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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
Software tool that helps users write experimental protocols.
Proper citation: Ready Set Potato (RRID:SCR_025289) Copy
https://www.yworks.com/products/yed
Software desktop application as general purpose diagramming program with multi-document interface. Cross-platform Java application to generate high-quality diagrams. Runs on Windows, Linux, Mac OS, and other platforms that support Java Virtual Machine.
Proper citation: yEd (RRID:SCR_025325) Copy
Operating software for Thermo Scientific NanoDrop 1000 Spectrophotometer. Free NanoDrop operating software to update your instrument.
Proper citation: Thermo Scientific NanoDrop 1000 Software (RRID:SCR_025282) Copy
https://github.com/BaselAbujamous/clust
Software package for automatic extraction of optimal co-expressed gene clusters from gene expression data. Automatic and optimised consensus clustering of one or more heterogeneous datasets.
Proper citation: Clust (RRID:SCR_025283) Copy
https://github.com/schwartzlab-methods/too-many-cells-interactive
Web browser-based JavaScript application for visualizing hierarchical cellular populations as interactive radial tree. Allows users to explore, filter, and manipulate hierarchical data structures through intuitive interface while also enabling batch export of high-quality custom graphics.
Proper citation: TooManyCellsInteractive (RRID:SCR_025315) Copy
https://whatshap.readthedocs.io/en/latest/
Software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. Used for long reads, but works also well with short reads.
Proper citation: WhatsHap (RRID:SCR_025319) Copy
https://www.bruker.com/en/products-and-solutions/preclinical-imaging/paravision-360.html
Software for preclinical imaging integrated with Bruker MRI spectrometers. Used with Bruker MRI, PET/MR, and PET/CT instruments. Enables easy and high throughput imaging. All images, protocols, and subjects are in one location with inherent co-registration, image fusion, data processing, and analysis.
Proper citation: ParaVision 360 (RRID:SCR_025295) Copy
https://github.com/schwartzlab-methods/too-many-cells-python
Software Python implementation of clustering tool named TooManyCells. Software package for spectral clustering.
Proper citation: too-many-cells-python (RRID:SCR_025327) Copy
https://gitlab.com/sysbiobig/movarsim
Software simulator that leverages data-driven information to set both variants and reads characteristics, producing realistic tumoral samples. Computational modelling of cancer-specific variants and sequencing reads characteristics for realistic tumoral sample simulation.
Proper citation: MOVARSim (RRID:SCR_025388) Copy
https://CRAN.R-project.org/package=glmulti
Software R package for model selection and multimodel inference. Used for automated model selection and model-averaging. Provides wrapper for glm and other functions, automatically generating all possible models with specified response and explanatory variables.
Proper citation: glmulti (RRID:SCR_025423) Copy
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
https://github.com/monologue0924/COMSOL-model-of-Magnetic-coil-
Software application as model of magnetic field distribution of magnetic coil visualized using COMSOL Multiphysics.
Proper citation: COMSOL model of Magnetic coil (RRID:SCR_025426) Copy
https://github.com/mtu-most/linear-actuator
Code and model files for open source linear actuator. Part of Pearce Lab Syringe Pump system.
Proper citation: linear actuator (RRID:SCR_021613) Copy
https://github.com/KravitzLab/ROBucket
Software tool as ROBucket source code.
Proper citation: Rodent Operant Bucket (RRID:SCR_021610) Copy
https://github.com/jf-lab/chendoscope
Software tool as part of CHEndoscope. Acquisition software that interfaces with CHEndoscope Ximea USB camera. This code is compatible with Linux and Windows systems.
Proper citation: chendoscope (RRID:SCR_021616) Copy
https://github.com/jamieboyd/AutoHeadFix
Software Python code for automated control of behavioural apparatus and imaging for mice in home cage environment.Part of Homecage Task Training and Mesoscale Imaging system.
Proper citation: AutoHeadFix (RRID:SCR_021617) Copy
https://github.com/bsbrl/craniobot
Software tool as part of Craniobot system.Generates, sends, and receives commands to communicate with the Craniobot.
Proper citation: craniobot (RRID:SCR_021609) Copy
https://murphylab.med.ubc.ca/automated-homecages/
Software tool as part of Automated Home Cage Functional Imaging system.
Proper citation: Automated Home-Cage Functional Imaging (RRID:SCR_021607) Copy
https://github.com/dublon/scintillate
Open source graphical viewer for time series calcium imaging evaluation and pre-processing.
Proper citation: Scintillate (RRID:SCR_021531) Copy
https://github.com/GuyButcher/alpha-helix-coordinate-frame-simulation
Source code for alpha-helix simulation framework written in Matlab. Specifically tested on Talin-1 Rod Domain.
Proper citation: alpha helix coordinate frame simulation (RRID:SCR_019320) Copy
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