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http://zhanglab.ccmb.med.umich.edu/I-TASSER/

Web server as integrated platform for automated protein structure and function prediction. Used for protein 3D structure prediction. Resource for automated protein structure prediction and structure-based function annotation.

Proper citation: I-TASSER (RRID:SCR_014627) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/us/en/home/technical-resources/software-downloads/applied-biosystems-7500-real-time-pcr-system.html

A software used to control and operate the Applied Biosystems 7500 Real-Time PCR system.

Proper citation: 7500 Real-Time PCR Software (RRID:SCR_014596) Copy   

•   Source: SciCrunch Registry

http://chemistry.unt.edu/~verbeck/LIMS/Manuals/XCAL_Quant.pdf

A software which acquires and processes data sets, primarily through the Xcalibur system.

Proper citation: Thermo Xcalibur (RRID:SCR_014593) Copy   

•   Source: SciCrunch Registry

http://cole-trapnell-lab.github.io/cufflinks/cuffmerge/

Software tool for transcriptome assembly and differential expression analysis for RNA-Seq. Includes script called cuffmerge that can be used to merge together several Cufflinks assemblies. It also handles running Cuffcompare as well as automatically filtering a number of transfrags that are likely to be artifacts. If the researcher has a reference GTF file, the researcher can provide it to the script to more effectively merge novel isoforms and maximize overall assembly quality.

Proper citation: Cufflinks (RRID:SCR_014597) Copy   

•   Source: SciCrunch Registry

http://cyberinncorp.com/SigmaGel.htm

Gel analysis software which can be used on a PC with TWAIN-compatible scanners without specialty equipment. Users scan or load an image which can then be calibrated. SigmaGel allows users to make lane measurements, spot measurements, and molecular weight measurements. After data analysis was completed, users can print or copy and paste data and images.

Proper citation: SigmaGel Software (RRID:SCR_014598) Copy   

•   Source: SciCrunch Registry

http://www.cbn-atl.org/research/stopwatch.shtml

A software which tracks the number of occurrences and duration of up to 16 defined events. The user can group events together so that turning on one event in a group will automatically turn off other active events in the group. Sessions can end after a fixed length of time, or the sessions can be ended manually, At the end of the session, the data can be saved in a comma-delimited file which can be easily imported into a spreadsheet application.

Proper citation: Stopwatch+ (RRID:SCR_014591) Copy   

•   Source: SciCrunch Registry

http://statplus-mac.en.softonic.com/mac

A statistical data analysis tool that works with Microsoft Excel and is designed especially for use in IOS systems. Tutorials and examples are provided within the program.

Proper citation: StatPlus Mac (RRID:SCR_014635) Copy   

•   Source: SciCrunch Registry

http://store.neurosky.com/products/neuroexperimenter

Software which provides an interface for MindWave Mobile hardware, allowing users to view and listen to brainwave output of different "mind states". Users can: view any or all brainwaves, specify a combination of brainwaves via a formula, compare a base line session to a performance session, and create a log and run it through the application to view different graphical outputs. NeuroExperimenter only runs on Windows

Proper citation: NeuroExperimenter (RRID:SCR_014759) Copy   

•   Source: SciCrunch Registry

http://www.jadesantiago.com/Electrophysiology/IonChannelLab/

Software for kinetic modeling of ion channels which operates on Windows XP or Windows Vista.

Proper citation: IonChannelLab (RRID:SCR_014762) Copy   

•   Source: SciCrunch Registry

http://libroadrunner.org/

Simulation engine for systems and synthetic biology to be used with other software applications. It retains the original functionality of RoadRunner but has changes in performance, back-end design, event handling, new C++ API, and stochastic simulation support.

Proper citation: libRoadRunner (RRID:SCR_014763) Copy   

•   Source: SciCrunch Registry

http://hmpdacc.org/resources/tools_protocols.php

A tool used to screen for core gene sets as an indicator of completeness of draft genomes. The download includes a Perl script and required archaeal and bacterial core genes fasta and cluster files.

Proper citation: Core Gene Evaluation Script (RRID:SCR_014604) Copy   

•   Source: SciCrunch Registry

http://cxidb.org

Database of Coherent X-ray Imaging (CXI) experiments. This data is widely accessible to researchers worldwide.

Proper citation: Coherent X-Ray Imaging Data Bank (CXIDB) (RRID:SCR_014722) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/invue/

An API and software suite for large scale data visualization and analysis.

Proper citation: inVUE (RRID:SCR_014608) Copy   

•   Source: SciCrunch Registry

http://rast.nmpdr.org

A SEED-quality automated service that annotates complete or nearly complete bacterial and archaeal genomes across the entire phylogenetic tree. RAST can also be used to analyze draft genomes.

Proper citation: RAST Server (RRID:SCR_014606) Copy   

•   Source: SciCrunch Registry

http://www.vicbioinformatics.com/software.prokka.shtml

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for the rapid annotation of prokaryotic genomes. It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank/DDJB/ENA. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Prokka (RRID:SCR_014732) Copy   

•   Source: SciCrunch Registry

http://computation.llnl.gov/projects/sundials/cvode

Solver for stiff and nonstiff ordinary differential equation (ODE) systems (initial value problem), given in explicit form y' = f(t,y), based on Adams and BDF methods. It is one of the programs that makes up the Suite of Nonlinear and Differential/Algebraic Equation Solvers (SUNDIALS)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CVODE (RRID:SCR_014696) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/SparseTracer

Software used to automatically trace single neurons. It supports VTK 3D visualization.

Proper citation: SparseTracer (RRID:SCR_014736) Copy   

•   Source: SciCrunch Registry

http://www.splitstree.org/

Application that uses molecular sequence data to compute unrooted phylogenetic networks. Given an alignment of sequences, a distance matrix, or a set of trees, the program will compute a phylogenetic tree or network using methods such as split decomposition, neighbor-net, consensus network, super networks methods or methods for computing hybridization or simple recombination networks., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SplitsTree (RRID:SCR_014734) Copy   

•   Source: SciCrunch Registry

http://biocore.github.io/SitePainter/

An interactive data visualization tool which allows users to create and upload pictures of their study site, load diversity analyses, and display both diversity and taxonomy results in a spatial context.

Proper citation: SitePainter (RRID:SCR_014618) Copy   

•   Source: SciCrunch Registry

http://aem.asm.org/content/71/12/8228.full

THIS RESOURCE IS NO LONGER IN SERVICE, documented Setember 8, 2016. A suite of tools for the comparison of microbial communities using phylogenetic information. It takes as input a single phylogenetic tree that contains sequences derived from at least two different environmental samples and a file describing which sequences came from which sample.

Proper citation: Unifrac (RRID:SCR_014616) Copy   

•   Source: SciCrunch Registry