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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://nationalmaglab.org/user-facilities/high-b-t-facility

Facility to conduct experiments in high magnetic fields up to 15 tesla and at very low temperatures down to 0.4 mK simultaneously. Located at University of Florida in Gainesville, it is operated as part of Physics Department Microkelvin Laboratory.

Proper citation: National High Magnetic Field Laboratory High B/T Core Facility (RRID:SCR_017360) Copy   

•   Source: SciCrunch Registry

https://amris.mbi.ufl.edu/

National High Magnetic Field Laboratory (MagLab) site. It provides researchers with advanced NMR, MRI, and spectroscopy tools (human/animal imaging) for biomedical studies, specializing in high-field magnetic resonance technology. Hosts spectrometers and scanners, including high-field NMR (up to 1.5 GHz), MR microscopy, and human/animal MRI systems (e.g., 3T and 900 MHz). Offers expertise in high-resolution solution NMR, solid-state NMR, and specialized imaging for in vivo animal models and humans.Features an RF coil lab that designs, builds, and tests custom MRI/NMR coils to optimize data collection. Supports research into Alzheimer's, cancer, metabolism, and brain development.

Proper citation: National MagLab University of Florida McKnight Brain Institute Advanced Magnetic Resonance Imaging and Spectroscopy AMRIS Core Facility (RRID:SCR_017362) 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

http://www.udel.edu/chem/beebe/surface.htm

Core provides consulting and services in X-ray Photoelectron Spectroscopy (XPS or ESCA), Time-of-Flight Secondary-Ion Mass Spectrometry (TOF-SIMS), X-ray Photoelectron Imaging, Auger Electron Spectroscopy (AES), Scanning Auger Microscopy or Imaging (SAM), Secondary-Electron Microscopy (SEM), Ion-Scattering Spectroscopy (ISS or LEIS), Scanning Probe Microscopy (STM and AFM).

Proper citation: Delaware University Surface Analysis Core Facility (RRID:SCR_017796) Copy   

•   Source: SciCrunch Registry

https://www.mccormick.northwestern.edu/materials-science/clammp/

Core provides mechanical testing machines and accessories for conducting educational, research, and outreach experiments on most solid materials.

Proper citation: Northwestern University Central Laboratory for Materials Mechanical Properties Core Facility (RRID:SCR_017877) Copy   

•   Source: SciCrunch Registry

http://crl.berkeley.edu/molecular-imaging-center/

Microscopy core specializing in laser based fluorescence techniques. Offers training and expertise in 20 different microscope systems, including live cell and in vivo imaging, laser scanning (LSM) and spinning disk (SDC) confocal, multi-photon (2p), fluorescent lifetime imaging (FLIM), light-sheet microscopy (SPIM), super resolution (Airyscan), slide scanning and patterned illumination for optogenetic manipulation and readout. Provides offline computer analysis workstations for image processing, visualization and analysis, including GPU workstations. MIC operates in 3 different buildings on campus, with primary locations in Life Sciences Addition (LSA), North-side core in Barker Hall, and small outpost in Li Ka Shing Center for Biomedical and Health Sciences (LKS).Provides equipment in categories:Confocal and multi photon laser scanning microscopes,Spinning disk confocal microscopes,Lightsheet (SPIM) microscopes,Epifluorescence/widefield scopes and Computer workstations.

Proper citation: University of California at Berkeley Cancer Research Laboratory Molecular Imaging Center Core Facility (RRID:SCR_017852) Copy   

•   Source: SciCrunch Registry

https://www.danforthcenter.org/our-work/core-facilities/advanced-bioimaging-laboratory/

Core provides instruments for live cell imaging including Leica SP8-X confocal microscope and other fluorescence microscopes. Facility provides workstation for confocal image processing, ancillary equipment required for transmission electron microscopy. Services are provided as self services after user training by IMF staff or as full services done by core facility staff.

Proper citation: Donald Danforth Plant Science Center Advanced Bioimaging Laboratory Core Facility (RRID:SCR_018951) Copy   

•   Source: SciCrunch Registry

https://pynwb.readthedocs.io/en/latest/

Software Python package for working with Neurodata stored in Neurodata Without Borders files. Software providing API allowing users to read and create NWB formatted HDF5 files. Developed in support to NWB project with aim of spreading standardized data format for cellular based neurophysiology information.

Proper citation: PyNWB (RRID:SCR_017452) Copy   

•   Source: SciCrunch Registry

https://github.com/DeNardoLab/BehaviorDEPOT

Software tool for automated behavioral detection based on markerless pose tracking. Behavioral analysis tool to first compile and clean point-tracking output from DeepLabCut, and then classify behavioral epochs using custom behavior classifiers. Used to detect frame by frame behavior from video time series and can analyze results of common experimental assays, including fear conditioning, decision-making in T-maze, open field, elevated plus maze, and novel object exploration. Calculates kinematic and postural statistics from keypoint tracking data from pose estimation software outputs.

Proper citation: BehaviorDEPOT (RRID:SCR_023602) Copy   

•   Source: SciCrunch Registry

https://github.com/nlm-irp-jianglab/SpikeHunter

Software deep learning tool for identifying phage tailspike proteins. Used to identify phage tailspike proteins.

Proper citation: SpikeHunter (RRID:SCR_024831) 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://github.com/PhysiCell-Tools/PhysiCell-Studio

Software graphical tool to allow easy editing of (XML) model, create initial positions of cells, run simulation, and visualize results. To contribute, fork and make PRs to the development branch. Used to create, execute, and visualize multicellular model using PhysiCell.

Proper citation: PhysiCell Studio (RRID:SCR_025311) Copy   

•   Source: SciCrunch Registry

https://github.com/COMBINE-lab/maximum-likelihood-relatedness-estimation

C++ program to infer biological relatedness from low coverage 2nd generation sequencing data. It uses information from genotype likelihoods rather than observed genotypes in maximum likelihood framework in order to estimate the overall coefficient of relatedness as well as individual kinship components between two samples. Maximum Likelihood Estimation of Biological Relatedness from Low Coverage Sequencing Data.

Proper citation: lcMLkin (RRID:SCR_025418) Copy   

•   Source: SciCrunch Registry

http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/

Software tool for ultra fast eQTL analysis via large matrix operations.

Proper citation: MatrixEQTL (RRID:SCR_025513) Copy   

•   Source: SciCrunch Registry

https://github.com/sokrypton/ColabFold

Software application offers accelerated prediction of protein structures and complexes by combining homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. Used for protein folding.

Proper citation: ColabFold (RRID:SCR_025453) Copy   

•   Source: SciCrunch Registry

https://www.morphosource.org/

Publicly accessible 3D data repository where subject experts, educators, and general public can find, view, interact with, and download 3D and 2D media representing physical objects important to the world’s natural history, cultural heritage, and scientific collections. Media data are contributed by a community that includes museums, institutions, researchers, scholars, and other subject experts who use MorphoSource to archive data, share findings, and increase scholarly impact. Contributed media represent both biological objects such as fossils and representatives of living species, as well as artifacts and objects created by humans that are critical to our shared cultural heritage.

Proper citation: MorphoSource (RRID:SCR_025654) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/SomaticSignatures.html

Software R package for identifying mutational signatures of single nucleotide variants (SNVs) from high-throughput experiments.

Proper citation: SomaticSignatures (RRID:SCR_025620) Copy   

•   Source: SciCrunch Registry