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http://sciencedynamics.data4good.io

Portal for Science Dynamics projects with open source framework to provide way to query datasets. Code framework, including tutorials for project, titled Over Optimization of Academic Publishing Metrics Observing Goodhart Law in Action, to interactively explore and understand how various properties of journals have changed over time. Datasets, software implementations, code tutorials and interactive web interface for investigating studied networks.

Proper citation: Science Dynamics (RRID:SCR_016958) Copy   

•   Source: SciCrunch Registry

https://www.olympus-global.com/technology/museum/micro/2004/

FV1000 confocal laser scanning biological microscope features twin scan system which enables spectroscopy of living intercellular contents and analysis of objects down to a 2nm wavelength resolution. Image size is increased to 4096x4096 pixels.

Proper citation: Olympus: FV1000 Confocal Microscope (RRID:SCR_016840) Copy   

•   Source: SciCrunch Registry

https://www.leicabiosystems.com/us/histology-equipment/cryostats/leica-cm3050-s/

Instrument designed for cryosectioning in biomedical, neuro-anatomical and pharmaceutical research.

Proper citation: Leica: CM3050 S Research Cryostat (RRID:SCR_016844) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/bbmap

Software tool as a short read aligner for DNA and RNA seq data. Used for large genomes with millions of scaffolds. Can align reads from Illumina, PacBio, 454, Sanger, Ion Torrent, Nanopore. Fast and accurate, particularly with highly mutated genomes or reads with long indels, even whole gene deletions over 100kbp long. It has no upper limit to genome size or number of contigs. Written in Java, can run on any platform.

Proper citation: BBmap (RRID:SCR_016965) Copy   

•   Source: SciCrunch Registry

http://zhoulab.usc.edu/TopDom/

Software tool to identify Topological Domains, which are basic builiding blocks of genome structure. Detects topological domains in a linear time., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: TopDom (RRID:SCR_016964) Copy   

•   Source: SciCrunch Registry

http://cctop.enzim.ttk.mta.hu/

Web application providing transmembrane topology prediction. Server incorporates topology information from existing experimental and computational sources using the probabilistic framework of hidden Markov model. Provides the option to precede the topology prediction with signal peptide prediction and transmembrane globular protein discrimination. Given the amino acid sequence of a putative α helical transmembrane protein, CCTOP predicts its topology i.e. localization of membrane spanning regions and orientation of segments between them.

Proper citation: CCTOP (RRID:SCR_016963) Copy   

•   Source: SciCrunch Registry

https://www.btxonline.com/products/electroporation-systems/ecm-830-square-wave-electroporation-system.html

ECM 830 is a square wave pulse generator designed for in vitro and in vivo applications for gene, drug and protein delivery for mammalian cells, zebra fish tissue and embryos, nuclear transfer, embryo manipulation, plant protoplast and basic bacteria and yeast transformations. Used in ECM 830 SQUARE WAVE ELECTROPORATION SYSTEM.

Proper citation: HBio: Multichallel Systems: Electro Square Porator ECM 830, BTX (RRID:SCR_016841) Copy   

•   Source: SciCrunch Registry

https://pharos.nih.gov/

Program to improve understanding of properties and functions of proteins that are currently unannotated within three most commonly drug protein families: targeted G-protein coupled receptors, ion channels, and protein kinases. Includes Data and Resource Generating Centers (DRGC), Knowledge Management Center (KMC), and Resource Dissemination and Outreach Center (RDOC).

Proper citation: Illuminating the Druggable Genome (RRID:SCR_016924) Copy   

•   Source: SciCrunch Registry

https://plusconsortium.umn.edu

Research consortium from many different fields to plan, perform and analyze the studies that are needed to help researchers conduct future prevention and intervention for Lower Urinary Tract Symptoms (LUTS) in women.

Proper citation: Prevention of Lower Urinary Tract Symptoms (RRID:SCR_016923) Copy   

•   Source: SciCrunch Registry

https://commonfund.nih.gov/hubmap

Project to facilitate research on single cells within tissues by supporting data generation and technology development to explore the relationship between cellular organization and function, as well as variability in normal tissue organization at the level of individual cells. Framework for functional mapping the human body with cellular resolution.Designed to support diverse spatial and non-spatial omics and imaging data types and to integrate with a wide range of analysis workflows.

Proper citation: The Human BioMolecular Atlas Program (RRID:SCR_016922) Copy   

•   Source: SciCrunch Registry

http://dee2.io/

Software tool as a repository of uniformly processed RNA-seq data mined from public data obtained from NCBI Short Read Archive . DEE2 consists of three parts: Webserver where end-users can search for and obtain data-sets of interest, Pipeline that can download and process SRA data as well as users own fastq files, Back-end that collects, filters and organises data provided by contributing worker nodes.

Proper citation: Digital Expression Explorer 2 Project (RRID:SCR_016929) Copy   

•   Source: SciCrunch Registry

http://alggen.lsi.upc.es/cgi-bin/promo_v3/promo/promoinit.cgi?dirDB=TF_8.3

Web tool to identify putative transcription factor binding sites (TFBS) in DNA sequences from a species or groups of species of interest. Used for detection of known transcription regulatory elements using species-tailored searches.

Proper citation: ALGGEN-PROMO (RRID:SCR_016926) Copy   

•   Source: SciCrunch Registry

https://biii.eu/fibriltool

ImageJ plug-in to quantify fibrillar structures in raw microscopy images. Used to evaluate the orientation of fiber orientation pattern and plots the results in the image.

Proper citation: FibrilTool (RRID:SCR_016773) Copy   

•   Source: SciCrunch Registry

https://www.nzytech.com/

Commercially provides services and products for research in the fields of molecular biology, diagnostics, enzymes and proteins.

Proper citation: NZYTech (RRID:SCR_016772) Copy   

•   Source: SciCrunch Registry

https://github.com/ToolsVanBox/smMIPfil

Software tool for single molecule Molecular Inversion Probes data analysis. This is a stand-alone perl script. Except that this is dependent on the samtools, no installation required.

Proper citation: smMIPfil (RRID:SCR_016892) Copy   

•   Source: SciCrunch Registry

https://github.com/zitmen/thunderstorm

Software tool for automated processing, analysis, and visualization of data acquired by single molecule localization microscopy methods such as PALM and STORM. ImageJ interactive and modular plugin for SMLM data analysis and super-resolution imaging.

Proper citation: Thunder STORM (RRID:SCR_016897) Copy   

•   Source: SciCrunch Registry

https://crispr.cos.uni-heidelberg.de/

Web tool for CRISPR/Cas9 target prediction. Identifies and ranks all candidate sgRNA target sites according to their off-target quality and displays full documentation.

Proper citation: CCTop (RRID:SCR_016890) Copy   

•   Source: SciCrunch Registry

https://utex.org/

The UTEX Culture Collection of Algae includes different strains of living algae, representing most major taxa. Cultures in the Collection are used for research, teaching, biotechnology development, and various other projects throughout the world.

Proper citation: Culture Collection of Algae at the University of Texas (RRID:SCR_016782) Copy   

•   Source: SciCrunch Registry

http://crispr.hzau.edu.cn/CRISPR/

Web tool for synthetic single-guide RNA design of CRISPR-system in plants. Allows to search for high specificity Cas9 target sites within DNA sequences of interest, which also provides off-target loci prediction for specificity analyses and marks restriction enzyme cutting site to every sgRNA for further convenient in experiment.

Proper citation: CRISPR-P (RRID:SCR_016941) Copy   

•   Source: SciCrunch Registry

https://www.schrodinger.com/macromodel

Software package for molecular modeling. Computes free energy changes using free energy perturbation method. Used to examine molecular conformations, molecular motion, and intermolecular interactions, such as those in a ligand-receptor complex.

Proper citation: MacroModel (RRID:SCR_016747) Copy   

•   Source: SciCrunch Registry