Tools   Select Another Resource Report Type

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

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

https://www.proteinspire.org/MOPED/

An expanding multi-omics resource that enables rapid browsing of gene and protein expression information from publicly available studies on humans and model organisms. MOPED also serves the greater research community by enabling users to visualize their own expression data, compare it with existing studies, and share it with others via private accounts. MOPED uniquely provides gene and protein level expression data, meta-analysis capabilities and quantitative data from standardized analysis utilizing SPIRE (Systematic Protein Investigative Research Environment). Data can be queried for specific genes and proteins; browsed based on organism, tissue, localization and condition; and sorted by false discovery rate and expression. MOPED links to various gene, protein, and pathway databases, including GeneCards, Entrez, UniProt, KEGG and Reactome. The current version of MOPED (MOPED 2.5) The current version of MOPED (MOPED 2.5, 2014) contains approximately 5 million total records including ~260 experiments and ~390 conditions.

Proper citation: MOPED - Model Organism Protein Expression Database (RRID:SCR_006065) Copy   

•   Source: SciCrunch Registry

https://masst.gnps2.org/microbemasst/

Web taxonomically informed mass spectrometry search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging database of over 60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns.

Proper citation: microbeMASST (RRID:SCR_024713) Copy   

•   Source: SciCrunch Registry

http://www.sb.cs.cmu.edu/drem

The Dynamic Regulatory Events Miner (DREM) allows one to model, analyze, and visualize transcriptional gene regulation dynamics. The method of DREM takes as input time series gene expression data and static transcription factor-gene interaction data (e.g. ChIP-chip data), and produces as output a dynamic regulatory map. The dynamic regulatory map highlights major bifurcation events in the time series expression data and transcription factors potentially responsible for them. DREM 2.0 was released and supports a number of new features including: * new static binding data for mouse, human, D. melanogaster, A. thaliana * a new and more flexible implementation of the IOHMM supports dynamic binding data for each time point or as a mix of static/dynamic TF input * expression levels of TFs can be used to improve the models learned by DREM * the motif finder DECOD can be used in conjuction with DREM and help find DNA motifs for unannotated splits * new features for the visualization of expressed TFs, dragging boxes in the model view, and switching between representations

Proper citation: Dynamic Regulatory Events Miner (RRID:SCR_003080) Copy   

•   Source: SciCrunch Registry

http://www.ascidiancenter.ucsb.edu/index.html

Supplier of Ciona (C. robusta and C. savignyi) adults and stable transgenic animals expressing tissue-specific fluorescent proteins for research laboratories. This ascidian culturing facility is located at the marine laboratory of the University of California at Santa Barbara (UCSB).

Proper citation: Ascidian Stock Center (ASC) (RRID:SCR_014949) Copy   

•   Source: SciCrunch Registry

https://elegansvariation.org/

Supplier and researcher of wild C. elegans strains. CeNDR supplies organisms, analyzes whole-genome sequences, and facilitates genetic mappings to aid researchers in gene discovery.

Proper citation: Caenorhabditis elegans Natural Diversity Resource (CeNDR) (RRID:SCR_014958) Copy   

•   Source: SciCrunch Registry

http://www.ccg.unam.mx/tfmodeller

Web application that scans a library of protein-DNA complexes and builds comparative models of proteins bound to DNA. Its results include complex coordinates, schematic interface diagrams, interface alignments and DNA motifs.

Proper citation: TFmodeller (RRID:SCR_015715) Copy   

•   Source: SciCrunch Registry

http://amp.pharm.mssm.edu/gen3va/

Software tool for aggregation and analysis of gene expression signatures from related studies.Used to aggregate and analyze gene expression signatures extracted from GEO by crowd using GEO2Enrichr. Used to view aggregated report that provides global, interactive views, including enrichment analyses, for collections of signatures from multiple studies sharing biological theme.

Proper citation: GEN3VA (RRID:SCR_015682) Copy   

•   Source: SciCrunch Registry

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

Software resource that allows students or the general public find variants that may be significantly associated with some disease. CREEDS also visualizes and analyzes gene expression signatures.

Proper citation: CRowd Extracted Expression of Differential Signatures (RRID:SCR_015680) Copy   

•   Source: SciCrunch Registry

http://neuroexpresso.org/

Database of mouse brain cell type-specific gene expression datasets. NeuroExpresso is able to demonstrate the use of marker genes for acquiring cell type specific information from whole tissue expression.

Proper citation: NeuroExpresso (RRID:SCR_015724) Copy   

•   Source: SciCrunch Registry

https://www.rosettacommons.org/home

Molecular modeling software package for 3D structure prediction and high resolution design of proteins, nucleic acids, and non natural polymers. Used in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes.

Proper citation: Rosetta (RRID:SCR_015701) Copy   

•   Source: SciCrunch Registry

http://ontodog.hegroup.org/index.php

Ontodog is a web-based ontology view generator. It can generate inSubset annotation ontology, user preferred label annotation ontology and subset of source ontology. Simply provide Ontodog input term file (Microsoft Excel file or tab-delimited text file), select one source ontology or enter your own source ontology and SPARQL endpoint, then set the settings for Ontodog output files and get the OWL (RDF/XML) Output files. Ontodog performs the basic ontology modularization-like function, i.e.,it automatically extracts all axioms and related terms associated with user-specified signature term(s). In addition, Ontodog includes extra features: (1) extracting all instance data associated with the retrieved class terms and annotations; and (2) recursively extracting all axioms and related terms indirectly associated with signature terms. More features are being added to Ontodog, such as relabeling preferred names for various ontology terms to fit in with the needs from a specific community. The Ontodog input data requires a source ontology and a list of user-specified signature terms in tab-delimited format. Ontodog provides the template files for generating the signature terms as the input terms file to download. There are several output options that the users can choose based on their needs. With more and more ontologies being developed, Ontodog offers a timely web-based package of solutions for ontology view generation. Ontodog provides an efficient approach to promote ontology sharing and interoperability. It is easy to use and does not require knowledge of SPARQL, script programming, and command line operation. Ontodog is developed to serve the ontology community for ontology reuse. It is freely available under the Apache License 2.0. The source code is made available under Apache License 2.0.

Proper citation: Ontodog: A Web-based Ontology View Generator (RRID:SCR_005061) Copy   

•   Source: SciCrunch Registry

http://www.mouse-genome.bcm.tmc.edu/ENU/MutagenesisProj.asp

THIS RESOURCE IS NO LONGER IN SERVICE. For updated mutant information, please visit MMRRC or The Jackson Laboratory. Produces, characterizes, and distributes mutant mouse strains with defects in embryonic and postembryonic development. The goal of the ENU Mutagenesis project III is to determine the function of genes on mouse Chromosome 11 by saturating the chromosome with recessive mutations. The distal 40 cM of mouse Chr 11 exhibits linkage conservation with human Chromosome 17. We are using the chemical N-ethyl-N-nitrosourea (ENU) to saturate wild type chromosomes with point mutations. By determining the function of genes on a mouse chromosome, we can extrapolate to predict function on a human chromosome. We expect many of the new mutants to represent models of human diseases such as birth defects, patterning defects, growth and endocrine defects, neurological anomalies, and blood defects. Because many of the mutations we expect to isolate may be lethal or detrimental to the mice, we are using a unique approach to isolate mutations. This approach uses a balancer chromosome that is homozygous lethal and carries a dominant coat color marker to suppress recombination over a reasonable interval.

Proper citation: Mouse Mutagenesis Center for Developmental Defects (RRID:SCR_007321) Copy   

•   Source: SciCrunch Registry

http://cellprofiler.org

Software tool to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. It counts cells and also measures the size, shape, intensity and texture of every cell (and every labeled subcellular compartment) in every image. It was designed for high throughput screening but can perform automated image analysis for images from time-lapse movies and low-throughput experiments. CellProfiler has an increasing number of algorithms to identify and measure properties of neuronal cell types.

Proper citation: CellProfiler Image Analysis Software (RRID:SCR_007358) Copy   

•   Source: SciCrunch Registry

http://zhanglab.ccmb.med.umich.edu/EDTSurf/

Software that constructs triangulated surfaces for macromolecules. It generates three major macromolecular surfaces: van der Waals surface, solvent-accessible surface and molecular surface (solvent-excluded surface) and also identifies cavities which are inside of macromolecules. Used in accurate calculation of protein surfaces in the protein structural and functional studies including ligand-protein docking and virtual screening.

Proper citation: Edtsurf (RRID:SCR_016083) Copy   

•   Source: SciCrunch Registry

https://github.com/lh3/fermi-lite

Standalone C library as well as a command-line tool for assembling Illumina short reads in small regions. It is an overlap-based assembler used in sequencing to retain heterozygous events and to assemble diploid regions for the purpose of variant calling.

Proper citation: fermi-lite (RRID:SCR_016112) Copy   

•   Source: SciCrunch Registry

http://acb.qfab.org/acb/glam2/

Software package for finding novel, gapped (recurring, variable-length patterns) motifs in related groups of DNA or protein sequences (sample output from sequences). Used to perform motif based sequence discovery for gapped motifs on DNA or protein datasets.

Proper citation: Glam2 (RRID:SCR_016129) Copy   

•   Source: SciCrunch Registry