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http://doa.nubic.northwestern.edu/pages/search.php

Project portal for a collaborative database aiming to provide a comprehensive annotation to human genome.It uses the computable, controlled vocabulary of Disease Ontology (DO) and NCBI Gene Reference Into Function (GeneRIF).

Proper citation: DOAF (RRID:SCR_015666) Copy   

•   Source: SciCrunch Registry
  

http://pa.wishartlab.com/pa/pa/index.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 29,2025. Web-based tool that predicts subcellular localization and GO molecular function of proteins. Proteome Analyst has the ability to explain its predictions and gives users the ability to run a large set of tools on their proteins.

Proper citation: Proteome Analyst (RRID:SCR_013807) Copy   

•   Source: SciCrunch Registry
  

http://www.rhino3d.com/features

3D modeling software used to create, edit, analyze, document, render, animate, and translate surfaces, solids, point clouds, and polygon meshes. It can also be used to analyze and manufacture a variety of products.

Proper citation: Rhinoceros (RRID:SCR_014339) Copy   

•   Source: SciCrunch Registry
  

https://www.ncbi.nlm.nih.gov/UniGene/help.cgi?item=DDD

Software tool for comparing EST profiles in order to identify genes with significantly different expression levels.

Proper citation: Digital Differential Display (DDD) (RRID:SCR_016638) Copy   

•   Source: SciCrunch Registry
  

http://www.gelifesciences.co.kr/wp-content/uploads/2016/08/IN-Cell-Developer-Toolbox-v1.9.pdf

Image analysis software for developing new cellular assay analysis routines. This software provides a selection of advanced segmentation, pre-processing and post-postprocessing tools.

Proper citation: INCell Developer Toolbox (RRID:SCR_015790) Copy   

•   Source: SciCrunch Registry
  

http://asipro.software.informer.com/

An image analysis software.

Proper citation: ASIPro (RRID:SCR_014547) Copy   

•   Source: SciCrunch Registry
  

https://github.com/wdecoster/nanofilt

Software tool written in Python to perform its filtering based on mean read quality and GC content and read length. Used for filtering and trimming of long read sequencing data.

Proper citation: NanoFilt (RRID:SCR_016966) Copy   

•   Source: SciCrunch Registry
  

http://monogenicdiabetes.uchicago.edu/mody-registry-2/

Research project that aims to learn more about the number of people who have monogenic diabetes, why and how it happens, and how best to treat it. Any adult or child with a known genetic cause of diabetes may join the MODY Registry.

Proper citation: Monogenic Diabetes Registry (RRID:SCR_015883) Copy   

•   Source: SciCrunch Registry
  

https://github.com/mandricigor/ScaffMatch

Software tool as scaffolding algorithm based on maximum weight matching able to produce high quality scaffolds from next generation sequencing data (reads and contigs). Able to handle reads with both short and long insert sizes.

Proper citation: ScaffMatch (RRID:SCR_017025) Copy   

•   Source: SciCrunch Registry
  

https://www.adinstruments.com/products/dmt-normalization

Software tool for calculating optimal pretension conditions for microvascular or any small tubular tissue research. DMT Normalization Add-On, provided by ADInstruments, is included as part of LabChart Pro or can be purchased separately.

Proper citation: DMT Normalization (RRID:SCR_017024) Copy   

•   Source: SciCrunch Registry
  

https://github.com/cukie/SMIA

Software used to analyze and quantify images stained with multiple fluorophores in vitro or in vivo. It can output both image and value outputs.

Proper citation: SMIA-CUKIE (RRID:SCR_014795) Copy   

•   Source: SciCrunch Registry
  

http://www.ngsp.org

Project that aims to standardize Hemoglobin A1c test results to those of the Diabetes Control and Complications Trial (DCCT) and United Kingdom Prospective Diabetes Study (UKPDS) which established the direct relationships between HbA1c levels and outcome risks in patients with diabetes.

Proper citation: National Glycohemoglobin Standardization Program (RRID:SCR_015885) Copy   

•   Source: SciCrunch Registry
  

https://geomagic-studio.software.informer.com/12.0/

Software tool to convert 3D scans into parametric models. Transforms 3D scan data into highly accurate surface, polygon and native CAD models. Used for reverse engineering, product design, rapid prototyping and analysis.

Proper citation: GEOMAGIC Studio (RRID:SCR_016978) Copy   

•   Source: SciCrunch Registry
  

https://github.com/dvera/albacore

Data processing basecaller for the Oxford Nanopore sequencer that identifies DNA sequences directly from raw data. It enhances accuracy of the single-read sequence data, contributing to high consensus accuracy for nanopore sequence data.

Proper citation: Albacore (RRID:SCR_015897) Copy   

•   Source: SciCrunch Registry
  

http://alan-hadley.software.informer.com/

A software used to process stacks of digital images. All of the resulting images are processed to have the same dimensions and then are consolidated into a single image.

Proper citation: CombineZP (RRID:SCR_014567) Copy   

•   Source: SciCrunch Registry
  

https://www.nsrusa.org

Organization that provides instructions for and research on the Natural Stress Relief (NSR) meditation method.

Proper citation: Natural Stress Relief (RRID:SCR_015898) Copy   

•   Source: SciCrunch Registry
  

https://github.com/eulerlab/QDSpy

Software Python tool for scripting and presenting stimuli for visual neuroscience.

Proper citation: QDSpy (RRID:SCR_016985) Copy   

•   Source: SciCrunch Registry
  

http://www.nanoprobes.com

A nanoparticle research collaborative which engineers nanoparticle products in order to find cures for cancer and other diseases. The gold labels produced are uncharged molecules which are cross-linked to specific sites on biomolecules. Labels can be attached to any molecule with a reactive group (proteins, peptides, oligonucleotides, small molecules and lipids) for detection and localization. New probes can be engineered based on any fragment of a naturally occurring biomolecule, and the label can be positioned away from the binding site so it does not interfere with binding.

Proper citation: nanoprobes.com (RRID:SCR_014323) Copy   

•   Source: SciCrunch Registry
  

http://chemdata.nist.gov

A data center that develops evaluated mass spectral libraries and provides related software tools that assist compound identification by providing reference mass spectra for GC/MS (by electron ionization) and LC-MS/MS (by tandem mass spectrometry). It also provides gas phase retention indices for GC. Resources include the mass spectral library, the peptide library, and a standard refernece material guide.

Proper citation: NIST Mass Spectrometry Data Center (RRID:SCR_014680) Copy   

•   Source: SciCrunch Registry
  

http://ncmir.ucsd.edu/Software/btrack.htm

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. It analyzes and graphs time-lapse imaging data as acquired by a Bio-Rad confocal microscope, for experiments using nonratiometric fluorescent indicator dyes. Btrack can accommodate changes in the positions of imaged cells/tissue regions and can be used for analyzing an unlimited number of areas (cells/tissue regions) in an imaged field.

Proper citation: btrack (RRID:SCR_013591) Copy   

•   Source: SciCrunch Registry