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https://rise.bsc.gwu.edu/web/rise/home?p_p_id=58&p_p_lifecycle=0&_58_redirect=%2F

Consortium which includes 3 studies, each assessing the hypothesis that aggressive glucose lowering will lead to recovery of beta-cell function that will be sustained after treatment in those with prediabetes and early type 2 diabetes.

Proper citation: Restoring Insulin Secretion Consortium (RISE) (RRID:SCR_014383) Copy   

•   Source: SciCrunch Registry

http://msstats.org/

A package for statistical relative quantification of proteins and peptides in global, targeted, and data-independent proteomics. It handles shotgun, label-free, and label-based Selected Reaction Monitoring, as well as SWATH/DIA (Data Independent Acquisition) experiments. MSStats provide functionality for data processing and visualization, model-based statistical analysis, and model-based sample size calculations.

Proper citation: MSstats (RRID:SCR_014353) Copy   

•   Source: SciCrunch Registry

https://simthyr.sourceforge.io

Open source simulation software for thyroid homeostasis, based on published nonlinear model of pituitary thyroid feedback control. Simulates pituitary thyroid feedback control, which allows users to study relationship between structure and behaviour of thyroid homeostasis.

Proper citation: SimThyr (RRID:SCR_014351) Copy   

•   Source: SciCrunch Registry

http://cyberunits.sourceforge.net/

A cross-platform class library for development of high-performance life science computer simulations. It supports modelling for biomedical cybernetics and systems biology with Object Pascal. It contains a set of Pascal units for rapid programming of high-performance computer simulations called the Brick collection.

Proper citation: CyberUnits (RRID:SCR_014358) Copy   

•   Source: SciCrunch Registry

https://vdjserver.org/

A web application immune repertoire management, analysis, and archiving. Users can collaborate and share data either privately or publicly. Users can perform a variety of tasks, such as create and share projects with other users, conduct pre-processing tasks on single end reads, run IgBlast, and obtain basic repertoire characterization results for B cell receptor and T cell receptor repertoires.

Proper citation: VDJ Server (RRID:SCR_014356) Copy   

•   Source: SciCrunch Registry

https://cfn.upenn.edu/~zewang/BENtbx.php

A toolkit for mapping brain entropy using fMRI. It uses several functions from ASLtbx. At its core, the toolkit is a collection of batch scripts that implement a pipeline for processing fMRI data in order to get Sample entropy for each voxel.

Proper citation: Brain Entropy Mapping Toolbox (RRID:SCR_014470) Copy   

•   Source: SciCrunch Registry

http://technologies.kmi.open.ac.uk/rexplore/

An application which provides an environment to explore and organize scholarly data. Rexplore leverages solutions in large-scale data mining, semantic technologies and visual analytics, which allows users to detect and follow research trends, identify and map relationships between authors, perform expert searches, and analyze research performance.

Proper citation: Rexplore (RRID:SCR_014364) Copy   

•   Source: SciCrunch Registry

http://surfer.nmr.mgh.harvard.edu/optseq/

Software tool for automatically scheduling events for rapid-presentation event-related (RPER) fMRI experiments (the schedule is the order and timing of events). Events in RPER are presented closely enough in time that their hemodynamic responses will overlap. This requires that the onset times of the events be jittered in order to remove the overlap from the estimate of the hemodynamic response. RPER is highly resistant to habituation, expectation, and set because the subject does not know when the next stimulus will appear or which stimulus type it will be.

Proper citation: Optseq (RRID:SCR_014363) Copy   

•   Source: SciCrunch Registry

http://www.freepascal.org

Free Pascal is a 32, 64 and 16 bit professional Object Pascal compiler targeting multiple processor architectures and operating systems. Documentation, including guides and manuals, are available on the website.

Proper citation: Free Pascal Compiler (RRID:SCR_014360) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

https://www.nikoninstruments.com/Products/Software

Microscope imaging software suite used with Nikon products. NIS-Elements includes software applications for advanced and standard research, documentation, confocal microscopy, and high-content analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: NIS-Elements (RRID:SCR_014329) Copy   

•   Source: SciCrunch Registry

https://www.imagescience.de/imagic.html

An image analysis software that can process spectra and other multi-dimensional data-sets. The software package is aimed at processing large data sets from (cryo-) electron microscopy, especially in the field of single particle analyses. This software can be used with light and raster-tunneling microscopes, computer tomographs, FT-IR spectrometers and other signal collecting devices. This resource provides three-dimensional data processing and angular reconstitution modules that allow the three-dimensional reconstruction with point-group symmetry from the two dimensional electron microscopy projections. These models aid in the analysis of the macromolecules.

Proper citation: IMAGIC (RRID:SCR_014447) Copy   

•   Source: SciCrunch Registry

http://www.amtimaging.com/www11/english/product_e.html

AMT camera system software that performs digital image acquisition, processing, and storage. An operations manual and software specifications are available on the main site.

Proper citation: AMT Image Capture Software (RRID:SCR_014333) Copy   

•   Source: SciCrunch Registry

http://www.macrogen.com/

A company that provides a variety of next generation sequencing services. The company provides researchers with whole genome resequencing, exome sequencing, targeted sequencing, transcriptomics, and epigenome sequencing.

Proper citation: Macrogen (RRID:SCR_014454) Copy   

•   Source: SciCrunch Registry

http://scratch.proteomics.ics.uci.edu/index.html

Web protein structure and structural feature prediction server.Software suite includes predictors for secondary structure, relative solvent accessibility, disordered regions, domains, disulfide bridges, single mutation stability, residue contacts versus average, individual residue contacts and tertiary structure. User provides amino acid sequence and selects desired predictions, then submits to the server.

Proper citation: SCRATCH (RRID:SCR_014291) Copy   

•   Source: SciCrunch Registry

http://sysbio.rnet.missouri.edu/multicom_toolbox/NNCon%201.0.html

Protein contact map prediction is useful for protein folding rate prediction, model selection and 3D structure prediction. Here we describe NNcon, a fast and reliable contact map prediction server and software. NNcon was ranked among the most accurate residue contact predictors in the Eighth Critical Assessment of Techniques for Protein Structure Prediction (CASP8), 2008.

Proper citation: NNcon (RRID:SCR_014292) Copy   

•   Source: SciCrunch Registry

http://help.sap.com/saphelp_ve-author80/helpdata/en/bc/b3a5c7d8ec4dbebe54199d2ba9a58a/frameset.htm

A desktop application used to create and manage 2D and 3D animation and video and audio assets. SAP Visual Enterprise Author can be used to render visual content into common desktop documents, file formats, and business applications for secure downstream use. A variety of tools allows users to view, transform, optimize, animate, and publish in different formats.

Proper citation: SAP Visual Enterprise Author (RRID:SCR_014293) Copy   

•   Source: SciCrunch Registry

http://www.biobserve.com/products/viewer/

Software that provides subject tracking with body axis alignment and angle of view, which is then used to track body, nose and tail movements without marking the animal. Users may create the scoring system used by the software, as well as zones to observe, quantify, and compare the behavior of an animal in one or more areas. The software features several data acquisition and analysis tools to gather and interpret the data.

Proper citation: Biobserve Viewer (RRID:SCR_014337) Copy   

•   Source: SciCrunch Registry

http://www.andor.com/scientific-software/iq-live-cell-imaging-software

A live cell imaging software that allows for control of iXon EMCCD and sCMOS cameras in synchronized combination with a number of additional imaging hardware devices. iQ can be used to run experiments to investigate dynamic processes in both single cells and multicellular systems, image fixed samples, and generate 3 dimensional image volumes for analysis.

Proper citation: Andor iQ (RRID:SCR_014461) Copy   

•   Source: SciCrunch Registry

http://g6g-softwaredirectory.com/bio/cross-omics/biomarker/20241BrukerClinProTools.php

Biomarker detection and evaluation software which provides an advanced basis for mining unknown potential biomarkers in complex protein profiles. Visualization tools such as stack plots and box-and-whiskers plots can be used to interactively inspect and compare large data sets originating from samples that contain different clinical diagnoses. ClinProTools also supplies sophisticated mathematical algorithms for the discovery of complex biomarker pattern models. Besides validation, class-prediction tools are also integrated to allow the implementation of the whole biomarker detection and evaluation process.

Proper citation: ClinProTools (RRID:SCR_014341) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://www.embl.de/eamnet/html/body_image_browser.html

Software used to compile images obtained from the Zeiss LSM 510 confocal microscope. The browser can be used for general image archiving and handling and interactive measurement in labs and workgroups. Features include orthogonal sectioning, 3D cut function, 3D view with calculation of single projections, and interactive measurement functions in the overlay dialog, such as scale bar, distance, and area.

Proper citation: LSM Image Examiner (RRID:SCR_014344) Copy   

•   Source: SciCrunch Registry