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http://simbios.stanford.edu/index.html

Simbios is the NIH Center for physics-based Simulation of Biological Structures. Simbios provides infrastructure, software, and training to help biomedical researchers understand biological form and function as they create novel drugs, synthetic tissues, medical devices, and surgical interventions. Simbios is investigating a wide scale of biological structures - from molecules to organisms. Driving biological problems include RNA folding, protein folding, myosin dynamics, cardiovascular dynamics, and neuromuscular biomechanics. Investigators interested in collaborating with Simbios can apply for NIH funding. To encourage collaboration in building accurate biological models and simulations, Simbios also provides the biomedical community with https://simtk.org, a free, secure, distributed, development system for projects. Projects may include models, software, data, documentation, publications, and graphics and have automatic backups and off-site storage. Projects may be public or private and have project-specific mailing lists, forums, bug & feature databases, news, blogs, and source-code repositories. Simbios is developing and disseminating the SimTK core simulation toolkit, (simtk.org/home/simtkcore). SimTK core is open-source software developed by experienced professionals. The software includes advanced capabilities for modeling the geometry and physics of biological systems. To ensure utility and accuracy, the software and training material is being developed and tested in close collaboration with biomedical scientists. Simbios has developed OpenSim, an application for advanced neuromuscular modeling that uses the SimTK toolkit, and is making it openly available at simtk.org/home/opensim. Simbios also publishes the Biomedical Computation Review, a magazine devoted to the science and tools in biocomputation, aimed at the community which encompasses the diverse biocomputation disciplines. To help researchers find high quality software and tools Simbios has also establishes the Simbiome an inventory of high-quality commercial and academic bio-simulation tools. Simbios has recurring openings for postdoctoral researchers.

Proper citation: Simbios (RRID:SCR_004320) Copy   

•   Source: SciCrunch Registry

http://www.sci.utah.edu/cibc-software/scirun.html

A Problem Solving Environment (PSE) for modeling, simulation and visualization of scientific problems. SCIRun now includes the biomedical components formally released as BioPSE, as well as BioMesh3D. BioMesh3D is a free, easy to use program for generating quality meshes for the use in biological simulations. The most recent stable release is version 4.6.

Proper citation: SCIRun (RRID:SCR_002541) Copy   

•   Source: SciCrunch Registry

https://imagej.net/

Open source Java based image processing software program designed for scientific multidimensional images. ImageJ has been transformed to ImageJ2 application to improve data engine to be sufficient to analyze modern datasets.

Proper citation: ImageJ (RRID:SCR_003070) Copy   

•   Source: SciCrunch Registry

https://simtk.org/home/rna-viz-proto

A software application for animating and visualising RNA and other macromolecular structures. Users are able to use their intuition to interactively refold RNA structures and produce morphs from one structure to another. It allow researchers to explore and manipulate molecular structures Imported from BiositeMaps registry, to better understand structure:function relationships, folding pathways, and molecular motion.

Proper citation: ToRNADo (RRID:SCR_002706) Copy   

•   Source: SciCrunch Registry

https://github.com/WGLab/LongReadSum

Software fast and flexible QC and signal summarization tool for long read sequencing data.

Proper citation: LongReadSum (RRID:SCR_026408) Copy   

•   Source: SciCrunch Registry

https://scvi-tools.org/

Software Python library for deep probabilistic analysis of single-cell and spatial omics data. Used for probabilistic modeling and analysis of single-cell omics data, built on top of PyTorch and AnnData.

Proper citation: scvi-tools (RRID:SCR_026673) Copy   

•   Source: SciCrunch Registry

https://github.com/williamslab/ped-sim

Software tool to simulate pedigree structures. Used for simulating relatives that can utilize either sex-specific or sex averaged genetic maps and also either model of crossover interference or traditional Poisson model for inter-crossover distances.

Proper citation: ped-sim (RRID:SCR_026957) Copy   

•   Source: SciCrunch Registry

https://github.com/itmat/BEERS2

Software for simulation of RNA-seq reads. Combines flexible and highly configurable design with detailed simulation of entire library preparation and sequencing pipeline and is designed to include effects of polyA selection and RiboZero for ribosomal depletion, hexamer priming sequence biases, GC-content biases in polymerase chain reaction (PCR) amplification, barcode read errors and errors during PCR amplification.

Proper citation: BEERS2 (RRID:SCR_027287) Copy   

•   Source: SciCrunch Registry

https://github.com/RGLab/CytoML

Software R package that enables cross-platform import, export, and sharing of gated cytometry data. It currently supports Cytobank, FlowJo, Diva, and R, allowing users to import gated cytometry data from commercial platforms into R.

Proper citation: CytoML (RRID:SCR_027485) Copy   

•   Source: SciCrunch Registry

https://pepatac.databio.org/en/latest/

Software standardized pipeline for ATAC-seq data analysis with serial alignments. Leverages unique features of ATAC-seq data to optimize for speed and accuracy, and provides several unique analytical approaches. Downstream analysis is simplified by standard definition format, modularity of components, and metadata APIs in R and Python. Restartable, fault-tolerant, and can be run on local hardware, using any cluster resource manager, or in provided Linux containers. We also emphasize the advantage of aligning to the mitochondrial genome serially, which improves alignment and quality control metrics. Includes quality control plots, summary statistics, and variety of data formats.

Proper citation: PEPATAC (RRID:SCR_024758) Copy   

•   Source: SciCrunch Registry

https://github.com/TaliaferroLab/LABRAT

Software application to quantify usage of alternative polyadenylation and cleavage sites in RNAseq data and identify genes whose usage of these sites varies across experimental conditions.

Proper citation: LABRAT (RRID:SCR_025006) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/p/mageck/wiki/Home/

Software tool to identify important genes from genome-scale CRISPR-Cas9 screens. Used for prioritizing single-guide RNAs, genes and pathways in genome-scale CRISPR/Cas9 knockout screens.

Proper citation: MAGeCK (RRID:SCR_025016) Copy   

•   Source: SciCrunch Registry

https://reprint-apms.org/?q=chooseworkflow

Database of Mass Spectrometry contaminants and pipeline for Affinity Purification coupled with Mass Spectrometry analysis. Contaminant repository for affinity purification mass spectrometry data. Database of standardized negative controls. Used to identify protein-protein interactions.

Proper citation: CRAPome (RRID:SCR_025008) Copy   

•   Source: SciCrunch Registry

https://apps.cytoscape.org/apps/stringapp

Software application for network analysis and visualization of proteomics data. Cytoscape app that makes it easy to import STRING networks into Cytoscape, retains appearance and many of features of STRING, and integrates data from associated databases.

Proper citation: Cytoscape StringApp (RRID:SCR_025009) Copy   

•   Source: SciCrunch Registry

https://redu.ucsd.edu/

Software framework to find and re-analyze public Mass Spectrometry data. Used to find uniformly formatted public MS/MS data in the Global Natural Product Social Molecular Networking Platform (GNPS) via formatted metadata. New or previously collected data can be added provided they adhere to the ReDU metadata standards (the implemented drag-and-drop validator is applicable to any scientific data) and data are available in GNPS/MassIVE.

Proper citation: ReDU (RRID:SCR_025105) Copy   

•   Source: SciCrunch Registry

https://github.com/mwang87/MassQueryLanguage

Software application for universal searching of Mass Spectrometry data. Open source MS query language for flexible and mass spectrometer manufacturer-independent mining of MS data. Implements common MS terminology to build consensus vocabulary to search for MS patterns in single mass spectrometry run. Enables set of mass spectrometry patterns to be queried directly from raw data.

Proper citation: MassQL (RRID:SCR_025106) Copy   

•   Source: SciCrunch Registry

https://fmug.amaral.northwestern.edu/

Software data-driven tool to identify understudied genes and characterize their tractability. Users submit list of human genes and can filter these genes down based on list of factors. Code to generate Find My Understudied Genes app for Windows, iOS and macOS platforms.

Proper citation: Find My Understudied Genes (RRID:SCR_025047) Copy   

•   Source: SciCrunch Registry

https://github.com/willtownes/glmpca

Software R package for dimension reduction of non-normally distributed data. Generalized PCA for non-normally distributed data.

Proper citation: glmpca (RRID:SCR_025517) Copy   

•   Source: SciCrunch Registry

https://github.com/bmvdgeijn/WASP/

Software allele-specific pipeline for unbiased read mapping and molecular QTL discovery. Allele-specific software for robust molecular quantitative trait locus discovery.

Proper citation: WASP (RRID:SCR_025497) Copy   

•   Source: SciCrunch Registry

https://github.com/DevonsMo/IJOQ/releases

Software Python tool for fully automated analysis of cell-cell junction integrity. Used for fluorescence microscopy analysis.

Proper citation: Intercellular Junction Organization Quantification (RRID:SCR_026026) Copy   

•   Source: SciCrunch Registry