Tools   Select Another Resource Report Type

http://mmbios.org/

Biomedical technology research center that develops and makes available to the scientific community high performance computing algorithms, tools and software to leverage modeling efforts at disparate scales of structural biology, cellular microphysiology and large-scale bioimage processing and analysis, with the goal of advancing understanding of the molecular and cellular organization and functional mechanisms that underlie synaptic signaling and regulation.

Proper citation: National Center for Multiscale Modeling of Biological Systems (RRID:SCR_009005) Copy   

•   Source: SciCrunch Registry

http://msf.ucsf.edu/

Provides high-performance tandem mass spectrometry and proteomics, including multiplexed quantitative comparative analysis of protein and post-translational modifications, and a suite of tools for the analysis of mass spectrometry proteomics data. It provides both scientific and technical expertise and state-of-the-art high-performance, tandem mass spectrometric instrumentation. The facility also provides a service for small molecule analysis. Significant instrumentation in the facility includes three QSTAR quadrupole orthogonal time of flight instruments, and both an LTQ-Orbitrap platform with electron transfer dissociation (ETD) and an LTQ-FT linear ion trap FT-ICR instrument equipped with the ability to perform electron capture dissociation (ECD). The Center also has a 4700 Proteomic Analyzer MALDI tandem time of flight instrument; as well as a QTRAP 5500 hybrid triple quadrupole linear ion trap instrument; and a Thermo Fisher LTQ Orbitrap Velos. Major research focuses within the Center are the analysis of post-translational modifications, including phosphorylation and O-GlcNAcylation and development of methods for quantitative comparative analysis of protein and post-translational modification levels. The program also continues to develop one of the leading suites of tools for analysis of mass spectrometry proteomics data, Protein Prospector. The current web-based release allows unrestricted searching of MS and MSMS data, as well as the ability to perform comparative quantitative analysis of samples using isotopic-labeling reagents. It is the only freely-available web-based resource that allows this type of analysis.

Proper citation: National Bio-Organic Biomedical Mass Spectrometry Resource Center (RRID:SCR_009004) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/saint-apms/files/

Software tool for upgraded implementation of probabilistic scoring of affinity purification mass spectrometry data. Used for filtering high confidence interaction data from affinity purification mass spectrometry experiments. Used for assigning confidence scores to protein-protein interactions based on quantitative proteomics data in AP-MS experiments.

Proper citation: SAINTexpress (RRID:SCR_018562) Copy   

•   Source: SciCrunch Registry

http://www.pyrosetta.org/

Interactive Python based interface to Rosetta molecular modeling suite. Stand alone Python based implementation of Rosetta molecular modeling package that allows users to write custom structure prediction and design algorithms using major Rosetta sampling and scoring functions.

Proper citation: PyRosetta (RRID:SCR_018541) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3149502/

Software for comprehensive quantitative measure of splicing impact of complete set of RNA 6-mer sequences by deep sequencing successfully spliced transcripts.

Proper citation: ESRseq score (RRID:SCR_022270) Copy   

•   Source: SciCrunch Registry

https://faculty.chemistry.harvard.edu/shakhnovich/software/coarse-grained-co-translational-folding-analysis

Software for statistical approach to identify loci within genes that are both significantly enriched in slowly translated codons and evolutionarily conserved, and also co-translational protein folding model.

Proper citation: Coarse grained co-translational folding analysis (RRID:SCR_022271) Copy   

•   Source: SciCrunch Registry

https://psbweb05.psb.ugent.be/conet/microbialnetworks/spieceasi.php

Software R package estimates inverse covariance matrix from sequencing data.Statistical method for inference of microbial ecological networks from amplicon sequencing datasets.

Proper citation: Sparse Inverse Covariance Estimation for Ecological Association Inference (RRID:SCR_022646) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/BGLR/

Software R package implements large collection of Bayesian regression models, including parametric variable selection and shrinkage methods and semiparametric procedures.

Proper citation: Bayesian Generalized Linear Regression (RRID:SCR_022522) Copy   

•   Source: SciCrunch Registry

https://github.com/rondolab/MR-PRESSO

Software R package for performing Mendelian randomization pleiotropy residual sum and outlier method.Used to identify horizontal pleiotropic outliers in multi instrument summary level MR testing.

Proper citation: MR-PRESSO (RRID:SCR_023697) Copy   

•   Source: SciCrunch Registry

http://panomics.pnnl.gov/

Biomedical technology research center that develops and integrates new proteomic technologies for collaborative and service studies, disseminating the new technologies and training scientists in their use.

Proper citation: Proteomics Research Center for Integrative Biology (RRID:SCR_001098) Copy   

•   Source: SciCrunch Registry

http://www.cgl.ucsf.edu/

Biomedical technology resource center that develops software and web-based resources for the visualization and analysis of molecular structure, and related data, at scales ranging from the atomic to the supramolecular. They create tools for handling and integrating diverse types of biomolecular data, including atomic-resolution coordinates, density maps, sequences, annotations, and networks. Their primary efforts are in the visualization and analysis of structures of molecules and molecular assemblies, enzyme sequence-structure-function relationships, and network representations of protein similarity, binding interactions, and biological pathways. They provide technologies to enable identifying the molecular bases of disease and phenotypic variation, annotating proteins of unknown function, identifying targets for drug development, designing drugs, and engineering proteins with new functions. RBVI distributes software tools, including the popular UCSF Chimera visualization and analysis package, develops and hosts the Structure-Function Linkage Database, and provides access to state-of-the-art computational resources in support of research projects in these areas.

Proper citation: Resource for Biocomputing Visualization and Informatics (RRID:SCR_001374) Copy   

•   Source: SciCrunch Registry

http://anya.igsb.anl.gov/Geneways/GeneWays.html

System for automatically extracting, analzying, visualizing and integrating molecular pathway data from the research literature. System focuses on interactions between molecular substances and actions, providing a graphical consensus view on the collected information. GeneWays is designed as open platform, allowing researchers to query, review and critique integrated information.

Proper citation: GeneWays (RRID:SCR_000572) Copy   

•   Source: SciCrunch Registry

http://www.sci.utah.edu/cibc/software/231-biomesh3d.html

A free, easy to use program for generating quality meshes for use in biological simulations. It is currently integrated with SCIRun and uses the SCIRun system to visualize the intermediate results. The BioMesh3D program uses a particle system to distribute nodes on the separating surfaces that separate the different materials and then uses the TetGen software package to generate a full tetrahedral mesh.

Proper citation: BioMesh3D (RRID:SCR_009534) Copy   

•   Source: SciCrunch Registry

http://amp.pharm.mssm.edu/X2K/

Software tool to produce inferred networks of transcription factors, proteins, and kinases predicted to regulate the expression of the inputted gene list by combining transcription factor enrichment analysis, protein-protein interaction network expansion, with kinase enrichment analysis. It provides the results as tables and interactive vector graphic figures.

Proper citation: eXpression2Kinases (RRID:SCR_016307) Copy   

•   Source: SciCrunch Registry

http://compbio.cs.princeton.edu/conservation/

Software for scoring protein sequence conservation using the Jensen-Shannon divergence. It can be used to predict catalytic sites and residues near bound ligands.

Proper citation: Conservation (RRID:SCR_016064) 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://www.unmc.edu/vcr/cores/vcr-cores/animal-behavior/index.html

Provides investigators with expertise, equipment, and space that is required to conduct innovative acoustic, behavioral, and cognitive research with focus on rigor, reproducibility, and maintaining the highest standards of animal welfare.

Proper citation: University of Nebraska Medical Center Animal Behavior Core Facility (RRID:SCR_018830) Copy   

•   Source: SciCrunch Registry

http://cobre.pbrc.edu/cores/genomics/

Provides services which include Sanger and next-generation DNA sequencing,DNA fragment analysis,qualitative and quantitative analysis of DNA, protein, and RNA samples, quantitative PCR, microarray RNA labeling, hybridization, and scanning robotics,bioinformatics.Individual and small group training and consultation services are offered for sequence analysis, real-time PCR, next-generation sequencing and microarray analysis.

Proper citation: Louisiana State University Pennington Biomedical Research Center Genomics Core Facility (RRID:SCR_018675) Copy   

•   Source: SciCrunch Registry