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https://tracedrawer.com/product/tracedrawer/

Software for evaluating, comparing and presenting real-time interaction data. Used for quantification of kinetics and affinity through curve fitting, with large number of binding models to choose from. Can extract experimental information from measurement, requiring minimal user input.

Proper citation: TraceDrawer (RRID:SCR_025782) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/jrobust/

Software application for analysis of force microscopy recordings, including images and force curves. Allows for fast and reliable processing of single force curves and force maps, providing estimation of mechanical properties of sample.

Proper citation: AtomicJ (RRID:SCR_026023) Copy   

•   Source: SciCrunch Registry

https://www.seattlechildrens.org/research/resources/behavioral-phenotyping-core/

Core dedicated to the protocol driven collection, analysis, and reporting of behavioral data using a blend of classic and innovative assays. Supports neuroscience, psychology, pharmacology, genetics, cancer, and development by providing advanced tools and expertise for the precise measurement and interpretation of behavior.

Proper citation: Seattle Childrens Research Institute Behavioral Phenotyping Core Facility (RRID:SCR_026371) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages/release/bioc/html/singleCellTK.html

Software R package provides interface to popular tools for importing, quality control, analysis, and visualization of single cell RNA-seq data. Allows users to integrate tools from various packages at different stages of analysis workflow.

Proper citation: singleCellTK (RRID:SCR_026813) Copy   

•   Source: SciCrunch Registry

http://confocal.uconn.edu

Facility provides training and access to advanced light microscopy systems at an hourly rate. In addition, we are available to consult with and support users at every stage of a project including: experimental design, sample preparation, image acquisition, analysis, and data preparation.

Proper citation: University of Connecticut Advanced Light Microscopy Core Facility (RRID:SCR_027547) Copy   

•   Source: SciCrunch Registry

http://www.mtu.edu/mcff

Core facility provides tools for imaging, analysis, environmental testing, and micro/nanofabrication. Offers data, expertise, and hands-on training. From advanced materials to environmental systems, MCFF is the hub where discovery meets precision.

Proper citation: Michigan Technological University Materials Characterization and Fabrication Core Facility (RRID:SCR_027872) Copy   

•   Source: SciCrunch Registry

http://nmr.chem.cornell.edu

Core specializes in the analysis of small organic and organometallic analytes. Provides access to mass spectrometers for all.

Proper citation: Cornell University Chemistry MS Core Facility (RRID:SCR_028079) Copy   

•   Source: SciCrunch Registry

https://www.roswellpark.org/shared-resources/biostatistics-statistical-genomics

Core offers services in design, oversight, implementation, analysis, publication, and reporting of scientific studies including articulating study objectives and hypotheses, grant writing, conceiving appropriate cost-effective designs and models for achievement of study objectives, monitoring interim and final analyses, and co-authoring abstracts and manuscripts.

Proper citation: Roswell Park Comprehensive Cancer Center Biostatistics and Statistical Genomics Shared Resource BSGSR Core Facility (RRID:SCR_028371) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/as-peak/

A software that utilizes a peak detection algorithm to identify RNA-protein binding sites.

Proper citation: AS-Peak (RRID:SCR_000380) Copy   

•   Source: SciCrunch Registry

http://www.dnastar.com/t-seqmanpro.aspx

Software for analysis and DNA sequence assembly of Sanger data. It also provides visualizations and analysis of next-gen projects assembled by SeqMan NGen.

Proper citation: Lasergene's SeqMan Pro (RRID:SCR_000283) Copy   

•   Source: SciCrunch Registry

http://open-ms.sourceforge.net/documentation/knime-integration/

A graphical user interface (GUI) for rapid composition of HPLC-MS analysis workflows. Workflow construction is reduced to drag-and-drop of analysis tools and adding connections in between.

Proper citation: TOPPAS (RRID:SCR_000533) Copy   

•   Source: SciCrunch Registry

http://thomsonreuters.com/metadrug/

A leading systems pharmacology solution that incorporates extensive manually curated information on biological effects of small molecule compounds. Predictive and analytical algorithms look at chemical compounds from different angles in one integrated workflow are available for: * Individual previously described compounds to look up their known information and predict currently unknown properties * Individual newly synthesized or isolated compounds to predict their properties from its structures * Compound libraries to extract known and predict new properties of individual compounds and perform their comparison and prioritization

Proper citation: MetaDrug (RRID:SCR_000461) Copy   

•   Source: SciCrunch Registry

http://www.molmine.com/magma/

A collection of cook-book like manuals for various microarray designs. MAGMA is a collaboration between the Norwegian Microarray Consortium NMC and MolMine AS

Proper citation: Mini Analysis Guide for Microarrays (RRID:SCR_000596) Copy   

•   Source: SciCrunch Registry

http://linus.nci.nih.gov./BRB-ArrayTools.html

A software package for the visualization and statistical analysis of DNA microarray gene expression data. The tools have been developed from the R statistical system, in C and fortran programs and Java applications. They are integrated into Excel as an add-in.

Proper citation: Biometric Research Branch: ArrayTools (RRID:SCR_000778) Copy   

•   Source: SciCrunch Registry

http://megasoftware.net/

Software integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses. Used for comparative analysis of DNA and protein sequences to infer molecular evolutionary patterns of genes, genomes, and species over time. MEGA version 4 expands on existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. MEGA version 6 enables inference of timetrees, as it implements RelTime method for estimating divergence times for all branching points in phylogeny.

Proper citation: MEGA (RRID:SCR_000667) Copy   

•   Source: SciCrunch Registry

http://neuromorphometrics.org:8080/nvm/index.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6, 2023. Software tool for quantitative neuroanatomical measurements in volumetric image data. Used to draw regions of interest for subsequent fMRI analysis.

Proper citation: NVM (RRID:SCR_000600) Copy   

•   Source: SciCrunch Registry

http://www.bork.embl.de/j/

The main focus of this Computational Biology group is to predict function and to gain insights into evolution by comparative analysis of complex molecular data. The group currently works on three different scales: * genes and proteins, * protein networks and cellular processes, and * phenotypes and environments. They require both tool development and applications. Some selected projects include comparative gene, genome and metagenome analysis, mapping interactions to proteins and pathways as well as the study of temporal and spatial protein network aspects. All are geared towards the bridging of genotype and phenotype through a better understanding of molecular and cellular processes. The services - resources & tools, developed by Bork Group, are mainly designed and maintained for research & academic purposes. Most of services are published and documented in one or more papers. All our tools can be completely customized and integrated into your existing framework. This service is provided by the company biobyte solutions GmbH. Please visit their tools and services pages for full details and more information. Standard commercial licenses for our tools are also available through biobyte solutions GmbH. The group is partially associated with Max Delbr��ck Center for Molecular Medicine (MDC), Berlin.

Proper citation: EMBL - Bork Group (RRID:SCR_000810) Copy   

•   Source: SciCrunch Registry

http://kofler.or.at/bioinformatics/SciRoKo/

Comparative genomics software that assists in whole genome microsatellite search and investigation. The command line version is called SciRoKoCo. The perl script DesignPrimer can be used to design PCR primer pairs for the SciRoKo output.

Proper citation: SciRoKo (RRID:SCR_000941) Copy   

•   Source: SciCrunch Registry

http://www.scienceexchange.com/facilities/university-of-colorado-at-boulder

A portal for the core labs and facilities at the University of Colorado at Boulder.

Proper citation: University of Colorado at Boulder Labs and Facilities (RRID:SCR_001054) Copy   

•   Source: SciCrunch Registry

http://www.ezbioresearch.com

A biotechnology company that develops, manufactures and distributes molecular biology tool kits and laboratory consumable products. Services include DNA and RNA microarrays, PCR and transgenic genotyping, and DNA/RNA analysis and quality control.

Proper citation: EZ BioResearch (RRID:SCR_001050) Copy   

•   Source: SciCrunch Registry