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https://www.olympus-lifescience.com/en/microscopes/virtual/vs120/

VS120 Virtual Slide Microscope. Part of slide loader system for manually loading standard slides by Olympus.

Proper citation: Olympus: VS120 microscope (RRID:SCR_018411) Copy   

•   Source: SciCrunch Registry
  

https://www.sympy.org/en/index.html

Software Python library for symbolic mathematics. It aims to become full featured computer algebra system (CAS) while keeping code as simple as possible in order to be comprehensible and easily extensible.

Proper citation: SymPy (RRID:SCR_018417) Copy   

•   Source: SciCrunch Registry
  

https://www.beckman.com/liquid-handlers/biomek-i7/b87585

Liquid handling instrument designed to optimize dependability and walk-away time. Biomek i7 Hybrid with enclosure has up to 45 deck positions and includes both Multichannel and Span-8 pipette heads in enclosed work space.

Proper citation: Beckman Coulter: Biomek i7 Hybrid Automated Workstation (RRID:SCR_018094) Copy   

•   Source: SciCrunch Registry
  

https://pypi.org/project/pyflakes/

Software tool to check Python source files for errors. Passive checker of Python programs Used to analyze programs and detect various errors. Works by parsing source file, not importing it, so it is safe to use on modules with side effects.

Proper citation: Pyflakes (RRID:SCR_018422) Copy   

•   Source: SciCrunch Registry
  

https://github.com/smortezah/smashpp

Software tool to find and visualize rearrangements in DNA sequences.

Proper citation: smashpp (RRID:SCR_018307) Copy   

•   Source: SciCrunch Registry
  

https://www.fh-co.com/product/metal-microelectrodes/

A platinum/iridium electrode use for stimulating tissue samples. Manufactured by FHC Neural microTargeting Worldwide.

Proper citation: FHC: Platinum/Iridium microelectrode (RRID:SCR_018426) Copy   

•   Source: SciCrunch Registry
  

http://diana.imis.athena-innovation.gr/DianaTools

Collection of tools to provide algorithms, databases and software for interpreting and archiving data in systematic framework ranging from analysis of expression regulation from deep sequencing data, annotation of miRNA regulatory elements and targets to interpretation of role of ncRNAs in various diseases and pathways. Includes target prediction algorithms microT v4 and microT-CDS, databases of experimentally verified miRNA targets on coding and non-coding RNAs like TarBase v7.0 and LncBase, and software capable of identifying potentially altered molecular pathways by expression of single or multiple miRNAs , mirPath. Provides Web Server (v5.0) to support series of workflows enabling users to perform miRNA analyses.

Proper citation: DIANA Tools (RRID:SCR_018425) Copy   

•   Source: SciCrunch Registry
  

https://github.com/cramerlab/warp

Software tool that automates all preprocessing steps of cryo-EM data acquisition and enables real-time evaluation. Corrects micrographs for global and local motion, estimates local defocus and monitors key parameters for each recorded micrograph or tomographic tilt series in real time. Software includes deep-learning-based models for accurate particle picking and image denoising.

Proper citation: Warp (RRID:SCR_018071) Copy   

•   Source: SciCrunch Registry
  

https://biit.cs.ut.ee/gprofiler/page/r

Software R interface to g:Profiler. Uses publicly available APIs of g:Profiler web tool which ensures that results from all of interfaces are consistent. Used for gene list functional enrichment analysis and namespace conversion. gprofiler2 package supports all the same organisms, namespaces and data sources as the web tool.

Proper citation: gProfiler2 (RRID:SCR_018190) Copy   

•   Source: SciCrunch Registry
  

https://view.qiime2.org/

Web based serverless viewer of QIIME 2 artifacts and visualizations. Client side interface for viewing QIIME 2 artifacts and visualizations. Not needed working QIIME 2 installation to inspect QIIME 2 results. Supports viewing externally hosted files by automatically downloading and displaying them when links to files are provided.

Proper citation: QIIME 2 View (RRID:SCR_018074) Copy   

•   Source: SciCrunch Registry
  

http://flowpy.wikidot.com/

Software Python tool for flow cytometry data. Data generated by flow cytometer can be read by FlowPy. Used for data extraction, data visualization, data clustering, histogram subtraction.

Proper citation: FlowPy (RRID:SCR_018195) Copy   

•   Source: SciCrunch Registry
  

http://www.premierbiosoft.com/protein_quantification_software/index.html

Software package as comprehensive qualitative and quantitative suite for proteomics. Used to validate and quantify proteins by combining results from popular mass spectrometry platforms and database search engines. Provides customizable interface to support any form of biological annotation. Used to compare protein quantitative results in relation to biological pathways, protein localization, protein function, or to transcript abundance. Every protein identification can be linked to any external or internal knowledge database. Custom links are provided to GenBank, UniProt, IPI, and SwissProt databases or in-house LIMS.

Proper citation: PremierBiosoft Proteo IQ Software (RRID:SCR_018072) Copy   

•   Source: SciCrunch Registry
  

http://circadb.hogeneschlab.org/

Database of mammalian circadian gene expression profiles. Works with link outs to Wikipedia, HomoloGene, Refseq, etc.. Open source database of circadian transcriptional profiles from time course expression experiments from mice and humans.

Proper citation: CircaDB (RRID:SCR_018078) Copy   

•   Source: SciCrunch Registry
  

https://www.kicnet.co.jp/solutions/biosignal/biosignal-2/vitalrecorder2/

Sleep recording software by Kissei Comtech Co., Ltd. Can measure signals of up to 32 channels while monitoring wave forms in real time. Addition of video recording option enables simultaneous recording of biological signals and video.

Proper citation: VitalRecorder2 (RRID:SCR_018199) Copy   

•   Source: SciCrunch Registry
  

http://www.milesculabs.org/QuB.html

Integrated software platform for ion channel biophysics and neurophysiology.Used to explore dynamics of hidden states in memoryless system. Open source software suite for solving kinetic models, for report generation with publishable graphics, function fitting and scripting for new and repeated processing and AD/DA I/O. Can be applied to any data modeled with Markov kinetics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: QuB (RRID:SCR_018076) Copy   

•   Source: SciCrunch Registry
  

https://www.fibl.org/en/themes/sustainability-assessment-info/sustainability-assessment-smart.html

Web and offline tool for holistic sustainability assessment of farms. Tool operationalizes Sustainability Assessment of Food and Agriculture Systems Guidelines of Food and Agriculture Organisation of United Nations. Tool consists of questionnaire software, centralized database, pool of indicators and scientifically based assessment methodology. Different stakeholders can use results of this assessment e.g. for comparing different farms, production systems or for strategic development, improvement, monitoring and communication to business partners.

Proper citation: SMART-Farm Tool (RRID:SCR_018197) Copy   

•   Source: SciCrunch Registry
  

https://cran.r-project.org/web/packages/cowplot/index.html

Software R package as streamlined plot theme and plot annotations for ggplot2. Provides various features that help with creating publication quality figures with ggplot2, such as set of themes, functions to align plots and arrange them into complex compound figures, and functions that make it easy to annotate plots and or mix plots with images.

Proper citation: cowplot (RRID:SCR_018081) Copy   

•   Source: SciCrunch Registry
  

https://vivli.org/

Independent, non-profit organization that has developed global data-sharing and analytics platform to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through creation and implementation of sustainable global data-sharing enterprise. Our focus is on sharing individual participant-level data from completed clinical trials. Users can search listed studies, request data sets from data contributors, aggregate data, or share data of their own. Vivli (Center for Clinical Research Data) is launching a portal to share participant-level data from COVID trials.

Proper citation: Vivli (RRID:SCR_018080) Copy   

•   Source: SciCrunch Registry
  

http://cucurbitgenomics.org/

Database to facilitate genomic and genetic data distribution, analysis, mining and integration for cucurbits. To store, mine, analyze, integrate and disseminate Cucurbitaceae family datasets and to provide central portal for cucurbit research and breeding community. Central portal for comparative and functional genomics of cucurbit crops.

Proper citation: CuGenDB (RRID:SCR_018401) Copy   

•   Source: SciCrunch Registry
  

https://www.planmeca.com/software/

Software tool as 3D imaging software. Flexible and intuitive all-in-one dental software platform. Provides set of tools to meet imaging needs by any dental facility.

Proper citation: Planmeca Romexis (RRID:SCR_018403) Copy   

•   Source: SciCrunch Registry