biological matrices such as plasma/serum, tissue, cell lines and other biological material to gain understanding of physiological pathways, molecular interactions and regulatory signaling.

Proper citation: University of Nevada at Reno Nevada Proteomics Center Core Facility (RRID:SCR_017761) Copy   

•   Source: SciCrunch Registry

http://psf.cobre.ku.edu/cores/ppg/about

Core focuses on cloning, expression and purification of prokaryotic and eukaryotic proteins for COBRE and other investigators in Kansas and region. Laboratory maintains equipment to support production of properly folded proteins in quantities suitable for structural studies (X-ray and NMR), functional studies (catalytic or biological), label-free binding studies (SPR) and/or high throughput (HTP) screening studies.

Proper citation: Kansas University at Lawrence Protein Production Group Core Facility (RRID:SCR_017749) Copy   

•   Source: SciCrunch Registry

http://bioimaging.dbi.udel.edu

Microscopy facility that houses equipment including confocal microscopes: LSM780 confocal microscope (Located at CBBI),LSM880 confocal microscope (Located at DBI 117),electron microscopes and their accessory instrumentation:Thermo Scientific Apreo VS SEM microscope,Hitachi S-4700, Leica EM ACE600 and Tousimis Autosamdri-815B,CX7 high content analysis system. Our staff has technical expertise across different microscopy platforms and methodologies.

Proper citation: University of Delaware BioImaging Center Core Facility (RRID:SCR_017814) Copy   

•   Source: SciCrunch Registry

https://www.une.edu/research/cobre/histology

Core provides access to expertise, training and specialized instrumentation related to tissue processing, sectioning, staining, immunohistochemistry and microscopy. Offers services and training related to image analysis and image analysis software to guide investigators in choosing best methods for presenting their data.Services include Trimming of wet tissues,Tissue processing into paraffin, OCT and paraffin embedding, Sectioning of paraffin-embedded/frozen tissues, Routine and special histochemical staining, Immunohistochemistry/Immunofluorescence, Antibody optimization, Brightfield/ widefield/ confocal microscopy, Image capture and image analysis.Core has cryostats, microtomes and microscopes available for reservation.

Proper citation: University of New England COBRE Histology and Imaging Core Facility (RRID:SCR_017885) Copy   

•   Source: SciCrunch Registry

http://proteomics.northwestern.edu/collaborate

Core offers multiple types of experiments from simple protein identification to protein quantitation. Performs traditional bottom-up proteomics, where proteins are digested with enzyme prior to analysis and intact, top-down proteomics analyses. Services include proteins identification after in-gel or in-solution digestion, top-down mass spectrometry to preserve post-translationally modified forms of proteins present in vivo by measuring them intact, IP-MS Pulldown,BioID service to identify target of biotin ligase that has been tagged onto their protein via traditional cloning methods,Untargeted Quantitative Peptide Proteomics,Targeted Quantitative Peptide Proteomics,Epiproteomic Histone Modification Panel A,Epiproteomic Histone Modification Panel B,Untargeted Metabolomics,Phosphoproteomics,PTM Scan,ChIP-MS.

Proper citation: Northwestern University Proteomics Core Facility (RRID:SCR_017945) Copy   

•   Source: SciCrunch Registry